Clostridioides difficile Infection: Use of Inflammatory Biomarkers and Hemogram-Derived Ratios to Predict Mortality Risk in Hospitalized Patients.

BACKGROUND: Clostridioides difficile infection (CDI) is a significant cause of mortality, especially in healthcare environments. Reliable biomarkers that can accurately predict mortality in CDI patients are yet to be evaluated. Our study aims to evaluate the accuracy of several inflammatory biomarkers and hemogram-derived ratios in predicting mortality in CDI patients, such as the neutrophil-to-lymphocyte ratio (NLR), the systemic immune-inflammation index (SII), the platelet-to-neutrophil ratio (PNR), the derived neutrophil-to-lymphocyte ratio (dNLR), C-reactive protein (CRP), the platelet-to-lymphocyte ratio (PLR), and procalcitonin (PCT). RESULTS: NLR showed a sensitivity of 72.5% and a specificity of 58.42% with an area under curve (AUC) = 0.652. SII had a sensitivity of 77.5%, a specificity of 54.74%, and an AUC = 0.64. PNR, neutrophils, dNLR, and lymphocytes had lower AUCs which ranged from 0.595 to 0.616, with varied sensitivity and specificity. CRP, leukocytes, and platelets showed modest predictive values with AUCs below 0.6. PCT had a sensitivity of 100%, a low specificity of 7.41%, and an AUC = 0.528. METHODS: We conducted a retrospective analysis of CDI patients from two different hospital settings in Italy and Romania during the COVID-19 pandemic, from 1 January 2020 to 5 May 2023. Statistical analyses included t-tests, Wilcoxon rank-sum tests, χ2 tests, and multivariate logistic regression to identify predictors of mortality. ROC analysis assessed the accuracy of biomarkers and hemogram-derived ratios. A p value < 0.05 was considered significant. CONCLUSIONS: Neutrophils, dNLR, NLR, SII, and PNR are valuable biomarkers for predicting mortality in CDI patients. Understanding these predictors can improve risk stratification and clinical outcomes for CDI patients.

Artificial Intelligence for the Automatic Diagnosis of Gastritis: A Systematic Review.

Background and Objective: Gastritis represents one of the most prevalent gastrointestinal diseases and has a multifactorial etiology, many forms of manifestation, and various symptoms. Diagnosis of gastritis is made based on clinical, endoscopic, and histological criteria, and although it is a thorough process, many cases are misdiagnosed or overlooked. This systematic review aims to provide an extensive overview of current artificial intelligence (AI) applications in gastritis diagnosis and evaluate the precision of these systems. This evaluation could highlight the role of AI as a helpful and useful tool in facilitating timely and accurate diagnoses, which in turn could improve patient outcomes. Methods: We have conducted an extensive and comprehensive literature search of PubMed, Scopus, and Web of Science, including studies published until July 2024. Results: Despite variations in study design, participant numbers and characteristics, and outcome measures, our observations suggest that implementing an AI automatic diagnostic tool into clinical practice is currently feasible, with the current systems achieving high levels of accuracy, sensitivity, and specificity. Our findings indicate that AI outperformed human experts in most studies, with multiple studies exhibiting an accuracy of over 90% for AI compared to human experts. These results highlight the significant potential of AI to enhance diagnostic accuracy and efficiency in gastroenterology. Conclusions: AI-based technologies can now automatically diagnose using images provided by gastroscopy, digital pathology, and radiology imaging. Deep learning models exhibited high levels of accuracy, sensitivity, and specificity while assessing the diagnosis, staging, and risk of neoplasia for different types of gastritis, results that are superior to those of human experts in most studies.

Performance of 16S rRNA Gene Next-Generation Sequencing and the Culture Method in the Detection of Bacteria in Clinical Specimens.

Effective treatment of infectious diseases requires prompt and accurate bacterial identification and tailored antimicrobial treatments. Traditional culture methods are considered the gold standard, but their effectiveness diminishes for fastidious and hard-to-grow microorganisms. In recent years, molecular diagnostic tools such as 16S rRNA gene next-generation sequencing (16S NGS) have gained popularity in the field. We analysed data from samples submitted for 16S NGS between July 2022 and July 2023 at the Department of Advanced Translational Microbiology in Trieste, Italy. The study included samples submitted for both culture-based identification and 16S NGS. Conventional media were used for culture, and bacterial identification was performed using MALDI-TOF mass spectrometry. The V3 region of the 16S rRNA gene was sequenced using the Ion PGM platform. Among the 123 samples submitted, drainage fluids (38%) and blood (23%) were the most common, with requests predominantly from the Infectious Diseases (31.7%) and Orthopedic (21.13%) Units. In samples collected from patients with confirmed infections, 16S NGS demonstrated diagnostic utility in over 60% of cases, either by confirming culture results in 21% or providing enhanced detection in 40% of instances. Among the 71 patients who had received antibiotic therapies before sampling (mean 2.3 prior antibiotic days), pre-sampling antibiotic consumption did not significantly affect the sensitivity of 16S NGS. In routine microbiology laboratories, combining 16S NGS with culture method enhances the sensitivity of microbiological diagnostics, even when sampling is conducted during antibiotic therapy.

CRISPR-Cas System, Antimicrobial Resistance, and Enterococcus Genus-A Complicated Relationship.

(1) Background: The rise in antibiotic resistant bacteria poses a significant threat to public health worldwide, necessitating innovative solutions. This study explores the role of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) in the context of antibiotic resistance among different species from the Enterococcus genus. (2) Methods: The genomes of Enterococcus included in the study were analyzed using CRISPRCasFinder to distinguish between CRISPR-positive (level 4 CRISPR) and CRISPR-negative genomes. Antibiotic resistance genes were identified, and a comparative analysis explored potential associations between CRISPR presence and antibiotic resistance profiles in Enterococcus species. (3) Results: Out of ten antibiotic resistance genes found in Enterococcus species, only one, the efmA gene, showed a strong association with CRISPR-negative isolates, while the others did not significantly differ between CRISPR-positive and CRISPR-negative Enterococcus genomes. (4) Conclusion: These findings indicate that the efmA gene may be more prevalent in CRISPR-negative Enterococcus genomes, and they may contribute to a better understanding of the molecular mechanisms underlying the acquisition of antibiotic resistance genes in Enterococcus species.

Yokenella regensburgei-Past, Present and Future.

Yokenella regensburgei is a Gram-negative rod part of the Enterobacteriaceae family (order Enterobacterales) and a rare cause of human infections. Although improved diagnostic methods have led to an increase in reports of this elusive pathogen, information remains limited. In order to provide a better understanding of this bacterium, we developed the first comprehensive review of its biology, biochemical profile, antimicrobial resistance pattern, virulence factors, natural reservoir and involvement in various veterinary and human infections. Human infections with this bacterium are scarcely reported, most probably due to constraints regarding its identification and biochemical similarities to Hafnia alvei. Multiple systematic searches revealed 23 cases of human infection, with a seemingly worldwide distribution, mostly in middle-aged or elderly male patients, often associated with immunosuppression. To date, Y. regensburgei has been reported in skin and soft tissue infections, bacteremia and sepsis, osteoarticular infections and in others such as urinary tract and digestive infections. The unique ability of Y. regensburgei to degrade polystyrene presents a novel and promising avenue for addressing plastic pollution in the near future. However, large-scale applications of this bacterium will undoubtedly increase human exposure, highlighting the necessity for comprehensive research into its role in human and veterinary infections, pathogenicity and antibiotic resistance.

Risk Factors for 30-Day Mortality in Nosocomial Enterococcal Bloodstream Infections.

Enterococci commonly cause nosocomial bloodstream infections (BSIs), and the global incidence of vancomycin-resistant enterococci (VRE) BSIs is rising. This study aimed to assess the risk factors for enterococcal BSIs and 30-day mortality, stratified by Enterococcus species, vancomycin resistance, and treatment appropriateness. We conducted a retrospective cohort study (2014-2021) including all hospitalized adult patients with at least one blood culture positive for Enterococcus faecalis or Enterococcus faecium. We included 584 patients with enterococcal BSI: 93 were attributed to vancomycin-resistant E. faecium. The overall 30-day mortality was 27.5%; higher in cases of BSI due to vancomycin-resistant E. faecium (36.6%) and vancomycin-sensitive E. faecium (31.8%) compared to E. faecalis BSIs (23.2%) (p = 0.016). This result was confirmed by multivariable Cox analysis. Independent predictors of increased mortality included the PITT score, complicated bacteremia, and age (HR = 1.269, p < 0.001; HR = 1.818, p < 0.001; HR = 1.022, p = 0.005, respectively). Conversely, male gender, consultation with infectious disease (ID) specialists, and appropriate treatment were associated with reduced mortality (HR = 0.666, p = 0.014; HR = 0.504, p < 0.001; HR = 0.682, p = 0.026, respectively). In conclusion, vancomycin-resistant E. faecium bacteremia is independently associated with a higher risk of 30-day mortality.

Vancomycin-Resistant Streptococcus thoraltensis: A Case Report of Bacterial Endocarditis and Review of Literature on Infections Caused by This Pathogen.

Streptococcus thoraltensis is a rare species, part of the viridans streptococcus group, found initially in rabbits and pigs, which can be vancomycin-resistant. We present the case of a 65-year-old patient, a smoker and chronic alcohol consumer with chronic obstructive pulmonary disease (COPD) and multiple dental foci who had been diagnosed with bacterial endocarditis caused by Streptococcus thoraltensis. The particular elements of the case consisted of an atypical clinical presentation with diarrheal stools, abdominal pain, concomitant damage to the aortic and tricuspid valves, the presence of large vegetations (>2 cm), and a vancomycin-resistant strain of Streptococcus thoraltensis. The evolution of the patient was unfavorable due to septic embolisms, respiratory failure requiring orotracheal intubation, and septic and cardiogenic shock. Infections with Streptococcus thoraltensis are challenging to treat because of the severity of the clinical form it causes and the pattern of antibiotic resistance in this germ. Based on our brief review, Streptococcus thoraltensis is an extremely rare human pathogen previously described as the etiologic agent of infectious endocarditis in only one case.

Correlations between Dental Implant Infectious Pathologies and Maxillary Sinusitis: A Review Article.

(1) Background: The demands of patients for aesthetic and functional rehabilitation of edentulous areas led to the use of dental implants as therapeutic means on an increasingly large scale. This aspect determined the appearance of some infectious pathologies with a peri-implant starting point that can be complicated by various sinus diseases. The purpose of this review article is to synthesize the existing information in the specialized literature regarding the existing correlations between peri-implant and maxillary sinusitis. (2) Methods: The articles published in five databases were researched using different combinations of search terms. We selected 12 articles from the 250 found, by applying the inclusion and exclusion criteria and removing duplicates. (3) Results: We analyzed the included studies and we found that all of them reported a positive correlation between maxillary sinusitis and peri-implant infectious diseases. There are also reported other pathologies with a peri-implant infectious disease as a starting point such as abscesses, oro-antral communications, or foreign body reactions due to implant or bone graft materials migration. (4) Conclusions: This scoping review highlighted the existence of correlations between peri-implant and sinus pathology and the importance of preventing peri-implant diseases of an infectious nature to avoid the occurrence of these complications.

Sleep Deprivation-Induced Oxidative Stress in Rat Models: A Scoping Systematic Review.

Sleep deprivation is highly prevalent in the modern world, possibly reaching epidemic proportions. While multiple theories regarding the roles of sleep exist (inactivity, energy conservation, restoration, brain plasticity and antioxidant), multiple unknowns still remain regarding the proposed antioxidant roles of sleep. The existing experimental evidence is often contradicting, with studies pointing both toward and against the presence of oxidative stress after sleep deprivation. The main goals of this review were to analyze the existing experimental data regarding the relationship between sleep deprivation and oxidative stress, to attempt to further clarify multiple aspects surrounding this relationship and to identify current knowledge gaps. Systematic searches were conducted in three major online databases for experimental studies performed on rat models with oxidative stress measurements, published between 2015 and 2022. A total of 54 studies were included in the review. Most results seem to point to changes in oxidative stress parameters after sleep deprivation, further suggesting an antioxidant role of sleep. Alterations in these parameters were observed in both paradoxical and total sleep deprivation protocols and in multiple rat strains. Furthermore, the effects of sleep deprivation seem to extend beyond the central nervous system, affecting multiple other body sites in the periphery. Sleep recovery seems to be characterized by an increased variability, with the presence of both normalizations in some parameters and long-lasting changes after sleep deprivation. Surprisingly, most studies revealed the presence of a stress response following sleep deprivation. However, the origin and the impact of the stress response during sleep deprivation remain somewhat unclear. While a definitive exclusion of the influence of the sleep deprivation protocol on the stress response is not possible, the available data seem to suggest that the observed stress response may be determined by sleep deprivation itself as opposed to the experimental conditions. Due to this fact, the observed oxidative changes could be attributed directly to sleep deprivation.

An Overview of the Factors Involved in Biofilm Production by the Enterococcus Genus.

Enterococcus species are known for their ability to form biofilms, which contributes to their survival in extreme environments and involvement in persistent bacterial infections, especially in the case of multi-drug-resistant strains. This review aims to provide a comprehensive understanding of the mechanisms underlying biofilm formation in clinically important species such as Enterococcus faecalis and the less studied but increasingly multi-drug-resistant Enterococcus faecium, and explores potential strategies for their eradication. Biofilm formation in Enterococcus involves a complex interplay of genes and virulence factors, including gelatinase, cytolysin, Secreted antigen A, pili, microbial surface components that recognize adhesive matrix molecules (MSCRAMMs), and DNA release. Quorum sensing, a process of intercellular communication, mediated by peptide pheromones such as Cob, Ccf, and Cpd, plays a crucial role in coordinating biofilm development by targeting gene expression and regulation. Additionally, the regulation of extracellular DNA (eDNA) release has emerged as a fundamental component in biofilm formation. In E. faecalis, the autolysin N-acetylglucosaminidase and proteases such as gelatinase and serin protease are key players in this process, influencing biofilm development and virulence. Targeting eDNA may offer a promising avenue for intervention in biofilm-producing E. faecalis infections. Overall, gaining insights into the intricate mechanisms of biofilm formation in Enterococcus may provide directions for anti-biofilm therapeutic research, with the purpose of reducing the burden of Enterococcus-associated infections.

Antibacterial and Phytochemical Screening of Artemisia Species.

Taking into account the increasing number of antibiotic-resistant bacteria, actual research focused on plant extracts is vital. The aim of our study was to investigate leaf and stem ethanolic extracts of Artemisia absinthium L. and Artemisia annua L. in order to explore their antioxidant and antibacterial activities. Total phenolic content (TPC) was evaluated spectrophotometrically. Antioxidant activity was evaluated by DPPH and ABTS. The antibacterial activity of wormwood extracts was assessed by minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) in Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, and Salmonella enteritidis cultures, and by zone of inhibition in Klebsiella carbapenem-resistant enterobacteriaceae (CRE) and Escherichia coli extended-spectrum ß-lactamases cultures (ESBL). The Artemisia annua L. leaf extract (AnL) exhibited the highest TPC (518.09 mg/mL) and the highest expression of sinapic acid (285.69 ± 0.002 µg/mL). Nevertheless, the highest antioxidant capacity (1360.51 ± 0.04 µM Trolox/g DW by ABTS and 735.77 ± 0.02 µM Trolox/g DW by DPPH) was found in Artemisia absinthium L. leaf from the second year of vegetation (AbL2). AnL extract exhibited the lowest MIC and MBC for all tested bacteria and the maximal zone of inhibition for Klebsiella CRE and Escherichia coli ESBL. Our study revealed that AbL2 exhibited the best antioxidant potential, while AnL extract had the strongest antibacterial effect.

A Tale of Two Pandemics: Antimicrobial Resistance Patterns of Enterococcus spp. in COVID-19 Era.

Although the COVID-19 pandemic has held the spotlight over the past years, the antimicrobial resistance (AMR) phenomenon continues to develop in an alarming manner. The lack of strict antibiotic regulation added to the overuse of antimicrobials fueled the AMR pandemic. This paper aims to analyze and identify the impact of the COVID-19 pandemic on antibiotic resistance patterns of Enterococcus spp. The study was designed as a retrospective observational study. Enterococcus spp. infections data were collected from one academic hospital in Cluj-Napoca, Romania over 18 months. A statistical analysis was performed to compare antibiotic resistance phenotypes identified. We recorded an increase in the isolation rates of Enterococcus spp. strains, from 26 isolates (26.53%) during Period A (November 2020-April 2021) to 42 strains (42.85%) during Period C (November 2021-April 2022). The number of strains with resistance to vancomycin increased from 8 during Period A to 17 during Period C. Of the total 36 strains with resistance to vancomycin, 25 were identified as E. faecium. SARS-CoV-2 patients (n = 29) proved to be at risk to develop an E. faecium co-infection (n = 18). We observed that strains with resistance to ampicillin (n = 20) and vancomycin (n = 15) are more often isolated from these patients. All changes identified in our study are to be considered in the light of COVID-19 pandemic, highlighting the threatening AMR phenomenon in Romania. Further studies should be performed to quantify the worldwide effects of these pandemics.

Easy and Affordable: A New Method for the Studying of Bacterial Biofilm Formation.

BACKGROUND: Bacterial biofilm formation (BBF) proves itself to be in the spotlight of microbiology research due to the wide variety of infections that it can be associated with, the involvement in food spoilage, industrial biofouling and perhaps sewage treatment. However, BBF remains difficult to study due to the lack of standardization of the existing methods and the expensive equipment needed. We aim to describe a new inexpensive and easy to reproduce protocol for a 3D-printed microfluidic device that can be used to study BBF in a dynamic manner. METHODS: We used the SolidWorks 3D CAD Software (EducationEdition 2019-2020, Dassault Systèmes, Vélizy-Villacoublay, France) to design the device and the Creality3D Ender 5 printer (Shenzhen Creality 3D Technology Co., Ltd., Shenzhen, China) for its manufacture. We cultivated strains of Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae and Pseudomonas aeruginosa. For the biofilm evaluation we used optical coherence tomography (OCT), scanning electron microscopy (SEM), Fourier Transform Infrared (FTIR) spectroscopy and crystal violet staining technique. RESULTS: Based on the analysis, Enterococcus faecalis seems to produce more biofilm in the first hours while Pseudomonas aeruginosa started to take the lead on biofilm production after 24 h. CONCLUSIONS: With an estimated cost around €0.1285 for one microfluidic device, a relatively inexpensive and easy alternative for the study of BBF was developed.

The Main Bacterial Communities Identified in the Sites Affected by Periimplantitis: A Systematic Review.

(1) Background: Periimplantitis is an infectious condition that affects the periimplant tissue and is of bacterial etiology. However, to date, the exact bacterial flora involved in its occurrence is not known. The aim of this literature review was to summarize the articles published on this topic and to identify the main bacterial species isolated in periimplantitis. (2) Methods: The articles published in three databases were researched: Pubmed, Embase and Web of Science using Prisma guides and combinations of MeSH terms. We selected 25 items from the 980 found by applying the inclusion and exclusion criteria. (3) Results: We quantified the results of the 25 studies included in this review. In general, the most commonly identified bacterial species were Gram-negative anaerobic species, as Prevotella, Streptococcus, Fusobacterium and Treponema. (4) Conclusion: The most frequent bacteria in the periimplantitis sites identified in this review are Gram-negative anaerobic species, also involved in the pathogenesis of the periodontal disease.

Descriptive Analysis of Circulating Antimicrobial Resistance Genes in Vancomycin-Resistant Enterococcus (VRE) during the COVID-19 Pandemic.

COVID-19 offers ideal premises for bacteria to develop antimicrobial resistance. In this study, we evaluated the presence of several antimicrobial resistance genes (ARG) in vancomycin-resistant Enterococcus (VRE) isolated from rectal swabs from patients at a hospital in Cluj-Napoca, Romania. Rectal swabs were cultivated on CHROMID® VRE (bioMérieux, Marcy-l' Étoile, France) and positive isolates were identified using MALDI-TOF Mass Spectrometry (Bruker Daltonics, Bremen, Germany) and further analyzed using the PCR technique for the presence of the following ARGs: van A, van B, tet(M), tet(L), ermB, msrA, mefA, aac(6')-Im, aph(2)-Ib, ant(4')-Ia, sul1, sul2, sul3, and NDM1. We isolated and identified 68 isolates of Enterococcus faecium and 11 isolates of Enterococcus faecalis. The molecular analysis showed 66 isolates positive for the vanA gene and eight positive for vanB. The most frequent association of ARG in VRE was vanA-tet(M)-ermB. There was no statistically significant difference between Enterococcus faecium and Enterococcus faecalis regarding ARGs. Our work proves that during the COVID-19 pandemic, highly resistant isolates of Enterococcus were present in patients in the intensive care unit; thus, better healthcare policies should be implemented for the management and control of these highly resistant isolates in the future.

Enterococcus raffinosus, Enterococcus durans and Enterococcus avium Isolated from a Tertiary Care Hospital in Romania-Retrospective Study and Brief Review.

(1) Background: This paper aims to provide a description of non-faecalis non-faecium enterococci isolated from a tertiary care hospital in Romania and to briefly review the existing literature regarding the involvement of Enterococcus raffinosus, Enterococcus durans and Enterococcus avium in human infections and their antimicrobial resistance patterns; (2) Methods: We retrospectively analyzed all Enteroccocus species isolated from the "Prof. Dr. O. Fodor" Regional Institute of Gastroenterology and Hepatology from Cluj-Napoca during one year focusing on non-faecalis non-faecium Enterococci. A brief review of the literature was performed using case reports involving Enterococcus raffinosus, Enterococcus durans and Enterococcus avium; (3) Results: Only 58 out of 658 Enteroccocus isolates were non-faecalis non-faecium and met the inclusion criteria. These species were isolated more often (p < 0.05) from the surgical ward from mixed etiology infections with E. coli. In our review, we included 39 case reports involving E. raffinosus, E. durans and E. avium; (4) Conclusions: Isolation of non-faecalis non-faecium enterococci displays an emerging trend with crucial healthcare consequences. Based on the analysis of the case reports, E. avium seems to be involved more often in neurological infections, E. durans in endocarditis, while E. raffinosus displays a more heterogenous distribution.

Mixed Etiology COVID-19 Associated Pulmonary Aspergillosis (CAPA)-A Case Report and Brief Review of the Literature.

The SARS-CoV-2 pandemic has proved to be a significant risk addition for invasive infections with Aspergillus. Even though there are plenty of data about the COVID-19-associated pulmonary aspergillosis (CAPA), especially involving Aspergillus fumigatus, recent studies are presenting cases of CAPA involving more than one species of Aspergillus. We report the first case of a SARS-CoV-2 patient associating co-infection with, most likely, Aspergillus section Fumigati and Aspergillus section Flavi from Romania, and we review the existing medical literature in order to shed light upon mixed etiology cases of CAPA. Since mortality remains high in these cases, there is an acute need for more information about the interaction between SARS-CoV-2 and Aspergillus spp., and the therapies for CAPA. The emerging number of cases and the high mortality rate must be considered an incentive for future research.