Integrating whole genome sequencing and machine learning for predicting antimicrobial resistance in critical pathogens: a systematic review of antimicrobial susceptibility tests

BACKGROUND

Infections caused by antibiotic-resistant bacteria pose a major challenge to modern healthcare. This systematic review evaluates the efficacy of machine learning (ML) approaches in predicting antimicrobial resistance (AMR) in critical pathogens (CP), considering Whole Genome Sequencing (WGS) and antimicrobial susceptibility testing (AST).

METHODS

The search covered databases including PubMed/MEDLINE, EMBASE, Web of Science, SCOPUS, and SCIELO, from their inception until June 2024. The review protocol was officially registered on PROSPERO (CRD42024543099).

RESULTS

The review included 26 papers, analyzing data from 104,141 microbial samples. Random Forest (RF), XGBoost, and logistic regression (LR) emerged as the top-performing models, with mean Area Under the Receiver Operating Characteristic (AUC) values of 0.89, 0.87, and 0.87, respectively. RF showed superior performance with AUC values ranging from 0.66 to 0.97, while XGBoost and LR showed similar performance with AUC values ranging from 0.83 to 0.91 and 0.76 to 0.96, respectively. Most studies indicate that integrating WGS and AST data into ML models enhances predictive performance, improves antibiotic stewardship, and provides valuable clinical decision support. ML shows significant promise for predicting AMR by integrating WGS and AST data in CP. Standardized guidelines are needed to ensure consistency in future research.

A multilevel analysis of a randomized clinical trial comparing adjunctive moxifloxacin versus amoxicillin/metronidazole for the treatment of aggressive periodontitis

BACKGROUND

It was documented that the clinical outcomes of mechanical periodontal treatment can fluctuate not merely concerning patients but equally among various tooth sites in the subject. This trial evaluates the clinical parameters related with the patient, tooth, and site that generate more changes in clinical attachment level (CAL) gain and probing depth (PD) reduction, using moxifloxacin (MOX) versus amoxicillin plus metronidazole (AMOX + ME) as adjuncts to scaling and root planing (SRP), in comparison to SRP only, post-therapy in generalized aggressive periodontitis (GAgP).

MATERIALS AND METHODS

The analysis of this clinical trial included 6012 tooth sites at 1002 teeth in 36 patients; they were randomly assigned to three protocols: Systemically intake of MOX or AMOX + ME plus SRP, or SRP + placebo for 7 days. The clinical effect of the patient, tooth, and site characteristics, in terms of CAL gain and PD reduction, was explored using a multilevel linear model. P < 0.05 was statistically significant.

RESULTS

Following 6 months of treatment, the differences between the groups were statistically significant, favoring the MOX and AMOX + ME protocols (P < 0.0001). Moreover, the multilevel model showed that adjunctive MOX, AMOX + ME, non-molar, and interproximal sites were the features that contribute significantly to CAL improvement, and PD decreases in GAgP (P ≤ 0.001 for all).

CONCLUSION

The most relevant characteristics for the changes in CAL increase and PD diminution, after adjunctive antimicrobials, were ascribable to the features related to the tooth. MOX and AMOX + ME, non-multi-radicular-tooth, and interdental sites indicated superior clinical gains at the tooth and site levels in GAgP.

Addressing mucosal ulcers during orthodontic treatment: An urgent call for preventive strategies

Mucosal ulcers are a common yet often overlooked complication during orthodontic treatment, significantly impacting patient comfort and compliance. This letter aims to highlight the prevalence, potential causes, and management strategies for mucosal ulcers in orthodontic patients. By reviewing recent literature and clinical observations, we underscore the necessity for proactive measures and tailored interventions to mitigate the incidence and severity of these lesions. Emphasizing the role of patient education and the use of protective devices, we call for a multidisciplinary approach to enhance patient care and treatment outcomes. This discussion is particularly relevant in the context of evolving orthodontic techniques and materials, which necessitate continuous adaptation of clinical practices to ensure patient safety and well-being.

Comparison of Outcomes and Survival of Two Cohorts of Patients with Simultaneous Pancreas-Kidney Transplantation: A Retrospective Cohort Study in a Latin American Hospital

BACKGROUND

Simultaneous pancreas-kidney transplantation (SPKT) is a complex and demanding procedure with a considerable risk of morbidity and mortality. Advances in surgical techniques and organ preservation have introduced changes in care protocols. Two cohorts of patients receiving SPKT with two different protocols were compared to determine overall survival and pancreatic and renal graft failure-free survival.

METHODS

This retrospective observational study was conducted in two cohorts of SPKT recipient patients that underwent surgery between 2001 and 2021. Outcomes were compared in transplant patients between 2001 and 2011 (cohort 1; initial protocol) and 2012-2021 (cohort 2; improved protocol). In addition to the temporality, the cohorts were defined by a protocolization of technical aspects and medical management in cohort 2 (improved protocol), compared to a wide variability in the procedures carried out in cohort 1 (initial protocol). Overall survival and pancreatic and renal graft failure-free survival were the primary outcomes. These outcomes were determined using Kaplan-Meier survival analysis and the log-rank test.

RESULTS

Fifty-five SPKT were performed during the study period: 32 in cohort 1 and 23 in cohort 2. In the survival analysis, an average of 2546 days (95% CI: 1902-3190) was found in cohort 1, while in cohort 2, it was 2540 days (95% CI: 2100-3204) (p > 0.05). Pancreatic graft failure-free survival had an average of 1705 days (95% CI: 1037-2373) in cohort 1, lower than the average in cohort 2 (2337 days; 95% CI: 1887-2788) (p = 0.016). Similarly, renal graft failure-free survival had an average of 2167 days (95% CI: 1485-2849) in cohort 1, lower than the average in cohort 2 (2583 days; 95% CI: 2159-3006) (p = 0.017).

CONCLUSIONS

This analysis indicates that pancreatic and renal graft failure-free survival associated with SPKT decreased significantly in cohort 2, with results related to improvements in the treatment protocol implemented in that cohort.

Artificial Intelligence through Wireless Sensors Applied in Restorative Dentistry: A Systematic Review

The integration of wireless sensors with artificial intelligence could represent a transformative approach in restorative dentistry, offering a sophisticated means to enhance diagnostic precision, treatment planning, and patient outcomes. This systematic review was conducted to pinpoint and assess the efficacy of wireless sensors in restorative dentistry. The search methodology followed the guidelines outlined by PRISMA and involved the utilization of prominent scientific databases. Following the final phase of evaluating eligibility, the systematic review included six papers. Five experiments were conducted in vitro, while one was a randomized clinical trial. The investigations focused on wireless sensors for cavity diagnosis, toothbrush forces, facial mask applications, and physiological parameter detection from dental implants. All wireless sensors demonstrated efficacy in achieving the objectives established by each study and showed the validity, accuracy, and reproducibility of this device. The investigations examined in this systematic review illustrate the potential of wireless sensors in restorative dentistry, especially in the areas of caries detection, dental implant systems, face masks, and power brushes. These technologies hold promise for enhancing patient outcomes and alleviating the workload of dental practitioners.

A Case Report of a Lingual Cyst Lined by Respiratory Epithelium in a Child

The lingual cyst lined by respiratory epithelium is a rare pathology. It probably appears from the default of undifferentiated cells of the foregut during embryonic growth. This pathology is seen more often in males and children; however, only 5 patients younger than 4 years old have been reported. The pathophysiology and the management of this cyst were described in a 4-year-old girl. She presented with a soft mass on the dorsum of the tongue covered by normal mucosa, which existed since her birth, causing difficulty in eating, breathing, and talking. The magnetic resonance described a hyperintense image with an anteroposterior diameter of 27 mm, craniocaudal of 19 mm, and transversal of 26 mm in the midline groove of the tongue; the scintigraphy showed normality. The enucleation of the lesion was performed, eradicating the capsule of the cyst and obtaining a complete cleavage. The histopathologic examination defined a cyst lined predominantly by respiratory epithelium. Unlike in other cases, in this case their cystic lining and capsular constituents were contemplated considering the current histological recommendations. It is relevant to differentiate this pathology from other cysts with similar histological findings.

Efficacy of CAD/CAM Technology in Interventions Implemented in Orthodontics: A Scoping Review of Clinical Trials

OBJECTIVES

To evaluate the efficacy of computer-aided design/computer-aided manufacturing (CAD/CAM) technology in interventions implemented in orthodontics.

METHODS

A scoping review of scientific evidence was accomplished, involving different databases. MesH terms and keywords were provided to examine clinical trials (CTs) in all languages. Exclusively CTs that fulfilled the eligibility criteria were admitted.

RESULTS

Eight CTs were chosen. These experiments evaluated 542 patients. Four CTs compared the computer-aided indirect bonding method versus the traditional direct bonding of orthodontic brackets. Three CTs compared CAD/CAM retainers with other types of retainers, and one CT compared the CAD/CAM group with multistranded stainless steel wires versus stainless steel wires. Regarding the efficacy of the interventions with CAD/CAM technology used in orthodontics, variable results were found. The indirect bonded customized CAD/CAM brackets presented just a slight effect on the treatment efficacy and therapy results. Two CTs showed that an indirect bonding self-ligating standard system had a similar quality of therapy in comparison with the CAD/CAM customized bracket system. Concerning the clinical failure rate, no differences were presented between the CAD/CAM retainer and other retainers. A CAD/CAM system had more loose brackets than a noncustomized system and was observed also a greater amount of immediate debonding with CAD/CAM indirect bonding than with direct bonding. CAD/CAM fixed retainers revealed inferior relapse and fewer failures than lab-based and conventional chairside retainers. No changes between treatment groups were observed regarding the total therapy time, amount of appointments, and quantity of archwire bends.

CONCLUSIONS

In general terms, no greater efficacy of CAD/CAM technology was observed over traditional therapies used in orthodontics. However, it was found that gingival inflammation and the accumulation of bacterial plaque and dental calculus were lower when CAD/CAM retainers were used. When comparing interventions that include CAD/CAM systems with conventional therapies, no significant reduction in care times was found.

Comparison of light gradient boosting and logistic regression for interactomic hub genes in Porphyromonas gingivalis and Fusobacterium nucleatum-induced periodontitis with Alzheimer's disease

Introduction

Porphyromonas gingivalis and Treponema species have been found to invade the central nervous system through virulence factors, causing inflammation and influencing the host immune response. P. gingivalis interacts with astrocytes, microglia, and neurons, leading to neuroinflammation. Aggregatibacter actinomycetemcomitans and Fusobacterium nucleatum may also play a role in the development of Alzheimer's disease. Interactomic hub genes, central to protein-protein interaction networks, are vulnerable to perturbations, leading to diseases such as cancer, neurodegenerative disorders, and cardiovascular diseases. Machine learning can identify differentially expressed hub genes in specific conditions or diseases, providing insights into disease mechanisms and developing new therapeutic approaches. This study compares the performance of light gradient boosting and logistic regression in identifying interactomic hub genes in P. gingivalis and F. nucleatum-induced periodontitis with those in Alzheimer's disease.

Methods

Using the GSE222136 dataset, we analyzed differential gene expression in periodontitis and Alzheimer's disease. The GEO2R tool was used to identify differentially expressed genes under different conditions, providing insights into molecular mechanisms. Bioinformatics tools such as Cytoscape and CytoHubba were employed to create gene expression networks to identify hub genes. Logistic regression and light gradient boosting were used to predict interactomic hub genes, with outliers removed and machine learning algorithms applied.

Results

The data were cross-validated and divided into training and testing segments. The top hub genes identified were TNFRSF9, LZIC, TNFRSF8, SLC45A1, GPR157, and SLC25A33, which are induced by P. gingivalis and F. nucleatum and are responsible for endothelial dysfunction in brain cells. The accuracy of logistic regression and light gradient boosting was 67% and 60%, respectively.

Discussion

The logistic regression model demonstrated superior accuracy and balance compared to the light gradient boosting model, indicating its potential for future improvements in predicting hub genes in periodontal and Alzheimer's diseases.

Factors Associated with the Extent of Clinical Attachment Loss in Periodontitis: A Multicenter Cross-Sectional Study

Periodontitis has significant public health implications, affecting individuals' overall health, well-being, and quality of life. This study aimed to assess the risk factors associated with the extent of clinical attachment loss (CAL) in a population diagnosed with periodontitis. Six hundred and sixty-seven patients with different degrees of CAL (mild, n = 223; moderate, n = 256; and advanced, n = 188) were enrolled. Socio-demographics, lifestyle, microbiological profiles, specific immune response, obesity, and single-nucleotide polymorphism of the IL1 gene were determined. Unconditional logistic regression models were conducted to determine the factors associated with the extent of CAL. Aging, smoking, microbial factors, plaque index, and IgG2 antibodies against Aggregatibacter actinomycetemcomitans were associated with advanced CAL. IgG2 antibodies against A. actinomycetemcomitans (OR 1.50; CI 95% 1.23-1.81), plaque accumulation (OR 2.69; CI 95% 2.20-3.29), Porphyromonas gingivalis (OR 1.93; CI 95% 1.35-2.76), Tanerella forsythia (OR 1.88; CI 95%1.30-2.70), and current smoking (OR 1.94; CI 95% 1.31-2.87) were associated with advanced CAL. Gene IL polymorphisms, obesity, and stress were not associated with the extent of CAL. Aging, plaque accumulation, smoking, and having antibodies against A. actinomycetemcomitans were the most critical factors associated with advanced CAL. In contrast, obesity, stress, and gene polymorphisms were not associated with the extent of CAL.

Opportunistic pathogens are associated with deteriorated clinical parameters in peri-implant disease

OBJECTIVES

To assess the association between Gram-negative enteric rods and Pseudomonas with the clinical parameters in peri-implant disease.

MATERIALS AND METHODS

Patients treated with implants and diagnosed with peri-implant mucositis and/or peri-implantitis participate in this cross-sectional research. Unusual microorganisms from the implants were recognized using MALDI-TOF mass spectrometry. Linear regression models were applied.

RESULTS

A total of 103 implants were evaluated in thirty-one participants. Gram-negative enteric rods/Pseudomonas were observed in 47 implants (46%). Interestingly, there were differences in probing pocket depth (PPD), clinical attachment loss (CA), and bleeding on probing (BOP) between the groups, where implants with the presence of Gram-negative enteric rods/Pseudomonas presented deteriorated clinical parameters (p < .0001). The crude and adjusted linear regression models for PPD in peri-implant mucositis, PPD in peri-implantitis, CA in peri-implantitis, and BOP in peri-implant disease present significant βs, demonstrating deteriorated parameters (p < .0001) in the presence of Gram-negative enteric rods/Pseudomonas. Besides, the model for CA in peri-implantitis showed that cemented restored reconstructions were statistically significant (p = .009). Additionally, the R2 value in most models indicated a high degree of correlation (>85%).

CONCLUSION

The occurrence of Gram-negative enteric rods and Pseudomonas was associated with deteriorated clinical parameters in patients with peri-implant disease.

Efficacy of wireless sensors in assessing occlusal and bite forces: A systematic review

BACKGROUND

The noteworthy correlation between bite force and masticatory performance emphasizes its significance as a meaningful and objective method for assessing oral function. Furthermore, in the study of bruxism, the measurement of intraoral bite force assumes critical importance. Given the importance of assessing occlusal forces and bite force, this systematic review aims to assess the efficacy of wireless sensors in measuring these forces.

METHODS

The search methodology employed in this systematic review adhered to the guidelines outlined by PRISMA. The strategy involved the exploration of various databases, including PubMed/MEDLINE, SCOPUS and SCIELO. An assessment tool was employed to evaluate the bias risk and study quality.

RESULTS

This systematic review encompassed six prospective clinical studies involving a total of 89 participants. Wireless sensors for measuring occlusal forces and bite forces were predominantly employed in healthy adults or individuals with bruxism, along with children undergoing orthodontic treatment. All wireless sensors employed in the studies underwent validation and reproducibility assessments, affirming their reliability. The findings indicated that all wireless sensors exhibited efficacy in detecting occlusal forces and bite forces.

CONCLUSION

Wireless sensors offer real-time monitoring of occlusal and bite forces, aiding in understanding force distribution and identifying bruxism patterns. Despite limited studies on their application, these sensors contribute to evolving insights. Integration into clinical practice requires careful consideration of factors like calibration and patient compliance. Ongoing research is crucial to address limitations and enhance the efficacy of wireless sensors in measuring occlusal and bite forces and managing bruxism.

Primary Headache Approach in the Emergency Departments: A Systematic Scoping Review of Prospective Studies

This systematic scoping review aims to answer questions related to the main characteristics of primary headache, the need for neuroimaging, and the presence of red flags in these patients. A review of prospective studies including the MEDLINE/PubMed, Scopus, LILACS, and SCIELO databases, as well as the grey literature, was conducted. The methodological quality of the selected investigations was also assessed. Six investigations met the selection criteria. The mean age of people with primary headache was less than 43 years, with ages ranging from 39 to 46 years. Most of the studies reported the presence of nausea/vomiting, between 12% and 60% of the patients studied. To a lesser extent, there was also the presence of intense and moderate pain, loss of consciousness, stiff neck, presence of aura, and photophobia. The most frequent diagnoses were unspecified headache, migraine, and tension headache. The studies did not recommend neuroimaging and no red flags were reported. Primary headache occurred more frequently in women, in those under 46 years of age with a history of migraine and similar episodes. Moreover, the presence of red flags and the need for neuroimaging in patients with primary headaches were not evidenced.

Predicting the hub interactome of COVID-19 and oral squamous cell carcinoma: uncovering ALDH-mediated Wnt/β-catenin pathway activation via salivary inflammatory proteins

Understanding shared pathways and mechanisms involved in the pathogenesis of diseases like oral squamous cell carcinoma (OSCC) and COVID-19 could lead to the development of novel therapeutic strategies and diagnostic biomarkers. This study aims to predict the interactome of OSCC and COVID-19 based on salivary inflammatory proteins. Datasets for OSCC and COVID-19 were obtained from https://www.salivaryproteome.org/differential-expression and selected for differential gene expression analysis. Differential gene expression analysis was performed using log transformation and a fold change of two. Hub proteins were identified using Cytoscape and Cytohubba, and machine learning algorithms including naïve Bayes, neural networks, gradient boosting, and random forest were used to predict hub genes. Top hub genes identified included ALDH1A1, MT-CO2, SERPINC1, FGB, and TF. The random forest model achieved the highest accuracy (93%) and class accuracy (84%). The naive Bayes model had lower accuracy (63%) and class accuracy (66%), while the neural network model showed 55% accuracy and class accuracy, possibly due to data pre-processing issues. The gradient boosting model outperformed all models with an accuracy of 95% and class accuracy of 95%. Salivary proteomic interactome analysis revealed novel hub proteins as potential common biomarkers.

Predicting intensive care unit-acquired weakness: A multilayer perceptron neural network approach

In this editorial, we comment on the article by Wang and Long, published in a recent issue of the World Journal of Clinical Cases. The article addresses the challenge of predicting intensive care unit-acquired weakness (ICUAW), a neuromuscular disorder affecting critically ill patients, by employing a novel processing strategy based on repeated machine learning. The editorial presents a dataset comprising clinical, demographic, and laboratory variables from intensive care unit (ICU) patients and employs a multilayer perceptron neural network model to predict ICUAW. The authors also performed a feature importance analysis to identify the most relevant risk factors for ICUAW. This editorial contributes to the growing body of literature on predictive modeling in critical care, offering insights into the potential of machine learning approaches to improve patient outcomes and guide clinical decision-making in the ICU setting.

Evaluation of the clinical efficacy of green tea extract gel as local drug delivery for periodontitis

BACKGROUND

Periodontal disease is a chronic inflammatory condition characterized by periodontal pocket formation, clinical attachment loss, and destruction of alveolar bone. Its conventional treatment primarily involves mechanical debridement and plaque control, but localized antimicrobial therapy offers site-specific advantages. While antibiotics such as metronidazole and doxycycline are commonly used, green tea extract, which is rich in epigallocatechin gallate, has been proposed as a promising alternative for local drug delivery due to its anti-inflammatory and antimicrobial properties.

AIM

To compare the clinical efficacy of green tea extract gel and ornidazole gel as adjuncts to scaling and root planing (SRP) in patients with periodontitis.

METHODS

Teeth with probing pocket depths (PPD) of 4-7 mm were selected. Participants’ baseline oral hygiene index-simplified, plaque index, clinical attachment loss, and PPD were recorded. The participants were randomized into two groups: One received green tea extract gel after SRP, and the other received ornidazole gel. Subgingival drug delivery was performed, and participants refrained from brushing or interproximal cleaning for ten days. Their clinical parameters were re-evaluated after one month.

RESULTS

The PPD decreased significantly from baseline to one month in both groups. However, the green tea extract gel group exhibited superior outcomes to the ornidazole gel group, with a mean difference in PPD of 0.28 ± 0.78 mm at one month (P < 0.007).

CONCLUSION

As an adjunct to SRP, green tea extract gel showed greater efficacy in improving clinical periodontal parameters than ornidazole gel.

Portal Vein Thrombosis in Liver Transplantation: A Retrospective Cohort Study

Portal vein thrombosis was considered a contraindication for liver transplantation. This study analyzes the perioperative complications and survival of liver transplant patients with portal vein thrombosis (PVT). A retrospective observational cohort study of liver transplant patients was conducted. The outcomes were early mortality (30 days) and patient survival. A total of 201 liver transplant patients were identified and 34 (17%) patients with PVT were found. The most frequent extension of thrombosis was Yerdel 1 (58.8%), and a portosystemic shunt was identified in 23 (68%) patients. Eleven patients (33%) presented any early vascular complication, PVT being the most frequent (12%). The multivariate regression analysis showed a statistically significant association between PVT and early complications (OR = 3.3, 95% confidence interval 1.4-7.7; p = 0.006). Moreover, early mortality was observed in eight patients (24%), of which two (5.9%) presented Yerdel 2. For Yerdel 1, patient survival according to the extent of thrombosis was 75% at 1 year and 3 years, while for Yerdel 2, it was 65% at 1 year, and 50% at 3 years (p = 0.04). Portal vein thrombosis significantly influenced early vascular complications. Furthermore, portal vein thrombosis Yerdel 2 or higher impacts the survival of liver grafts in the short and long term.