bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meningitis Multiplex-PCR: 3-Year Study of Cost and Correlation With Traditional Cerebrospinal Fluid Analysis
Authors: DeRosa P A , Annitsakis D , Chi S , Akselrod H 
Published: November 2022

Abstract

Introduction/Objective
Physicians often rely on Cerebrospinal Fluid (CSF) cytology, chemistry, and culture. While cheap, these methods lack high sensitivity/specificity or have long turnaround times. PCR evaluation of CSF has become more common and is often touted as a way to save money, decrease turnaround times and quickly target antibiotics. PCR systems may cost $200,000, with $150 in disposables per test. As a new, fast, test it may be over ordered.

Methods/Case Report
Case-control study using retrospective chart review. All adults, aged 18 and over, who had undergone both PCR based testing and cytochemical testing between 3/1/2017 and 9/7/2019 were included.

Results (if a Case Study enter NA)
From 3/1/2017-9/7/2019, there were 381 available PCR results for adult GWUH patients. Demographic data showed that the patient sample was majority black (195/320, 60.94%), had an average age of 49.8 ± 17.2, and was majority female (172/320, 53.75%). The PCR results were 85.31% negative (273/320) and the CSF cultures were 94.38% negative. The most common PCR positive organism was Varicella zoster virus (11/47 positive results) and the most common CSF culture organism was Streptococcus pneumoniae (5/18 positive cultures).

Conclusion
In a population with clinical symptoms and at least 1 abnormality on CSF analysis, 6.5 tests were run for every positive PCR test. No single variable was found to significantly predict PCR results. Within a high initial cost, a disposable cost of $150 per test and detection rate of 14.7%, the cost to detect a single positive test by PCR could approach $4,500. PCR should be used judiciously following history, physical exam and standard CSF workup, rather than as a screening tool.
In-vitro Activity of Ceftolozane-Tazobactam Against Multi-Drug ResistantPseudomonas aeruginosa in a Tertiary Care Center in Al-Ahsa, KSA
Authors: Jaber F , Aljawad H 
Published: November 2022

Abstract

Introduction/Objective
Pseudomonas aeruginosa is a major nosocomial pathogen often causing serious multi-drug resistant (MDR) infections. Resistant strains, including carbapenem-resistant (CR), are increrasing especially in intensive care units (ICU) which limits treatment options to nephrotoxic aminoglycosides and polymyxins, and results in failure of initial therapy, significant mortality, morbidity and cost. Ceftolozane-tazobactam (CT) is a novel antimicrobial showing good activity against MDR and CR isolates; however, reports of resistance are increasing. Data from KSA is scarce. The aim of this study is to determine the in-vitro activity of CT against MDR and CR P. aeruginosa

Methods/Case Report
Single-center retrospective observational study of patients with P. aeruginosa infection in 2020 and 2021. Data including susceptibility to anti-pseudomonal drugs were retreived from medical records. Non-duplicate consecutive first isolates from all clinical specimens were included. MDR strains were labeled following international guidelines. Data was analyzed using the Statistical Package for the Social Sciences software (SPSS®).

Results (if a Case Study enter NA)
Out of 538 isolates collected, 98 (18.2%) were CR and 62 (11.5%) were MDR. MDR isolates were mainly retrieved from respiratory samples (44%), bedsores (29%) and urine (21%). 62% of CR and 76% of MDR isolates were from patients &gt;60 years of age; significantly higher than younger patients. 85% (83/98) of CR and 81% (50/62) of MDR isolates came from ICU patients where the prevalence of CR and MDR was 34% and 20%, respectively; significantly higher than other areas. Overall sensitivity to CT was 97%, 85% for CR and 71% for MDR isolates. Only amikacin performed better with 98% sensitivity overall, 92% for CR and 86% for MDR. Sensitivity to CT in ICU was 94%. CT was effective against 83% of CR and 70% of MDR isolates second only to amikacin (90% and 84%, respectively). Other tested antimicrobials were ineffective against MDR and CR isolates.

Conclusion
CT shows good in-vitro activity against MDR and CR P. aeruginosa isolates. It may provide a therapeutic option to treat urinary tract infections and hospital-acquired or ventilator-associated pneumoniae especially in critically ill elderly patients. More studies on treatment responses and emergence of resistance are required to establish the role of CT as an effective treatment of serious P. aeruginosa infections.
In Vitro Activity of Clinically Used Farnesol and Other Antifungals Against Pre-formedCandida albicans Biofilms
Authors: Abdelmonem M , Eldaly R , Wasim H , Elhusseny A , Abdelmageed M , Saleh Abdelfattah M 
Published: November 2022

Abstract

Introduction/Objective
Introduction: The emergence of antifungal resistance patients after long-term antifungal treatment shows an urgent need to develop new antifungal therapies. The ability of Candida albicans cells to form biofilm is resistant to many antifungal agents; it causes about 90% of vaginal yeast infections. Farnesol has a critical regulatory (quorum-sensing) molecule in C. albicans biofilm formation, a phenomenon that may be relevant to C. albicans biofilm formation. This study aims to prophesy the effect of Farnesol against pre-formed Candida albicans biofilms on the Intra-uterine devices (IUDs) users in Egypt.

Methods/Case Report
The study was carried out in The Delta region, Egypt, and included 325 females using IUDs with vaginitis syndromes with a median age of 20 to 45 years. About 291 (58.75%) Candida albicans were isolated from all cases. Vaginal swabs and IUDs were collected. The cultural characters identified the isolated organisms; the formation of biofilm in vitro was identified by (polystyrene multiwell microtitre plates (96 flat bottoms wells & Polymetheylmethacrylate strips (PMMA)). Antifungal susceptibility testing of plaktonic cells was identified by (The broth microdilution method, Spectrophotometric Modified Microdilution Method, and Colorimetric Modified Microdilution Method). In vitro activity of clinically used fluconazole, amphotericin B, and farnesol against pre-formed biofilms formed using RPMI was assessed using the XTT-reduction assay.

Results (if a Case Study enter NA)
Values of Candida biofilm untreated with antifungals were 11 independent biofilms formed in each of 8 different rows of the same 96 wells microtiter plate. The experiments showed the increased resistance of sessile C. albicans cells to fluconazole and amphotericin B. Farnesol was the only antifungal agent which showed potent activity indicated by the low SMIC80 values (0.03125μg/ml).

Conclusion
This study highlights the drastic reduction of Franesol on C.albicans biofilm. We recommend using Franesol as an antifungal agent for C.albicans in Egypt.
Commonly Isolated Organisms Isolated from Urine Cultures In United Arab Emirates (UAE)
Authors: Abdelmonem M , Saleh Abdelfattah M , Wasim H , Eldaly R , Elhusseny A , Abdelmageed M 
Published: November 2022

Abstract

Introduction/Objective
Urinary tract infection is the most common reason for infection in the hospital setting, nursing home residents, and the second most common infection in the overall population. Females are more at risk of getting urinary tract infections (UTIs) than males. UTIs remain very common as 50% of women report having at least one UTI in their lifetimes. The risk is higher for older patients, especially when they have a catheter.

Objectives
The current study aimed to determine the commonly isolated organisms from urine cultures In United Arab Emirates (UAE).

Methods/Case Report
The study was performed on 4885 urine cultures collected from patients in the United Arab Emirates. The system has identified the micro-organisms using a fluorogenic methodology for organism identification and a turbidimetric method for susceptibility testing using a 64-well card that is barcoded with information on card type, expiration date, lot number, and unique card identification number.

Results (if a Case Study enter NA)
A total of 4885 urine cultures were collected; 3793 (77.6%) urine samples were collected from females and 1092 (22.4%) from males. We identified 81 organisms that have been isolated from all urine cultures. The most frequently isolated organisms were eight organisms 4017 times out of the 4885 (82.2%), whereas the other 73 organisms were found in 868 cultures representing only (17.8%) of the whole samples. E. coli was the most isolated organism by 2078 times, representing (42%) of total isolated organisms. The number of samples in the other seven common isolated organisms was 762 for Klebsiella pneumonia, 330 for group B streptococci, 307 for Enterococcus faecalis, 218 for Candida albicans, 197 for Pseudomonas aeruginosa, 84 for Staphylococci aureus, and 41 for Staphylococci saprophyticus representing (16%), (7%), (6%), (4.5%), (4%), (1.7%), (1%) respectively of the total number.

Conclusion
The study revealed that E. coli was the most common cause of urinary tract infection, followed by Klebsiella pnumonaie. Women with recurrent UTIs are worth concern for antimicrobial prophylaxis. This study gave us a clear picture of the main causative agents of UTIs so that it might help select medication.
Crisis of Vaginitis;Candida albicans in Intrauterine Device (IUD)
Authors: Abdelmonem M , Abdelmageed M , Elhusseny A , Eldaly R , Wasim H , Saleh Abdelfattah M 
Published: November 2022

Abstract

Introduction/Objective
Fungal infection is usually caused by an overgrowth of yeast typically found in the vaginal flora. The major pathogen C. albicans is the best-characterized member of the Candida clade. Candida species are common inhabitants of the female genital tract, and the use of intrauterine devices (IUDs) has been associated with pelvic inflammatory diseases. This study explored the relationship between insertion (IUDs) and candidiasis.

Methods/Case Report
350 female patients using IUDs suffering from vaginitis from The Delta region, Egypt, were enrolled in this study. The median age was 20 to 43 years old. Vaginal swabs and IUDs were collected. Patients were classified according to the period of using IUDs as the following. Group 1: 46 users of IUDs for a period of one month to one year. Group 2: 85 users for one year to 5 years. Group 3: 171 users for five years to 10 years. Group 4: 52 users for 10 years to 20 years. The cultural characters identified the isolated organisms (morphological characters of the purified fungal isolates were carried out according to the organism's colony characters and biochemical tests).

Results (if a Case Study enter NA)
: 292 patients were positive for Candida albicans. We observed that 38 (5.59 %), 41 (11.2 %), 163 (7.6 %), and 48 (5.93 %) cases have positive Candida albicans for group1, group2, group2, and group4 respectively. There was a statistically significant difference between the occurrence of Candidiasis and IUDs in all studied groups P-value was ≤ 0.05.

Conclusion
In Egypt, women who use intrauterine devices have a higher chance of developing vaginitis. The findings indicated that women who used IUDs for longer periods of time had a higher risk of developing candidiasis. We advocate for the regulation of IUDs and the education of women on how to recognize the symptoms of candidiasis vaginosis and how to properly treat it.
Fluctuations of SARS-CoV-2 Antibody Concentrations with Age in Vaccine Naïve Population with SARS-CoV- 2 Infection
Authors: Akinyemi A , Wantuch A , Errath A , Manjee K , Benirschke R C , Lee H 
Published: November 2022

Abstract

Introduction/Objective
Notable differences have been observed in the severity of COVID-19 disease across age groups. This study’s aim was to investigate the antibody dynamics in children versus adults after natural infection with SARS-CoV-2.

Methods/Case Report
Charts of patients who had SARS-CoV-2 spike protein antibody (SPA) testing at our institution were reviewed. Patients with positive SPA and no documented evidence of SARS-CoV-2 vaccination were selected. SARS-CoV-2 nucleocapsid antibody (NA) testing was performed on the same SPA positive blood specimens to confirm that positive SPA was due to SARS-CoV-2 infection. In cases where NA testing could not be performed, SARS-CoV-2 polymerase chain reaction results were used to confirm previous infection. Patterns involving age, NA, and SPA concentrations were detected using scatter and box-and-whisker plots. Wilcoxon signed-rank tests were subsequently used to assess for statistical significance in the different age groups. This study was approved by our institution's IRB.

Results (if a Case Study enter NA)
There were 372 patients who had SPA testing and previous SARS-CoV-2 infection. SPA concentrations were not uniformly distributed but showed significantly higher concentrations in younger patients with a visually determined inflection point of around 20 years old. This was statistically confirmed by binning ages by decade of life and comparing their medians (p-value&lt;0.05). Within the cohort, 107 patients were 20 years old or younger while 265 were older. Patients 0-20 years old had higher median SPA levels (262.9 U/mL vs. 108.2 U/mL, p-value&lt;0.05) and significantly more variation (interquartile range 535 U/mL vs. 235 U/mL). NA levels showed a similar pattern in the overall distribution, but there was no statistically significant difference between the age groups (medians 45.835 U/mL vs. 30.3 U/mL, p-value=0.44).

Conclusion
These findings suggest that patients up to 20 years old have significantly higher SPA levels following SARS-CoV-2 infection, which may explain the milder symptoms of COVID-19 disease in children.
Unusual Combination of Gastrointestinal Pathogens Detected by Multiplex PCR
Authors: Akgun Y , Tao L , Maris A , Humphries R , Schmitz J 
Published: November 2022

Abstract

Introduction/Objective
Infectious gastroenteritis (IGE) is a common but complex entity which is a major cause of global morbidity and mortality. IGE is caused by a wide range of etiologic agents such as viruses, bacteria, and parasites. In the United States there are approximately 373 million of IGE cases per year. Most cases of IGE resolve without identification of a specific pathogen. Multiplex molecular assays allow identification of multiple possible pathogens with rapid turnaround time and increased sensitivity, facilitating to formulate an effective treatment plan and control measures.

Methods/Case Report
We present a case of a pediatric patient with no significant past medical history who has been having runny stools that have progressively worsened in the last 3 months and 2 days history of bloody stools with mucus before emergency room presentation. She had no fever, vomiting, joint pain, oral ulcer, and rash. Physical exam showed that the patient appeared well, nontoxic, and vital signs were within normal limit. Copious rhinorrhea was noted. She was at 50th percentile for age on the growth chart. Family denied any recent travel or sick contacts however stated that all the family members have been on well water. Complete blood count was obtained and showed a platelet count of 669 x 10(3)/mcL and WBC of 16.6 x 10(3)/mcL with differential showing absolute lymphocytosis, absolute monocytosis and absolute eosinophilia. Biofire FilmArray gastrointestinal panel performed on the stool detected Giardia lamblia, Campylobacter, Shiga-like toxin producing E. coli and Adenovirus F 40/41. Repeat of the panel per protocol detected the same four pathogens.

Results (if a Case Study enter NA)
N/A.

Conclusion
This case report highlights the significance of detecting multiple causative pathogens. While long term watery diarrhea may guide clinicians to malabsorptive process and the use of well water to Giardia, a sensitive and specific multiplex assay can detect all the pathogens involved in the disease process and greatly simplify the treatment plan for patients. This unusual combination of pathogens can explain the unique symptomology of the patient including long term watery diarrhea, recent bloody diarrhea as well as copious rhinorrhea and failure to thrive.
Salmonella Infantis Meningitis in a Pediatric Patient After in-Utero Exposure to Ustekinumab
Authors: Akgun Y , Tao L 
Published: November 2022

Abstract

Introduction/Objective
Salmonella meningitis is associated with a significant neurological sequelae, subdural effusions, cerebral infarction, encephalitis, cerebral abscess, and high mortality. It is a rare complication of Salmonella sepsis and occurs almost exclusively during early infancy. Salmonella is identified as pathogen in less than 1% of confirmed cases of bacterial meningitis in infants. Immunocompromised individuals have higher risk of having invasive salmonellosis.

Methods/Case Report
We present a case of 4-month-old male with no significant past medical history who was presented to emergency department with five days history of fever, cough and decreased oral intake. At the time of admission, complete blood count was obtained and showed a platelet count of 702 x 10(3)/mcL, hematocrit of 25% and WBC of 17.0 x 10(3)/mcL with differential showing absolute neutrophilia and absolute monocytosis. Head ultrasound was concerning for meningoencephalitis with bilateral parenchymal echogenicity and bilateral subdural collections. Lumbar puncture showed WBC cell count of 229 (36 % PMNs, 52% lymphocytes, 12% monocytes), red blood cells of 0, glucose of 13 mg/dL, protein of 151 mg/dL. Meningitis multiplex PCR panel of the CSF was negative. MRI of the brain showed findings suggestive of meningitis with associated subdural empyema and ventriculitis without hydrocephalus. CSF culture identified Salmonella species that is susceptible to ampicillin and ceftriaxone which later identified as Salmonella infantis by the State laboratory. Immunodeficiency workup including next generation sequencing immunodeficiency panel did not reveal any known causes. Of note, mother has psoriasis and was treated with ustekinumab; an antibody against a cytokine subunit shared by IL12 and IL23, during pregnancy. The patient responded to antibiotic treatment and was discharged in a stable condition.

Results (if a Case Study enter NA)
N/A.

Conclusion
This case report highlights Salmonella infantis meningitis in a pediatric patient who was exposed to ustekinumab in utero which could cause drug induced immunodeficiency state as IL-12 is known to activate macrophages and macrophages are critical for Salmonella clearance. Although ustekinumab level was undetected in the patient right prior to discharge, the long half-life and mechanism of action of this medication could have caused an immunodeficiency state which allowed rare Salmonella infantis meningitis.
The Assessment of the Diagnostic Accuracy of Antigen-Detecting Rapid Diagnostic Test using Nasopharyngeal Swab Specimen in Detecting SARS-CoV-2 among Patients in a Private Hospital in Bulacan, Philippines
Authors: Magpoc R M , Murzo M , Jayag A P , Lee S P , Manguiat A M , Oloteo E M , Mendoza A , Hizon J S , Macalalad J C , Sison R G , Nieto X A 
Published: November 2022

Abstract

Introduction/Objective
Continuous progression of the COVID-19 outbreak prompted an expensive, limited, and slow-moving laboratory-based molecular testing capacity of the gold standard, Real-time Reverse Transcription- Polymerase Chain Reaction (rRT-PCR), in detecting SARS-CoV-2. The vital step in mitigation is utilizing an accurate diagnostic detection assay to deploy various preventive measures. Therefore, there is a need to evaluate an accessible, fast, and inexpensive point-of-care immunoassay, such as Antigen-detecting Rapid Diagnostic Tests (Ag- RDTs). Thus, the study aimed to assess the diagnostic accuracy of Ag-RDT in detecting SARS-CoV-2.

Methods/Case Report
A non-experimental, quantitative, and cross-sectional cohort study utilized 272 SARS-CoV-2 Ag-RDT with rRT-PCR confirmation collected from April 2021 to February 2022 in a private primary hospital laboratory database in Bulacan, Philippines. Diagnostic accuracy parameters of Ag-RDT included in the study are sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV).

Results (if a Case Study enter NA)
The overall sensitivity and specificity of Ag-RDT were 69.6% and 98.8%, respectively. Additionally, it exhibited a PPV of 84.2% and an NPV of 97.2%. With a hypothetical 1% prevalence, PPV and NPV were 36.8% and 99.7%. Meanwhile, PPV and NPV were 86.5% and 96.7% at 10% prevalence. High specificity denotes that positive Ag-RDT test results can be confidently considered in true SARS-CoV-2 infection, while low sensitivity entails that a negative result must be subjected to confirmatory tests. Furthermore, when prevalence increases, PPV increases while NPV decreases.

Conclusion
The study primarily encapsulated that the Ag-RDT cannot replace rRT-PCR in detecting SARS-CoV-2 infections. Despite its shortcomings, Ag-RDT is still valuable in areas with moderate-to-high disease prevalence and with limited access to confirmatory test due to its high predictive values and advantages. A larger number of positive results of rRT-PCR, evaluation of factors correlating to low sensitivity, and a prospective study are recommended for future studies.
Rapid Detection of Uropathogens and Antibiotic-resistant Genes Using Open Array Multiplex PCR Technology
Authors: Neopane P , Nypaver J , Beqaj S S , Shrestha R 
Published: November 2022

Abstract

Introduction/Objective
Introduction: Standard diagnostic practices for Urinary Tract Infection (UTI) take 2–3 days for pathogen identification and antibiotic susceptibility testing leading to delayed diagnosis and an increase in healthcare expenditures. The rapid diagnostics tool is highly desirable to identify the pathogen and its antibiotic-resistant genes directly from the samples. Our objective is to validate and evaluate the performance of Open array multiplex PCR for pathogen identification and antibiotic resistance genes.

Methods/Case Report
Method: Open array multiplex PCR method for 20 UTI pathogens was validated using ATCC organisms and inter-laboratory correlation using 50 urine samples. Briefly, samples were homogenized using Omni bead ruptor 96, and DNA was extracted using Hamilton Vantage. Customized open array and UTI chips with 20 most common urinary tract pathogen target and 13 resistant genes target specifically for UTI treatment were filled with Taqman open array PCR master mix and extracted DNA in a 1:1 ratio. UTI chips were prepared on Accufill and real-time PCR was performed on Quantstudio 12K flex. A total of 116 de-identified patient samples were analyzed.

Results (if a Case Study enter NA)
Result: The sensitivity, specificity, and accuracy of this method were more than 90% considering the reference method as the standard method. A total of 14 different types of organisms were detected. Escherichia coli (n=49) was the highest among all. Multiple pathogens were identified in 27 urine samples. Organisms such as Ureaplasma and Megasphaera 1 were detected in nine and four samples, respectively. All positive samples were resistant to at least one or two resistant genes. tetM and tetS were resistant among 72 samples, erm A, B, and C in 60 samples, ESBL in 30 and fosfo A in 21 samples.

Conclusion
Conclusion: The open array multiplex PCR technology may help in the early diagnosis and treatment that can improve patient care, shorten hospitalization, and reduces the economic burden.