bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Validation and Comparison of Bacterial Vaginosis Detection
Authors: Figueroa C I , Moore N , Flaws M 
Published: October 2024

Abstract

Introduction/Objective
Bacterial vaginosis (BV) is considered a top reason for women’s gynecological visits, causing symptoms such as vaginal discharge, foul odor, itching, and burning associated with the alteration of the normal vaginal microbiome. It is often presented as a decrease in Lactobacillus spp. and an increase in anaerobic organisms such as Gardnerella vaginalis and Atopobium vaginae. In response to the demand for more automated and less subjective testing, molecular methods have recently been developed to aid in BV testing. The objectives of this study are to validate and compare the molecular Aptima® Bacterial Vaginosis Assay by Hologic® to the established BV Screen via a Gram stained vaginal smear graded through Nugent scoring at RUSH University Medical Center in Chicago, IL and perform a cost analysis between the testing methods.

Methods/Case Report
Samples of known BV value were tested on the Panther® instrument to validate the Aptima® Bacterial Vaginosis Assay for accuracy and precision. Clinical samples of vaginal swabs were used to make a Gram stained BV screen for Nugent scoring, then afterwards were placed into Hologic Multitest Aptima® probes for molecular testing on the Panther® instrument. Nugent scoring was performed blind by the molecular test. Molecular results of negative, positive, and invalid were then compared to the Nugent scores: scores of 0-3 for negative/normal vaginal flora, 7-10 for positive BV, and 4-6 for intermediate/altered scores were screened for discrepancy.

Results (if a Case Study enter NA)
The Aptima® BV Assay tested 52 known samples with 97% accuracy and 100% precision. A total of 80 clinical samples of vaginal swabs used for Gram stained BV screens were run on the Aptima® BV Assay; 61 provided conclusive data for comparative analysis. When compared to the original Nugent scores, the positive percent agreement (PPA) was 77.0% and negative percent agreement (NPA) was 92.9%.

Conclusion
The Aptima® BV Assay proved to be both accurate and precise in its validation testing. Clinically, it was able to screen for BV in vaginal samples with a good percent agreement to Gram stained BV screens. Further testing of additional clinical samples are to be done to continue analysis. Although the supplies needed to perform a Gram stain cost less than molecular testing, the reimbursement payment for molecular testing is much greater and overall reduces employee time costs for performing the test, making it the more cost effective choice for the laboratory.
Lack of Diagnostic Value from Fungal and Mycobacterial Cultures in Cases of Suspected Prosthetic Joint Infection
Authors: Nava A , Graf E , Burnett K 
Published: October 2024

Abstract

Introduction/Objective
Infections of prosthetic joints cause significant morbidity and often result in removal of the infected joint. In many cases, an infectious etiology can be difficult to definitively identify. As a result, providers suspecting prosthetic joint infections (PJI) often place large order sets of microbiology tests, including fungal and mycobacterial cultures. Fungal and mycobacterial cultures are labor-intensive for the laboratory taking up to 28 days and 42 days, respectively, to complete. As a potential area for a diagnostic stewardship intervention, we wanted to evaluate how often a fungal or mycobacterial culture produced actionable information in cases of suspected PJI.

Methods/Case Report
Data reports were retrieved from both the Electronic Health Record (EHR) and the Laboratory Information System (LIS) from May 2022 to May 2023. As sources submitted by the provider often do not specify that the joint is prosthetic, data from LIS was evaluated to identify microbiology culture test sets ordered on joint sources, while data from EHR was examined to isolate patients with implanted joints. Using Microsoft Excel, data from both systems was compared in order to match microbiology culture test sets to the known implanted joints. LIS data from implanted joint sources was assessed to record negative (no growth) and positive (growth) cultures, and to register all organisms isolated.

Results (if a Case Study enter NA)
Of 794 order sets for cultures collected from prosthetic joint sources, 430 included requests for fungal culture and 79 included requests for mycobacterial culture. Of these 79 requests for mycobacterial culture, 0 organisms were isolated (0%). Of these 430 requests for fungal culture, 7 grew yeast (1.6%) and 7 out of 7 (100%) of these yeasts were also isolated on general (aerobic bacterial) culture. No molds were isolated.

Conclusion
Discontinuing the routine practice of ordering fungal and mycobacterial culture for prosthetic joint sources would have no negative impact on patient care but would reduce unnecessary work in the microbiology laboratory and potentially avoid additional costs to the patient. Education to the orthopedic provider group as well as best practice alerts in the EHR will be pursued, based on the findings from this study, in order to reduce unnecessary culture orders.
Increasing Burden of Antibiotic Resistance in Children Suffering from Septicemia in Tertiary Care Hospitals
Authors: Khan H , Mazhar K , Ullah R , Sajjad Naqvi S , Noorul Hasan T 
Published: October 2024

Abstract

Introduction/Objective
Invasion of the bloodstream by microorganisms constitutes one of the most serious situations in infectious disease. Children are the most susceptible groups to contract diseases specifically Blood Stream Infections (BSIs). BSIs have been considered to be the main cause of morbidity and mortality in children. It is associated with a high mortality rate of 20%–50%. The emerging causative agents and resistance to various antimicrobial agents are increasing from time to time.

Methods/Case Report
The present study was carried out to confirm the causative agents and their antibacterial susceptibility pattern in children with septicemia at Tertiary Care Hospitals, Peshawar, KP, Pakistan. This cross- sectional study involved about 873 pediatric patients (≤ 13 years). BACTEC BD 9050 system was used to identify the causative organism, and sub-cultures were done on MacConkey Agar and Blood Agar. The antibiotic susceptibility test was done using the Kirby Bauer Disk diffusion method as per CLSI guidelines.

Results (if a Case Study enter NA)
Among 873 study subjects 568 (65.06 %) were males followed by 305 (34.93 %) females. Out of the 873 tested blood samples, blood cultures were positive in 83 (9.51%) followed by 122 (13.98%) skin contaminants, and no growth was observed in 668 (76.51%) cases. The majority 43 (51.80 %) of them were neonates (≤ 28 days). Gram-positive and Gram-negative bacteria constituted 58 (69.87%) and 25 (30.13%), respectively. The most frequent pathogen found was Staphylococcus aureus 54 (65.06 %), followed by Klebsiella spp., E. coli, and Pseudomonas aeruginosa 6 (7.22 %), Salmonella spp. 5 (6.02 %) Enterococcus faecalis 3 (3.61 %), Acinetobacter baumannii 2 (2.40 %) and Staphylococcus epidermidis 1 (1.20 %). In Staphylococcus aureus about 6 (11.11) were MRSA. The majority of bacterial isolates showed high resistance to Ciprofloxacin, Ceftazidime, Cefuroxime, Co-trimoxazole, Cefepime, Cefotaxime, Minocycline, Tobramycin, Cefoxitin and Cephradine that are commonly used in the study area.

Conclusion
The majority of the isolates were multidrug resistant. These higher percentages of multi-drug resistant emerged isolates urge us to take infection prevention measures and to conduct other large studies for appropriate empiric antibiotic choice.
Case Series: Emerging Pathogens Aerococcus urinae and Aerococcus sanguinicola at a Canadian tertiary care hospital
Authors: Tariq J , Kakodkar P , Scott J , LU L , Wu F , Mehta N , Hamula C 
Published: October 2024

Abstract

Introduction/Objective
Background: Aerococcus urinae and sanguinicola are emerging opportunistic pathogen linked with urinary tract infections. Unmanaged Aerococcus infections have the propensity to precipitated into urosepsis. The ongoing gestalt of managing these infections needs standardization. We reviewed A. urinae and sanguinicola isolates from our clinical microbiology laboratory to better characterize its spectrum of clinical presentation, sources of infection, microbiological characteristics, and antimicrobial management.

Methods/Case Report
Methods: The electronic microbiology database was utilized to review the retrospective clinical data of patients that grew positive cultures for Aerococcus urinae and sanguinicola on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) in Saskatchewan from January to July 2023.
Demographic variables, site of presentation, microbiological parameters surrounding culture and sensitivities, and antimicrobial management were recorded. The results were analyzed on SPSS 28 software.

Results (if a Case Study enter NA)
Results: This cohort (n=115) had a median age 82 years [Range: 7 to 103] with a female predilection (F:M = 78:37). A. urinae and sanguinicola were primarily involved in UTI (n=96), obstructive uropathy (n=9), and urosepsis (n=6). The hypothyroidism (26.9%, n = 31) rate in this population was 3-fold higher than the age-matched background rate for our province. Aerococcus infections were predominantly monomicrobial (73.9%, n= 85 out of 115) and showed sensitivity for ceftriaxone, penicillin G, and vancomycin. Antimicrobials were seldom used in the UTI cohort (31.2%, n=30 out of 96). Amoxicillin-clavulanate (29.8%, n=25 out 84) was the most popular choice at patient discharge in monomicrobial Aerococcus infections only.

Conclusion
Conclusion: Aerococcus urinae and sanguinicola are emerging uropathogen. Despite this, the clinical significance of these Aerococcus species remains undervalued. Our case series shows that untreated or recurrent A. urinae and A. sanguinicola infections can precipitate into urosepsis. Clinicians should utilize the antimicrobial susceptibility profiles for these Aerococcus species to provide appropriate antimicrobial coverage and manage these pathogens effectively. Further studies should explore the link between hypothyroidism and these aerococcal infections.
Molecular Characterization of Endophytic Fungal Strains for Green Synthesis of ZnO and Au Nanoparticles
Authors: Abdelmonem M , EL-Rouby M N , Hammad S E , Elshikh H H , Mostafa M A , Wasim H , Abdelmageed M , Eldaly R 
Published: October 2024

Abstract

Introduction/Objective
Introduction: Traditional methods for nanoparticle synthesis often involve hazardous compounds, posing environmental risks and limiting their biomedical applications due to instability. The exploration of green synthesis approaches using natural products and eco-friendly solvents presents a challenging yet imperative pursuit in nanoparticle research.

Methods/Case Report
Methods: Endophytic fungi were isolated from healthy Eucalyptus sideroxylon plants collected from the Desert Research Center. Cultivation of fungi in malt extract broth was conducted at 28°C with agitation for 96 hours. Subsequently, fungal DNA was extracted, and ITS-rDNA regions were PCR-amplified for identification. Sequencing and phylogenetic analysis were performed to characterize the fungal isolates. Fungal filtrates were utilized for the biosynthesis of ZnO and Au nanoparticles (NPs) from ZnSO4 and HAuCl4 solutions, respectively.

Results (if a Case Study enter NA)
Results: Among the 13 fungal isolates, Fusarium chlamydosporum (FI-03) exhibited the most efficient synthesis of ZnO and Au NPs. Sequencing confirmed the identity of the fungal strain. The synthesized NPs displayed uniform spherical shapes, with ZnO NPs averaging 19.3 nm and Au NPs averaging 22.1 nm in size. Transmission electron microscopy (TEM) analysis further elucidated the morphology of the NPs.

Conclusion
Conclusion: Fusarium chlamydosporum emerged as a promising candidate for the green synthesis of ZnO and Au NPs. This environmentally friendly approach offers a cost-effective and biocompatible alternative to conventional nanoparticle synthesis methods.
Novel Effects of Chlorhexidine Gluconate on Gram-Positive vs Gram-Negative Microorganisms
Authors: Patel H V 
Published: October 2024

Abstract

Introduction/Objective
Chlorhexidine Gluconate (CHG) is a widely used antiseptic for the skin, oral areas, and cleansing oneself for surgery. Uses of CHG throughout healthcare centers have proven to reduce potential pathogens and lessen risks of central venous catheter blood infections. Gram-positive and gram-negative microorganisms can lead to major diseases such as prostatitis, candidiasis, endocarditis, and more. It is crucial to understand the effects that CHG has on these organisms so we can accurately apply it to treat these various illnesses. It also allows us to better understand the source of surgical site infections (SSIs) and prevent them.

Methods/Case Report
A minimum bactericidal concentration (MBC) was employed to see how various CHG concentrations (0% (control), 1%, 3%, 5%, 7%, and 9%) would affect the gram-positive (C. albicans and S. aureus) and gram-negative (P. aeruginosa and E. coli) microorganisms. First, a 1.0 McFarland suspension was created for each organism. Then, the various CHG concentration wells for each microorganism would be created within 96 well plates. In each well, there was always 300 μL of solution (containing the McFarland suspension and CHG liquid formula (HibiClensTM). After 4 minutes of CHG exposure in each well, an inoculating loop was used to streak a petri dish. One trial was completed after all concentrations were done for each microoganism. Each trial was incubated for 24 hours and there were a total of 6 trials.

Results (if a Case Study enter NA)
The substantial results challenged the previously assumed hypothesis that gram- negative microorganisms are more resistant to CHG. The separation between the two types of microorganisms became evident at even the 1% CHG concentration. C. albicans and S. aureus are thriving with averages of approximately 74,333 CFU/mL and 70,333.3 CFU/mL respectively for 1% CHG in comparison to the 1% CHG concentration for P. aeruginosa (2,500 CFU/mL) and E. coli (22,334.3 CFU/mL). Additionally. P. aeruginosa and E. coli had no colonies in any of the trials at 7% and 9% CHG, while C. albicans and S. aureus were present in numerous amounts.

Conclusion
Through numerous trials using an MBC as a new method, dose response curves for E. coli, P. aeruginosa, S. aureus, and C. albicans were deduced. The curves displayed how gram-positive microorganisms are more resistant to CHG than gram-negative microorganisms, defying what was previously assumed. In regards to various diseases and infections caused by these various bacteria, CHG may now be assesed for potential forms of treatment.
Anticancer Efficacy of Biosynthesized Zinc Oxide and Gold Nanoparticles
Authors: Abdelmonem M , Hammad S E , Elshikh H H , Mostafa M A , EL-Rouby M N , Wasim H , Abdelmageed M 
Published: October 2024

Abstract

Introduction/Objective
Introduction: Advancements in nanoscale materials have led to the exploration of metal oxides for cancer diagnosis and therapy. Zinc oxide nanoparticles (ZnO NPs) and gold nanoparticles (Au NPs) are particularly promising due to their biocompatibility and anticancer properties demonstrated across various cancer cell lines.

Objectives
This study aimed to isolate fungal endophytes from Eucalyptus sideroxylon leaves and utilize them for the biosynthesis of nanoparticles (ZnO NPs and Au NPs) to assess their anticancer activity.

Methods/Case Report
Methods: Healthy Eucalyptus sideroxylon samples were collected from a desert research center, and endophytes were isolated and cultivated. The fungal biomass was processed to synthesize ZnO NPs and Au NPs. Cell lines were propagated for cytotoxicity experiments using the MTT assay in a 96-well plate format.

Results (if a Case Study enter NA)
Results: Biosynthesized ZnO and Au NPs exhibited anticancer activity against HCT-116 and CACO2 cell lines. The IC50 values for ZnO NPs were 5.06 μg/mL for HCT-116 and 6.07 μg/mL for CACO2, while Au NPs showed IC50 values of 5.9 μg/mL for HCT-116 and 1.1 μg/mL for CACO2. ZnO NPs demonstrated dose-dependent toxicity on HCT-116 cells, with increasing concentrations leading to a reduction in cell viability. Similarly, Au NPs exhibited dose-dependent cytotoxicity on both cell lines.

Conclusion
Conclusion: This study underscores the potential of endophytic fungi for biosynthesizing metal nanoparticles with significant anticancer effects. ZnO NPs displayed superior efficacy against colon cancer cells compared to Au NPs, indicating their potential as therapeutic agents. The findings highlight the importance of exploring natural sources for nanoparticle synthesis and their application in cancer therapy.
Synchronous endometrial and minor salivary gland carcinomas – role of molecular diagnostics amid lack of clinical suspicion
Authors: Singh P , Stewart J , Nelson A , Mogrovejo D O 
Published: October 2024

Abstract

Introduction/Objective
Synchronous malignancies account for 3-5% of all tumor diagnoses but can be challenging to detect if one or both tumors are rare histologic subtypes and clinical suspicion is lacking. Molecular diagnostics are critical for accurate diagnosis in these difficult cases to guide appropriate patient care.

Methods/Case Report
We report the case of a 49-year-old female who was diagnosed with a high-grade, mixed- histology endometrial adenocarcinoma a few years back. She was found to have hilar and mediastinal nodal carcinoma of uncertain differentiation a couple of months after her initial diagnosis, clinically labelled as metastatic endometrial carcinoma. Following neoadjuvant chemotherapy, her hysterectomy showed complete pathologic response, and was found to be POLE ultramutated on NGS. Follow-up PET scan in 2023 showed progression of hilar/endobronchial thickening, as well as interval increase in size of mediastinal nodes, again presumed to be endometrial metastases, despite the POLE mutant status. Repeat sampling was performed from both the sites, along with comprehensive molecular profiling. Cytology from the nodes and surgical pathology from the endobronchial lesion showed similar morphology consisting of hyperchromatic basaloid cells in cribriform arrangement with tubular structures containing myxoid stromal material, negative for PAX-8, ER, p40, and TTF1 immunostains, inconsistent with endometrial metastasis. Molecular studies including FISH and NGS showed MYB1::NFIB fusion characteristic of adenoid cystic carcinoma and absence of POLE mutation, definitively refuting the clinically suspected progression of endometrial metastasis. Molecular testing confirmed that the endobronchial tumor and mediastinal nodal involvement were caused by a second primary, distinct from her POLE-ultramutated endometrial carcinoma which disappeared with chemotherapy. Her extended molecular workup also revealed a pathogenic mutation in BRIP1, suggesting a genetic cancer predisposition syndrome requiring referral for genetic counseling.

Results (if a Case Study enter NA)
NA

Conclusion
Molecular pathology is an invaluable tool for unravelling diagnostic complexity. Pathologists must integrate cytomorphology, molecular genetics and knowledge of cancer biology to steer the clinical teams towards the best patient care.
Malignant Rhabdoid Tumor masquerading as Neuroblastoma: A rare Case-report
Authors: Rahman J , Wei E , Knowles K 
Published: October 2024

Abstract

Introduction/Objective
Malignant rhabdoid tumors (MRT) predominantly impact infants and young children, typically occurring around the age of 15 months. While they can emerge from soft tissues throughout the body, but commonly initiate in the kidneys. Neuroblastoma-like characteristics are seldom observed within the varied phenotypes of malignant rhabdoid tumors. Here, we present an exceptionally rare and distinctive subtype of malignant rhabdoid tumor exhibiting features akin to neuroblastoma localized within the unusal parapharyngeal space.

Methods/Case Report
A 2-month-old female presented to the ED with an enlarging right cervical neck mass. The mother reported a one-week history of upper respiratory tract symptoms and noticed an enlarging mass of her right neck. CT reported a “parapharyngeal abscess with airway compression”. The patient was started on Augmentin with no significant improvement. Repeat CT with contrast demonstrated an enlarging rim-enhancing 3 cm mass involving the right parapharyngeal space, trachea, and right carotid arteries. Laryngoscopy and incisional biopsy of right neck lymph nodes demonstrated a high-grade malignancy with prominent nucleoli, high N/C ratio and scant cytoplasm. The tumor tested positive for CD 99, synaptophysin, and neurofilament, leading to the initial diagnosis of neuroblastoma. However, molecular analysis uncovered the loss of INI-1 on 22q11.2, prompting a reevaluation and a final diagnosis of MRT with neuroblastoma-like characteristics was made.

Results (if a Case Study enter NA)
NA

Conclusion
A range of tumors displaying distinct “rhabdoid” cytological features are collectively termed as malignant rhabdoid tumors (MRTs). Conventional immunohistochemistry (IHC) staining for CD99, synaptophysin, neurofilament, and myogenin might suggest neuroblastoma, Ewing sarcoma, or rhabdomyosarcoma. However, the absence of INI-1 expression provides a definitive diagnosis. INI-1 loss, a purported tumor suppressor gene located on chromosome 22q11.2, solidifies the tumor’s classification as malignant rhabdoid tumor (MRT). Additionally, a positive neurofilament stain in MRT is crucial for diagnostic and therapeutic assessments. This differentiation is vital, given the dismal prognosis of MRT with a 5-year survival rate of less than 10%.
Bladder cancer`s genetic Tapestry: Insights from two Cases with Ataxia Telangiectasia Mutated Gene Alterations
Authors: Elsafy H , Sami F I , Lack M , Hamza A 
Published: October 2024

Abstract

Introduction/Objective
Ataxia-telangiectasia mutated (ATM) plays a central role in the cellular response to DNA damage and is common in several tumor types including bladder cancer. The specific impact of ATM alterations on prognosis and therapy response in bladder cancer is uncertain. However, some data suggests shorter overall survival and benefit in patients treated with immune checkpoint inhibitors. This abstract explores the clinicopathologic features of two young patients of bladder cancer, harboring the ATM gene mutation.

Methods/Case Report
The institutional database was searched for diagnosis of urothelial carcinoma from January 2020 to December 2023. Only patients under the age of 30 years were included. Two cases were identified. Data such as patient age, gender, clinical history and presentation, histologic features, and gene mutations were collected.

Results (if a Case Study enter NA)
One patient was a 21-year-old male who presented with hematuria and the other was 17-year-old female who presented for work up vaginal bleeding. Both were non-smokers and had no family history of bladder cancer. Cystoscopy showed papillary tumors in both patients and TURBT specimens showing low grade non-invasive urothelial carcinoma in both patients. Genetic testing revealed ATM mutation in both patients. The male patient had recurrent disease twice and received intravesical BCG therapy, the female patient remains without recurrence 12 months later. Both patients remain under surveillance cystoscopy every three months.

Conclusion
These cases contribute to the growing body of evidence emphasizing the need for personalized therapeutic approaches and further research to unravel the complexities of bladder cancer in the context of ATM gene mutation among young patients.