bluuebunny/crossref_metadata_2025 huggingface dataset:
Applying Deep Learning Cancer Subtyping Algorithms Trained on Physical Slides to Multiphoton Imaging of Unembedded Samples
Authors: Mahmood F , Robbins C J , Perincheri S , Torres R
Published: November 2022

Introduction/Objective

Deep learning algorithms on digital images of physical tissue slides have shown potential improvements in accuracy and precision of diagnostic interpretation of neoplastic histology. Clustering-constrained- attention multiple-instance learning (CLAM) is one such method that identifies diagnostic sub-regions to accurately classify whole slides. Often, algorithm performance degrades when deployed on datasets that differ from the original set and it is subject to physical slide preparation variability. New multiphoton imaging modalities have potential workflow and quality advantages over physical slides, producing images analogous to whole slide imaging (WSI) without cutting artifacts, but performance of existing algorithms trained on digitized physical slides and applied to multiphoton images remains completely unknown. Given this, we aimed to test the performance of CLAM algorithms for subtyping renal cell carcinoma (RCC) and lung cancer (LC) applied to pseudo-colored multiphoton WSI.

Methods/Case Report

Clinical RCC and LC surgical resection samples were processed and imaged by Clearing Histology with MulitPhoton microscopy (CHiMP, Applikate Technologies, Fairfield, CT), producing digital images of un- cut, un-embeded tissue to generate H&E-like optical slices. Multiphoton images were downscaled to 0.5 um/px to match algorithm target resolution. CLAM models for subtyping RCC (chromophobe, clear cell, papillary) and LC (squamous & adenocarcinoma) previously trained using TCGA and CPTAC whole slide images of physical slides were applied directly to CHiMP multiphoton images without adjustment. Reference cancer subtype classifications were provided from physical and digital slides.

Results (if a Case Study enter NA)

For the subtypes included during training, multiphoton WSIs of RCC and LC were accurately subtyped by the CLAM models without stain normalization nor network fine tuning producing high prediction levels. Subtypes not included during the training (namely oncocytoma for RCC) resulted in low scoring model predictions (below 0.85), indicating specificity of identification. Multiple slide levels improved interpretation of several difficult cases for CLAM predictions.

Conclusion

This preliminary data suggests that CLAM models trained on standard H&E WSIs for RCC and LC subtyping are applicable to pseudo-H&E multiphoton WSIs without domain adaptations. This implies that diagnostic histologic features have been learned by these CLAM models and are efficiently recognized in digital histology images produced via CHiMP.
Exploration and Practice of Electronic, Networked and Intelligent Methods for Basic Medical Science Education to Develop Pathology Interest
Authors: Zhu M Y
Published: November 2022

Introduction/Objective

In response to the sudden COVID-19 pandemic, the Chinese government has restricted student visas for international students as part of an emergency "zero COVID" plan. As a result of these border closures, most international students enrolled in Chinese medical universities have not returned to campus for more than 2.5 years and have continued their medical education online. Basic medical science study has continued relatively smoothly compared to clinical apprenticeships, which focus more on clinical traineeship and practice. How to turn the crisis caused by the pandemic into an opportunity to improve the level of basic medical science education and level of pathology interest in our school is the topic explored in this paper.

Methods/Case Report

The methods proposed in this study include the intelligence of artificial intelligence technology and adaptive teaching tools for teaching students in accordance with their aptitude, interactive microscopic slides and gross pathology recognition methods based on computer graphics technology, and Internet-based group learning and large group discussions. All the advantages of traditional classroom teaching are therefore included and some overcome the shortcomings of traditional classroom teaching.

Results (if a Case Study enter NA)

Grades in 2019-2020 school year basic medical science courses were obtained. In this school year, the first semester was traditional education on campus and the second semester was online using the method described in this paper. Second semester grades were 17.2% higher than the first. USMLE Step 1 performance was another measured outcome because it focuses on basic science and pathology. A good outcome on this exam was obtained and the teaching method proposed in this paper is verified.

Conclusion

The author is preparing to expand the sample size to further verify, improve, and perfect the method proposed in this paper, so as to promote the depth and breadth of basic medical education and continuing success from education into success in pathology careers.
Tumor-to-Tumor Metastasis in the Central Nervous System: A 21-Year Single-Institutional Experience
Authors: Galev G , Prayson R
Published: November 2022

Introduction/Objective

Tumor-to-tumor metastasis (TTM) has two distinct morphologic appearances. In strict terms, it is a phenomenon where one tumor (donor tumor) metastasizes to another tumor (recipient tumor). Another pattern of TTM is collision tumor, where two tumors occur in immediate proximity with infiltration at the border between the two. TTM is a rare event, particularly in the central nervous system (CNS). Herein, we present a series of cases from our institution encountered in the past 21 years.

Methods/Case Report

The institutional archives were searched for CNS tumors that bear metastatic deposits or are collision tumors. The hematoxylin and eosin and any available immunohistochemical slides were reviewed. Relevant demographic and clinical data were obtained from patient medical records.

Results (if a Case Study enter NA)

Four cases were identified. The findings are summarized in the Table. The median age at presentation was 67 years (range, 60-74 years). Three patients were male. All metastases were carcinomas. Three cases were TTM in strict terms and one was a collision tumor. All TTM cases were an unexpected finding with no prior clinical or radiological suspicion for primary or metastatic neoplasm. In the collision tumor case, the metastatic tumor was an expected finding and the primary CNS tumor was an incidental one.

Conclusion

TTM in the CNS is a rare but important entity to recognize, as it often represents the presentation of an unknown primary malignancy. Further workup should aim at identifying the primary source of the malignancy, which warrants clinicopathologic correlation.
Performance Evaluation ofB. burgdorferi Serology Test Using Zeus Modified Two-Tier Testing (MTTT) Against Standard Two-Tier Testing (STTT) by Immunoblot Method
Authors: Karki S
Published: November 2022

Introduction/Objective

Lyme disease (LD) is a multisystem infection caused by tick-transmitted spirochete Borrelia burgdorferi. Serologic testing of LD is the primary diagnostic approach, and two-tiered testing is required to optimize specificity. The FDA cleared a variation of standard two-tiered testing (STTT) known as modified two-tier testing (MTTT) replacing the second tier immunoblot testing with a second enzyme immunoassay either ELISA or chemiluminescence format that can detect IgM and IgG simultaneously (MTTT-1) or separately (MTTT-2). The objective of this study is to evaluate the MTTT-2 assay performance against the predicate immunoblot method.

Methods/Case Report

Positive and negative quality controls (QC) were used to perform within and between day precision. 96 serum specimens were screened using ZEUS ELISA Borrelia VlsE1/pepC10 IgG/IgM Test System followed by method comparison using ZEUS B. burgdorferi IgG and IgM, separate test systems (ZEUS scientific, Branchburg, NJ) with the predicate MarDX Lyme Western Blot kit on Biotech Trinblot analyzer (Trinity Biotech USA, Jamestown, NY). Interference study was performed using 17 serum samples: 4 HIV positive, 5 ANA positive with high titer, 2 EBV IgG positive, 1 CMV IgG positive, 2 EBV & CMV IgG positive, and 3 reactive syphilis samples. Patient clinical chart was reviewed on results that disagreed.

Results (if a Case Study enter NA)

Within and between day precision studies were acceptable. Method comparison between MTTT-2 vs. immunoblot demonstrated 73% agreement (70/96). The remaining 26 samples showed disagreement either by IgM or IgG alone, or both. Upon clinical chart review, 8/26 samples that disagreed were likely true positive and 3/26 samples were likely false positive by MTTT-2 assay; the remaining 15/26 samples either cannot be confirmed due to lack of clinical history or inappropriately ordered as routine test. No cross-reactivity was observed on the MTTT-2 assay.

Conclusion

Our study demonstrated MTTT-2 assay is equivalent or slightly better than the predicate immunoblot method, if ordered appropriately when clinically indicated.
Clinical Lab Decision Support System for Quality Test Ordering and Utilization with Increase Reimbursement
Authors: Shrestha R , Hamill T , Beqaj S S
Published: November 2022

Introduction/Objective

It is estimated that at least 20% of the 5 billion lab orders submitted annually are inappropriate. Use of an appropriate laboratory test utilization management system (TUMS) can significantly overcome this. Laboratory Decision System (LDS) is the only automated TUMS to assist providers understand, select, order, and optimally utilize tests for disease diagnosis and management. This algorithm-based LDS rates and scores potential tests for any given disease and assigns an interpretable numeric score based on clinical relevance, medical necessity, and indication. Importantly, every orders using LDS will also have right CPT and ICD-10 codes assigned to meet the medical necessity and improve reimbursement. Therefore, in this study, we evaluated the performance of LDS as a testing utilization management system and its ability to improve the reimbursement.

Methods/Case Report

A total of 96,170 lab orders were analyzed from a reference laboratory. Of these, 814 tests were accompanied by an invalid ICD10 code and 44,671 tests or were accompanied by ICD10 that are described by Medicare as “never covered” because of inability to meet medical necessity. A total of 160,449 tests were subject to an Medicare policy review from which 112,400 tests met coverage criteria and 48,049 tests did not. These orders were then reevaluated using LDS, which can be accessed from app.medicaldatabase.com/site/api/cpoe or interfaced with EMR to determine if the system would have improved test selection and reimbursement.

Results (if a Case Study enter NA)

Of the original test order sample, 91.5% had an associated LDS score. Of these scored tests, 47.80% met coverage and 43.73% failed to meet coverage, according to the LDS Ranking System. Importantly, LDS provided recommendations for alternative diagnostic ICD10 codes or tests which could have aided physicians in choosing a more appropriate test or submitting a different ICD10 diagnostic code to meet medical necessity. 96.4% with an alternative ICD10 code or test with a score above 5, meeting medical necessity. 80.5% were recommended by the LDS system which would meet Medicare policies.

Conclusion

Use of such algorithm-based testing selection and ordering database that rates and scores potential tests for any given disease based on clinical relevance, medical necessity, and testing indication, would eventually help providers to select and order right test and reduce miss-utilization of tests.
Association Between Daily Sample Collection Time and Results of Testosterone Testing in Adult Males
Authors: Windham A K , Brimhall B , Nguyen K
Published: November 2022

Introduction/Objective

Serum testosterone levels in men have diurnal fluctuation with levels peaking between 7 AM and 10 AM, reaching an early evening nadir around 7 PM. For evaluation of male hypogonadism, fasting total testosterone levels should be measured in the early morning (8 to 10 AM). Testosterone measurements made beyond peak times may yield misleading results. We aim to investigate specimen collection times and compare with testosterone levels.

Methods/Case Report

We examined specimen collection times for testosterone testing (n=3075) for adult males (age >16 years) over a four-year period (July 2016-June 2020). Collection times were grouped into 2-hour intervals and test interpretations were grouped as either “low” or “high/normal”. Collection times were categorized as either morning (between 6 AM and 12 PM) or non-peak times (between 12 PM and 6 AM) A chi-square analysis was performed to investigate the possible relationship between low testosterone levels and specimen collection time.

Results (if a Case Study enter NA)

Approximately two-thirds of testosterone test samples were collected outside the recommended timeframe of 8-10 AM and accounted for 70% of low testosterone levels. The chi-square test showed that there is a significant (p=0.005) overall relationship between specimen collection times and testosterone levels. A correspondence plot of chi-square residuals showed a positive relationship between low testosterone levels collected at non-peak times. Conversely, there was a negative relationship between low testosterone levels collected in the morning.

Conclusion

Low testosterone levels measured on specimens collected outside of peak morning hours may be difficult to interpret and may lead to additional unnecessary repeat testing or treatment.
Diagnostic Testing for Gastrointestinal Surgery Patients at Academic and Non-Academic Health Systems
Authors: Zhou Y , Windham A K , Whitted M , Brimhall B , Podichetty A , Clark K
Published: November 2022

Introduction/Objective

Comparisons of surgical inpatient clinical laboratory test and radiology imaging utilization between multiple academic and non-academic health systems are very uncommon.

Methods/Case Report

Using the Vizient Clinical Data Base®, with permission from Vizient, Inc. (All rights reserved.), we compared clinical laboratory and imaging utilization over 3 years (2019-2021) for adult patients hospitalized for major GI surgical procedures at mid-size (250-450 hospital beds) academic (N=12; 8,706 hospitalizations) and non- academic (N=18; 7,930 hospitalizations) hospitals across the US. We used Medicare Severity Diagnosis Related Groups (MSDRG), employed by the US Centers for Medicare and Medicaid Services (CMS), to identify hospitalizations for major small and large bowel procedures (MSDRG triplet 329-331). Using single MSDRGs, we stratified patients by comorbid conditions and complications into high, moderate, and low severity groups. We compared the mean number of laboratory tests (CPT codes 80000-89999), and imaging studies (CPT codes 70000- 79999) per hospitalization and per hospital day. We measured aggregate Clinical Resource Intensity Weight (RIW) per hospitalization to quantify diagnostic resource consumption for each encounter. The RIW is based on the CMS Ambulatory Payment Classification weights.

Results (if a Case Study enter NA)

Academic hospitals had significantly (p<.01) higher mean laboratory tests per encounter (65.6 vs. 43.0 tests, 52.6% higher) and per hospital day (7.6 vs. 5.1 tests, 49.0% higher). Laboratory RIW was also higher at academic hospitals per hospitalization (12.8 vs. 10.3, 24.3% higher) and per hospital day (1.7 vs. 1.5, 13.3% higher). Mean imaging studies were also higher at academic centers per case (3.5 vs. 3.1 studies, 12.9% higher) and per day (0.37 vs. 0.33, 12.1% higher), but lacked statistical significance. Imaging RIW was not significantly different between academic and non-academic hospitals either by encounter (6.5 vs.6.2, 4.8% higher) or per day (0.697 vs. 0.700, 0.4% lower). Analysis of utilization after stratification by severity revealed similar patterns with larger differences at higher severity levels.

Conclusion

Mean diagnostic tests per hospitalization are greater at academic hospitals. These differences persist after adjustment for hospital length of stay and severity level. Laboratory test RIW is higher at academic hospitals. However, differences are not significant for imaging RIW.
The Value of Virtual Meetings during COVID-19 Pandemic in Healthcare Settings
Authors: Sughayer M A , Dabbagh T Z , Souan L , Alsughayer A
Published: November 2022

Introduction/Objective

The coronavirus pandemic led to an unprecedented rise in using virtual meeting technology in the healthcare sector for conferences, business meetings, and continuous medical education. This study aims to understand the practices and individual preferences and to highlight the benefits and challenges of virtual meetings compared to in-person ones.

Methods/Case Report

This cross-sectional study was disseminated via email as an online survey, using SurveyMonkey (Momentive Inc. San Mateo, California, USA) and targeted healthcare providers at the King Hussein Cancer Center-Amman, Jordan.

Results (if a Case Study enter NA)

A total of 342 healthcare providers took part in this questionnaire. 82.5% of respondents reported participating in virtual meetings; of those, only 33.5% preferred virtual over in-person meetings (PrV). Whether virtual meetings were equivalent to in-person ones, 33.2% of all participants (71.4% of the PrV) said virtual meetings were equivalent to in-person meetings in terms of participants’ attention (p<0.001). Additionally 54.8% of all participants believed their gain level was less in virtual meetings compared to the conventional in-person ones; this percentage differs significantly between the participant's group who preferred in-person (PrP) over virtual meetings and the PV group who believed otherwise (75.0% vs 13.2%, p<0.001). Nonetheless, when respondents were asked about their meeting preferences in the event of a pandemic, 49.5% of all healthcare providers preferred virtual over in-person meetings (91.3% of the PrV group p<0.001). Almost half the participants (54.3%) reported that they tend to temporarily leave virtual meetings before it is over, yet, this percentage rockets to 70.0% if the meeting is over 2 hours long. On the other hand 43.3% of respondents admitted to leaving the meeting physically while keeping themselves logged in on their mobile/computer. An interesting result of the survey was that 58.3% of all respondents preferred to attend virtual meetings during working hours (85.7% of the PrV group, p<0.001). Finally, when asked about performing other tasks while in a virtual meeting, the vast majority (82.6%) of respondents confirmed either answering the phone, reading/sending emails, or checking a social media outlet at least once, which contributes to a lack of adequate concentration.

Conclusion

Healthcare providers still prefer and attach more value and benifit to in-person interactions
Primary Hepatic Carcinosarcoma: A Rare Diagnosis With Unique Morphology
Authors: Asghar I A , Qu H , Ishtiaq H , Palmateer B
Published: November 2022

Introduction/Objective

The terminology and pathogenesis of primary hepatic carcinosarcoma remain controversial, as they are less than 1% of all hepatic cancers. The diagnostic challenges include interpreting their distinct morphology, immunohistochemical staining and excluding the differential diagnosis.

Methods/Case Report

Our case is of a 72-year-old man with history of smoking and occasional alcohol use. There was no history of viral hepatitis. He came with the complaint of abdominal pain and found to have 20 cm confluent mass in the left lobe of liver on imaging studies. Needle core biopsy was performed on the liver mass and showed biphasic malignant neoplasm with geographic necrosis. The tumor displayed two distinct patterns of growth. Portions of tumor exhibit vesicular nuclei with prominent nucleoli and abundant granular cytoplasm forming sheets and pseudoglandular structures. There were also separate well-demarcated foci of undifferentiated malignant epithelioid to spindle cells with abundant mitosis and apoptosis. The areas of hepatocellular differentiation were positive for Hep- Par-1, arginase and cytokeratin cam 5.2 and weak staining for glypican-3. They were negative for vimentin and smooth muscle actin. In contrast, the undifferentiated component is negative for Hep-Par-1, arginase, cytokeratin cam 5.2 and positive for vimentin (but not smooth muscle actin). The morphology and immunohistochemical staining pattern were consistent with a hepatic carcinosarcoma with undifferentiated sarcomatous component. The patient was put on palliative care due to the advanced nature of his disease.

Results (if a Case Study enter NA)

NA.

Conclusion

Despite the advancements in diagnostic techniques and treatment modalities, hepatic carcinosarcoma still is a rare occurrence with very dismal prognosis.
The SARS-CoV-2 Pandemic and Its Impact on the Incidence of Parasitic Gastrointestinal Illnesses in Pediatric and Adult Populations
Authors: Parsons D , Lavik J
Published: November 2022

Introduction/Objective

The initial months of the SARS-CoV-2 pandemic entailed unprecedented changes to the way lives are lived worldwide, resulting in new means of social and economic engagement. For instance, stay-at-home orders led to youths (and staff) attending school virtually. Likewise, entire sectors of the workforce were blocked from their offices and jobs went online. The aim of these public health policies was to reduce the transmission of SARS- CoV-2; however, less attention has been given to how these policies have impacted the spread of other communicable illnesses. As such, we hypothesized that stay-at-home orders, in conjunction with increased hygiene surveillance and other public health guidelines, altered the transmission cycles of communicable gastrointestinal parasites. We anticipated that when plotted against time, a decrease in positive cases would occur concomitantly with known periods of lockdown; similarly, an increase in positive cases would follow efforts to re-open society.

Methods/Case Report

To probe this hypothesis, the laboratory information system was queried for positive and negative cases of Giardia and Cryptosporidium identified within the Indiana University Health System based on the Surve-Vue Signature™ Crypto/Giardia assay (Fisher Healthcare, Waltham, MA).

Results (if a Case Study enter NA)

Results were categorized by patient age: 0 to 18-years-old and 19-110-years-old. Initial review of the pediatric data set reflected that pandemic-related public health measures did not meaningfully alter the incidence of positive test results for these two parasites, though notable observations suggested patterns buried more deeply within the data.

Conclusion

The findings of this study have broad implications regarding the perceived and actual communicability of Giardia and Cryptosporidium (as well as other gastrointestinal parasites) in both normal and pandemic-times.
The Changing Epidemiology of the Respiratory Syncytial Virus in Light of the COVID-19 Pandemic
Authors: Irfan A , Lankachandra K
Published: November 2022

Introduction/Objective

The epidemiology of a virus can be based on its evolving virulence, environmental and societal factors. Here we analyze the impact of the COVID-19 pandemic on the Respiratory Syncytial Virus (RSV).

Methods/Case Report

A 5-year retrospective study performed at Truman Medical Center, Kansas City, Missouri, analyzed 390 RSV positive cases by Lab PCR (polymerase chain reaction) for adult and pediatric patients, between the months of July- December, 2017-2021. Cases were divided into two groups - pre-pandemic and pandemic. Data was collected for both groups and categorized by age, gender, admission rate, summer months (July-September), winter months (October-December) and COVID-vaccination-status. A chi-square analysis was used to compare the above categorized data between both groups.

Results (if a Case Study enter NA)

Out of 390 cases, the annual incidence of RSV, pre-pandemic averaged at 71. This number fell drastically to 9 cases in 2020 followed by an overwhelming 168 cases in 2021. The incidence of cases in 2021 was higher in the summer months compared to pre-pandemic days, p<.00001. Additionally, the incidence of cases in children <5 years was greater during 2021, p=0.0014. Of note, no individuals <20 years of age, reported positive in 2020. Of the population eligible for the COVID19 vaccine, 24% of those who tested positive had also been vaccinated. There was no significant difference reported with regards to other age groups, gender or admission rates.

Conclusion

Adequate social distancing and non-pharmaceutical interventions (masks, handwashing etc.) can explain the sharp decline in cases in 2020. RSV appears to have evolved to a more virulent strain ever since, resulting in more infections during the summer months, especially targeting children under the age of 5.
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

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

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 >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

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

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

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

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<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<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

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

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

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

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.