bluuebunny/crossref_metadata_2025 huggingface dataset:
The Association Between Serum Hyaluronic Acid Levels and Routine Liver Function Tests in Liver Fibrotic HCV Patients
Authors: Abdelmonem M , Wasim H , Elhusseny A , Eldaly R , Saleh Abdelfattah M , Abdelmageed M
Published: November 2022

Introduction/Objective

Liver fibrosis is the excessive accumulation of extracellular matrix proteins, including collagen, that occurs in most types of chronic liver diseases. Advanced liver fibrosis results in cirrhosis, liver failure, and portal hypertension and often requires liver transplantation. Markers (NIM) of Liver Fibrosis, such as hyaluronic acid, help evaluate the stage of fibrosis in patients with liver fibrosis. This study aims to investigate whether or not there is a correlation between serum hyaluronic acid levels and liver function tests in patients who suffer from chronic HCV-induced liver fibrosis.

Methods/Case Report

This study was conducted on 118 (60 males and 58 females) patients recruited from Internal Medicine Dept., Mansoura University Hospitals, Egypt. The patients were diagnosed with chronic HCV-induced liver fibrosis. Also, we included 50 healthy comparable control subjects (27 males and 23 females). Routine laboratory tests such as AST, ALT, albumin, total bilirubin, and platelets count were performed. The APRI was calculated as [AST/ (upper limits of normal)/ platelets count 109/L]×100. The AST-ALT ratio was calculated as [AST/ ALT]. According to the manufacturer's instructions, the serum levels of hyaluronic acid were measured by radioimmunoassay.

Results (if a Case Study enter NA)

We observed a statistically significant positive correlation was found between serum hyaluronic acid levels and APRI (r=0.3, p=0.001), ALT (r=0.3, p=0.003), AST (r=0.3 and p=0.01), and total bilirubin (r=0.3 and p=0.002). Furthermore, there was a statistically significant negative correlation between serum hyaluronic acid levels and albumin (r= -0.43, p=0.0001), and platelets count (r= -0.4, p=0.0001).

Conclusion

The levels of hyaluronic acid in the body and the results of other liver function tests tend to rise in tandem, which suggests a significant relationship between the two. This may assist us in constructing an accurate picture of the patient's condition, which will lead to a more precise diagnosis.
Quality Improvement at the Laboratory’s Specimen Reception Station
Authors: Ong S , Pasaribu S , Tan S , Aw T , Huang J , Woo M , Koh S , Khoo K
Published: November 2022

Introduction/Objective

In our 1000-bed acute care tertiary hospital, physicians order laboratory tests via the computerized-provider-order-entry (CPOE) system and print barcode labels (patient demographics/tests ordered) at the computer-on-wheel printer. When tubes with unsuitable barcodes (misaligned, poor quality) are received at the laboratory specimen reception area a fresh barcode is re-printed by our laboratory staff. An incident involving a re- printed barcode label pasted on the wrong blood tube prompted an investigation into the quality of barcodes.

Methods/Case Report

We initiated ‘an opportunity for improvement (OFI) project’ at the laboratory specimen reception station. The OFI team involved Nursing, Information Technology (IT) and Pathology departments aimed to eliminate re-printing of barcode labels by 75% within 6 months. We collated and analyzed reasons for re-printing of barcodes on 3 separate 48-hour periods (27-28 April 2020, 24-25 June 2020, and 13-14 June 2022). A series of interventions and initiatives were implemented.

Results (if a Case Study enter NA)

Re-printed barcodes were from the Emergency Department (56%), Out-patient clinics (7%) and Wards (57%). Root cause analysis(RCA) using the “5 whys” technique categorized re-print causes into staff-related (misaligned barcodes) and printer-related (faint barcodes lines/truncated un-verifiable patient demographics). The team mass-emailed clinicians an educational “Do-You-Know” guide on proper pasting of barcodes on blood tubes and instructions on how to obtain help for printer rectification. These guide documents were placed in the hospital-wide document-sharing portal - Docupedia. Immediate close follow-up with sites that had poor barcodes was done in real-time. Barcode reprints decreased 83% within 2 months - from 174 (27-28 Apr 2020) to 30 (24-25 Jun 2020). A recent audit showed sustained elimination of barcode re-printing: 25 cases (13-14 Jun 2022).

Conclusion

The OFI project has successfully raised the quality of CPOE labels on specimen tubes contributing to process efficiency and safer patient care. Close communication with all care sites and their representatives on the OFI team are critical success factors.
Laboratory Testing for Obstetrics Patients at Academic and Non-Academic Health Systems
Authors: Windham A K , Staker C , Zhou Y , Whitted M , Brimhall B , Podichetty A
Published: November 2022

Introduction/Objective

Evaluation of obstetric clinical laboratory test utilization differences between academic and non-academic health systems would provide important benchmarking information for healthcare leaders and policy makers.

Methods/Case Report

Over a 3-year period (2019-2021), using the Vizient® Clinical Data Base with permission from Vizient, Inc. (All rights reserved.), we compared clinical laboratory utilization for adult obstetrics inpatients at mid-size (250-450 hospital beds) academic (N=9; 27,036 hospitalizations) and non-academic (N=17; 50,462 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 Cesarean section (MSDRG triplet 786-788) and vaginal delivery (MSDGR triplet 805-807) patient groups. For both groups, we stratified by comorbid conditions and complications into high, moderate, and low severity subgroups. We compared the mean number of laboratory tests (CPT codes 80000-89999) per hospitalization and per hospital day. We measured aggregate Clinical Resource Intensity Weight (RIW) per hospitalization to quantify laboratory resource consumption for each encounter. The RIW is based on the CMS Ambulatory Payment Classification (APC) weights.

Results (if a Case Study enter NA)

Academic hospitals had a significantly (p<.01) higher mean number of lab tests per Cesarean section hospitalization (20.3 vs. 10.3 tests, 97.1% higher) and hospital day (4.7 vs. 3.3 tests, 42.4% higher). Laboratory RIW per case was also significantly (p<.01) higher at academic hospitals (4.8 vs. 3.6 RIW, 33.3% higher); however, RIW per day did not differ between academic and non-academic hospitals. Significant differences (p<.01) persisted after adjusting for severity level. Although differences were smaller, academic hospitals had greater lab tests per case (12.1 vs. 8.1 tests, 49.4% higher) and day (4.3 vs. 3.6 tests, 19.4% higher) for vaginal delivery hospitalizations. Laboratory RIW per case was also significantly (p<.01) higher at academic hospitals (3.4 vs. 2.8 RIW, 21.4% higher). Laboratory RIW per day did not differ significantly. Significant differences remained for the high and moderate severity vaginal delivery groups.

Conclusion

Academic hospitals have greater laboratory test utilization for obstetrics patients. This difference appears to be largely due to a longer mean length of stay as well as use of tests with higher RIW.
High-Volume Laboratory Tests as Baseline for Benchmarking Less-Common Tests
Authors: Windham A K , Zhou Y , Brimhall B , Podichetty A
Published: November 2022

Introduction/Objective

Benchmarking establishes baseline laboratory utilization patterns across health systems. Nicholas et al. (2021) recently evaluated the use of test volume ratios to identify utilization intervention targets at VA hospitals. We aim to investigate potential differences of reported test volume ratios with those of non-VA hospitals.

Methods/Case Report

Using the Vizient® Clinical Data Base with permission from Vizient, Inc. (All rights reserved.), we obtained aggregated annual test and patient volumes from 2019-2021. To assess the accuracy of high-volume tests as a surrogate for patient volumes, we compared mean annual sodium and MCV test volumes with mean annual number of patient encounters at 712 hospitals (7,685,149 mean annual patient volume). We then calculated test volume ratios for eight less common analytes (homocysteine, prolactin, vitamin D (25-OH), HCV viral load, HIV viral load, Lyme disease serology, CD4, and HSV serology) at hospitals with patient encounters greater than 10,000 (279 hospitals, 6,046,670 mean annual patient volume). We calculated ratios using mean annual number of 1) sodium tests and 2) patient encounters as the denominator for comparison to reported ratios. All analytes are included in Choosing Wisely™ guidelines.

Results (if a Case Study enter NA)

There was strong positive correlation between mean annual sodium and MCV test volumes and mean annual patient volume (R = 0.92 and R=0.96, respectively). Our analyte-to-sodium volume ratios were smaller than expected. However, the analyte-to-patient volume median ratios were similar to those reported. A comparison of the calculated ratios showed a strong positive correlation (R=0.90), but the sodium ratios were nearly 4x smaller than the patient volume ratios. On average, the two methods agreed nearly 70% of the time for institutions with ratios greater than the 90th percentile- the intervention threshold. In comparison to previously reported median ratios, five analytes (homocysteine, prolactin, vitamin D (25-OH), Lyme disease serology and HSV serology) showed a significant difference from previously published ratios.

Conclusion

In comparison to VA hospitals, significant differences in median ratios were found. For calculating test volume ratios, high-volume tests are an adequate surrogate for patient volumes but may pose a challenge for inter- institution comparisons. Standardization for quantifying high-volume tests would improve the use of test volume ratios for benchmarking.
Safety Concerns for Laboratory Professionals in Rural Practice Settings During Covid-19
Authors: Williams J , Nunez-Argote L , Campbell J L , Brooks J
Published: November 2022

Introduction/Objective

The COVID-19 pandemic exacerbated the health risks of laboratory professionals. This study aimed to understand the impact increased workload and decreased staffing levels have, specifically in rural areas where clinical laboratory testing is performed, and to document how these changes affect the wellbeing of laboratory professionals.

Methods/Case Report

The study integrated responses from a cross-sectional study of laboratory professionals which employed an anonymous electronic survey deployed between November of 2021 and February of 2022. Specific items asked if participants had worked in clinical laboratories since the public health emergency started, if they were concerned regarding Covid-19 transmission, adequate staffing, and support at their workplace. A subsequent qualitative study including focus groups and an interview questionnaire targeted laboratory professionals working in rural laboratories in four states of the Mid-west to further understand any immediate health impacts on wellbeing for these professionals.

Results (if a Case Study enter NA)

Among 438 participants in the survey that indicated they worked in the laboratory since March of 2020, 20% said they worked in non-metro US counties (RUCC 4-9). Among the non-metro laboratory professionals, 70% indicated that staffing levels in their laboratories were inadequate, with over 50% of them expressing concern about contracting Covid-19 at their workplace, and 53% saying they had been told to work despite a possible or confirmed exposure to the virus. The analysis of thirteen focus groups (N=59) and qualitative written interviews (n=15) found that workplace changes impacted the health of laboratory professionals in rural areas. These included lack of availability of laboratory equipment and increased work hours, which increased self-reported levels of stress. Recommendations for improvement included flexibility in scheduling of hours and proper compensation for overtime work.

Conclusion

Working in rural clinical laboratories during the Covid-19 pandemic exposed laboratory professionals to stress that was exacerbated by a work environment operating in scarcity.
Metastatic Common Bile Duct Melanoma Presenting as Obstructive Jaundice: A Case Report and Review
Authors: Kaur N , Rahmanov N , Varshney N , Tang S J
Published: November 2022

Introduction/Objective

Malignant melanomas (MM) account for 4-7% of all new cancer cases. The most common primary site is the skin, however, in 1.3% of cases, these tumors originate from the mucous membranes of the respiratory, genitourinary, and gastrointestinal tracts. The metastatic spread to the biliary system is extremely infrequent, with rare reports in the literature. Herein, we report a case of history of cutaneous MM with metastasis to the biliary tract.

Methods/Case Report

A 35-year-old Caucasian female presented with pruritis, dark urine, and jaundice. Laboratory results favored the cholestatic process (total bilirubin – 10 mg/dL, alkaline phosphatase – 500 U/L, AST- 400 U/L, ALT – 1000 U/L). She had a remote diagnosis of MM of the left chest with metastases to bilateral axillary and periclavicular lymph nodes 8 years ago. She underwent wide local excision of the skin lesion and lymph node dissection then. ERCP with direct cholangioscopy revealed a 3 x 2 cm obstructive mass in the common bile duct which was biopsied to reveal cohesive, pleomorphic, epithelioid cells containing black-brown pigment with enlarged, irregular, and hyperchromatic nuclei. These atypical cells stained strongly with SOX10 and Mart-1 immunohistochemical stains, confirming the diagnosis of metastatic malignant melanoma.

Results (if a Case Study enter NA)

NA.

Conclusion

MM is cancer that originates from melanocytes, derived from the neural crest during embryogenesis. The pathogenesis of metastatic spread to the biliary system is still unknown due to the paucity of literature describing this. Diagnosis is often difficult, with many patients completely asymptomatic or occasionally presenting with biliary symptoms. There should be a detailed history, and extensive clinical workup along with extensive histological and immunoprofile, esp. in cases with a history of cutaneous melanoma for early detection of a potential metastasis leading to adequate management.
Correlation of SARS-CoV2 Viral Growth on Cultures, Ct Values, SARS-CoV-2 Variant and Vaccination Status in Asymptomatic, Pre-Symptomatic and Post-Infection Asymptomatic COVID Patients
Authors: Kaur H , Morris C P , Gallagher N , Norton J , Eldesouki R , Mostafa H , Sachithanandham J , Pekosz A
Published: November 2022

Introduction/Objective

COVID-19 large scale immunizations have helped control the infectious spread, but breakthrough infections are still observed and some of these patients remain asymptomatic. In this study, we compared the viral growth characteristics with vaccination status in asymptomatic patients.

Methods/Case Report

We searched our institutional laboratory database for asymptomatic patients infected with delta variant (November-December 2021, n=65) and omicron variant (December 2021, n=68), that were further classified as “truly asymptomatic”, “pre-symptomatic” and “post-infection asymptomatic” based on detailed chart reviews. The patients’ left-over nasopharyngeal swab samples’ cycle threshold values and the recovery of infectious virus in cell culture were compared.

Results (if a Case Study enter NA)

In the delta cohort, out of 65 asymptomatic patients, 36 were truly asymptomatic, 26 presymptomatic and 3 post infection asymptomatic patients. In the omicron cohort, out of 68 asymptomatic patients, 45 were truly asymptomatic and 23 were presymptomatic patients. The vaccination rate was 59% in truly asymptomatic (delta cohort=56%, omicron cohort=62%), 55% in presymptomatic (delta cohort=50%, omicron cohort=61%) and 67% in post-infection patients (delta cohort only). There was no significant difference in the Ct values of truly asymptomatic (mean Ct=21.08), presymptomatic (mean Ct=20.30) and post-infection asymptomatic patients (mean Ct=20.84) in the combined cohort (p=0.78) and in the delta (p=0.95) or omicron (p=0.45) subcohorts. The Ct values were not correlated with the vaccination status of the patients (vaccinated patients mean Ct=20.56, non-vaccinated patients mean Ct=20.16, p=0.68). Samples with positive viral growth on cultures had significantly lower Ct values (mean Ct= 17.16), compared to samples with negative viral culture results (mean Ct= 24.61) (p<0.0001). The viral growth on culture was not associated with the symptom status, SARS-CoV-2 variant type (delta vs omicron) and vaccination status of the patients in the delta and omicron subcohorts.

Conclusion

Our findings show that there is no significant correlation between vaccination status and viral loads and culture results in asymptomatic patients.
Serum Lipid & Hematological Profiles in Assessing Single & Multiple Soil-Transmitted Helminth Infections among Direct Fecal Smear Positive Patients in a Tertiary Provincial Hospital in Sorsogon, Philippines
Authors: San Pedro R S , Nicolas R F , Ramos A M , Robles T D , Rosales D S , Sagabaen R C , Santos G T , Sison R G , Nieto X A
Published: November 2022

Introduction/Objective

Soil-transmitted helminth (STH) infections have been recognized to be a global phenomenon and are still prevalent in tropical countries, particularly those with low human development index such as the Philippines. Previous literature have reported changes in the hematologic and serum lipid parameters of individuals with STH infections, however, there has yet to be a study in the Philippines regarding the association of said parameters to STH infections. This correlation could be valuable in evaluation, diagnosis, and treatment of STH infected patients.

Methods/Case Report

The study assessed single and multiple helminth infections caused by STH, particularly A. lumbricoides, T. trichiura, and hookworm direct fecal smear (DFS) positive patients and its correlation to hematologic and serum lipid parameters. The researchers followed a retrospective and systematic approach wherein data readily available from DFS positive patients aged 5-19 years old with complete serum lipid profile (total cholesterol, HDL, LDL, and triglycerides) and complete blood count (RBC count, hemoglobin, hematocrit, MCV, MCH, MCHC, WBC count, neutrophil count, lymphocyte count, monocyte count, eosinophil count, and platelet count) from the tertiary provincial hospital were utilized. Mean and standard deviation were used for the age and hematologic parameters. One-way analysis of variance (ANOVA) with Tukey’s HSD was used for post hoc analysis while Fisher exact test was used to compare the percentages among the groups of patients. Statistical tests were performed using RStudio, at 5% level of significance.

Results (if a Case Study enter NA)

Patients with multiple STH infection have greater risk of lymphopenia than patients with single helminth infection (p=0.053). Moreover, eosinophilia is more observed in patients infected with T. trichiura, hookworm, or with multiple STH infections compared to patients infected with A. lumbricoides alone (p=0.023).

Conclusion

This study demonstrated significant differences among DFS positive patients with single and multiple STH infections in both serum and hematological profiles.
In-vitro Activity of Ceftazidime-Avibactam Against Carbapenem-Resistant K. pneumoniae in a Tertiary-Care Center in Al-Ahsa, KSA
Authors: Jaber F , Aljawad H
Published: November 2022

Introduction/Objective

Carbapenem-resistant Enterobacteriaceae (CRE) represents an urgent global threat. Klebsiella pneumoniae is a common cause of various clinical infections showing increased rates of resistance. Carbapenem-resistant Klebsiella pneumoniae (CR-KP) is often multi-drug resistant and sometimes becomes pan-drug resistant causing serious infections with substantial morbidity, mortality and cost. Ceftazidime-avibactam (CZA) is considered to be a good alternative to standard CRE therapy. In our region, CRE is mostly due to OXA-type carbapenemases which are inhibited by CZA, however, metallo-beta-lactamases (MBLs) are being increasingly reported and against which CZA is inactive. The aim of this study is to determine the activity of CZA against CRE-KP isolated in our hospital.

Methods/Case Report

Single-center, prospective study on consecutive non-duplicate CRE-KP isolates recovered from various clinical specimens in 2020 and 2021. BD Phoenix® system was used for initial Identification and susceptibility testing. E-test was done to confirm susceptibility and determine the minimum inhibitory concentration (MIC) for CZA. The standards of the Clinical and Laboratory Standards Institute were followed.

Results (if a Case Study enter NA)

95 CRE-KP isolates were collected. CRE-KP was mostly isolated from: Respiratory samples: 36% (n=34), bedsores: 28% (n=27), urine: 23% (n=22) and 11% (10 isolates) were retrieved from blood cultures. 65% of patients were admitted to the intensive care unit (ICU), 13% were in long-term care wards and 13% were admitted for management of infected bedsores. 88 isolates were susceptible to CZA (93%) with MIC50= 1.5 μg/mL and MIC90= 4.0 μg/mL. 26 isolates (27%) were sensitive only to CZA. Susceptibility to tigecycline was 54%, amikacin 18% and gentamicin 17%. Other antimicrocbials including ceftolozane-tazobactam were basically ineffective.

Conclusion

Ceftazidime-avibactam shows excellent in-vitro activity against CR-KP isolates tested in this study. Further clinical studies on treatment efficacy and emergence of resistance are needed. Moreover, with the recent increase in reported MBLs-mediated resistance in our region, infection control measures, resistance-surveillance programs, and molecular testing may prove essential in the fight against carbapenem-resistant Enterobacteriaceae.
Biofilm Formation on Intrauterine Devices in Diabetic and Nondiabetic Patients with Vulvovaginal Candidiasis
Authors: Abdelmonem M , Eldaly R , Wasim H , Elhusseny A , Abdelmageed M , Saleh Abdelfattah M
Published: November 2022

Introduction/Objective

Women with diabetes mellitus (DM) are more susceptible to vulvovaginal candidiasis (VVC) than non-diabetics. This could be due to higher glucose levels predisposing VVC by damaging basic host defense mechanisms and stimulating Candida adhesion to vaginal cells.

Objectives

Investigating the prevalence of Candida albicans and biofilm formation in diabetic and nondiabetic IUD users.

Methods/Case Report

A total of 325 vaginal swabs and IUDs were enrolled in this study from the Delta region in Egypt. Females with a median age of 17 to 45 years were divided into two groups; diabetic (29.8%) and nondiabetic (70.1%). They were all vaginitis having one of these symptoms; irritation on the surface of the genital tract, uterine cervix ulcer, vaginal bleeding, and acute vaginal exudates. C. albicans were isolated and identified using cultural characters. Biofilm formation by Candida on removed IUDs and swabs was examined by XTT-reduction assay, scanning electron microscope (SEM), and transmission electron microscope (TEM). Antifungal susceptibility to fluconazole and amphotericin B (AMB) to isolated strains and in vitro experimental biofilm formation was performed.

Results (if a Case Study enter NA)

In diabetic cases, the highest percentage (91.1%) of isolated C.albicans was found among patients with irritation on the surface of the genital tract, whereas the lowest one (83.3%) was in the symptoms of acute vaginal exudates. In nondiabetic cases, the highest percentage of isolated C.albicans (51.7%) was found among patients with symptoms of acute vaginal exudates. In contrast, the lowest one (32.5%) was in the symptoms of irritation on the surface of the genital tract. XTT method illustrated the biofilm formation; SEM revealed a heterogeneous thick biofilm. Biofilm MIC to strains with AMB >1μg\ml was considered resistant, while those for which AMB concentration were ≤1μg\ml were deemed sensitive. Strains with Fluconazol 64 μg\ml were considered resistant, while those for which Fluconazol concentration was ≤8 μg\ml were deemed sensitive.

Conclusion

There was a significant direct relationship between diabetic cases and C.albicans prevalence in the current study. Furthermore, the ability to form biofilm was found to be the same in diabetic and nondiabetic patients.
Optimizing Detection of MEC-Mediated Methicillin Resistance in Coagulase Negative Staphylococcus Species
Authors: Givi J P , LaSala R , Miller B , Rybakov I
Published: November 2022

Introduction/Objective

Parenteral therapy for invasive staphylococcal infections often comprises lipo/glycopeptides for methicillin resistant (MR) organisms, with extended spectrum penicillins reserved for those confirmed as methicillin susceptible (MS). While phenotypic antimicrobial susceptibility testing (AST) using cefoxitin has high accuracy for differentiating MR/MS for S. aureus, the same, simple approach does not reliably distinguish resistance among all coagulase negative Staphylococcus species (CoNS). As such, clinicians may work under an assumption that MS CoNS cannot be reliably predicted by laboratories, leading to lipo/glycopeptide therapeutic use for invasive infections caused by both MR and MS isolates. To better inform laboratory practice, this study aimed to establish the accuracy of multiple phenotypic and genotypic tests for differentiation of MR/MS among commonly recovered CoNS species producing invasive infections.

Methods/Case Report

A convenience sample of 155 unique invasive CoNS isolates with historic Vitek 2 and/or disc diffusion (DD) AST results (~50% MR) were retrieved from frozen storage and tested by: (1) cefoxitin and oxacillin DD, (2) a lateral flow immunoassay for PBP2a without beta-lactam induction, and (3) a lab-developed PCR for mecA. A commercial real-time PCR for mecA/C was also employed for a subset of isolates.

Results (if a Case Study enter NA)

A total of 144 isolates belonging to 11 taxa were evaluated by all tests after accounting for missing, non-viable, and incorrectly cataloged isolates. Using PCR mecA/C detection as the reference standard, categorical agreement for MR/MS status was 95.5% (127/133) for original Vitek GP75 results, 98.6% (142/144) for DD interpreted using updated, species-specific CLSI guidelines, and 100% (144/144) for the lateral flow PBP2a assay. Six MR isolates from five different taxa that were repeatedly mecA-negative by lab-developed PCR confirmed as mecA/C-positive by a commercial assay.

Conclusion

Although all methods evaluated distinguish MR/MS CoNS with sufficient accuracy, definitive determination is best achieved using off-label/lab-developed PCR for mec or lateral flow immunoassay for PBP2a.
To Be or Not to Be Resistant: CLSI Versus EUCAST Guidelines for Staphylococcus lugdunensis
Authors: Benitez Barzaga M , Yee R
Published: November 2022

Introduction/Objective

Staphylococcus lugdunensis is a coagulase-negative Staphyloccocus, but infections can be as severe as S. aureus. Performing antimicrobial susceptibility testing (AST) is paramount to appropriate treatment. Recently, the College of American Pathologists is requiring clinical labs to implement updated guidelines. We evaluated how the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines would impact our hospital’s resistance rates for S. lugdunensis.

Methods/Case Report

Cultures with S. lugdunensis isolated between 04/2018 to 02/2022 were included. Minimal inhibitory concentrations (MICs) (Vitek2 and Microscan Walkaway) reported (clindamycin, doxycycline, daptomycin, linezolid, and vancomycin) were interpreted using CLSI (M100Ed32) and EUCAST (v12.0) guidelines. The range of MICs (95% Confidence Interval) was calculated.

Results (if a Case Study enter NA)

A total of 125 isolates from 120 patients from specimen types including wound (49%), tissue (42%), blood (6%), and body fluid (3%) were identified. Five patients had multiple cultures of S. lugdunensis, four from two wound/tissue sites and one with blood and biopsy positive. For clindamycin (0.7-1.3 ug/mL), EUCAST guidelines determined two more isolates (from blood and wound, MIC=0.5 ug/mL) as resistant. Most drastically, the rate of resistance for doxycycline (0.6-1.0 ug/mL) was 11% higher per EUCAST guidelines (susceptible: 89% EUCAST vs 100% CLSI). The difference was seen in isolates > 2 ug/mL, all isolated from wound and tissue. Regardless of the guidelines used, 100% of the isolates were susceptible to daptomycin (0.4-0.5 ug/mL), linezolid (1.2-1.4 ug/mL), and vancomycin (0.6-0.7 ug/mL); 23% were resistant to oxacillin (1.7-2.0 ug/mL).

Conclusion

EUCAST guidelines would have reported more resistant doxycycline and clindamycin isolates at our institution. To ensure that clinical teams are utilizing AST results to provide appropriate care, a team effort consisting of the microbiology lab, infectious diseases physicians, and antibiotic stewardship committee is needed to determine which guidelines should be followed.
Thermal Shock Viral RNA Release in COVID-19 Testing
Authors: Ledesma C J , Cavazos M , Chase L
Published: November 2022

Introduction/Objective

The public health emergency of the COVID-19 pandemic emphasized the crucial role of medical laboratory professionals and scientists in molecular diagnostics laboratories to ensure success in infection control strategies. The demand for laboratory testing using nucleic acid amplification tests to detect SARS-CoV-2 RNA imposed strains in laboratory supplies. Here, we explored an alternative cost-effective solution that will simplify the pre-PCR steps by using a simple heating method to release viral RNA.

Methods/Case Report

Samples tested using the reference automated extraction method were used:100 samples identified as positive for SARS-CoV-2 RNA and 500 samples tested negative for SARS-CoV-2 RNA were used for the study and sorted with equal distribution according to Ct values of (a) <20, (b) 20–30, and (c) >30.100 ul from swab preserved in Universal Transport Medium was treated with 30 μg of proteinase K, and another set was tested without proteinase K pre-treatment. All samples with or without proteinase K were diluted to minimize PCR inhibitors. The thermal shock protocol was set at (98°C, 5 minutes; 4°C, 2 minutes) and screened for purity. Performance and method verification studies were performed. Internal extraction, positive template, and no template controls were markers used for testing quality. The experimental study was performed by qualified testing personnel and all under the same experimental conditions.

Results (if a Case Study enter NA)

The Ct values from the thermal shock RNA release were compared to the automated extraction method and statistically analyzed.The criteria for acceptability for validation of this new RNA extraction proceeding were set to 100% concordance compared to the commercial kit using an automated extraction. PCR efficiency was at 98% and a slope of -3.3. Within run precision of 2% and limits of detection from 200 to 20,000 copies/uL The method 100% (50/50) concordance on samples previously identified as negative by automated methods and identified 86% (86/100) with a mean difference of 3 Ct.

Conclusion

Our findings suggest that the thermal shock treatment of nasopharyngeal swabs in viral transport media can successfully extract viral nucleic acid for nucleic acid amplification and is a reasonable alternative for chemical extraction methods when molecular diagnostic laboratories persistently encounter supply chain issues.
Analysis of microRNAs by the Stem-Loop Real-Time Quantitative Reverse Transcription Polymerase Chain Reaction Using A Double Quencher Probe
Authors: Kikuchi A , Naruse A , Takagi K
Published: November 2022

Introduction/Objective

We created a universal probe that can be used with mature micro RNAs (miRNAs) using a double quencher incorporating the ZEN quencher into the hydrolysis probe required for miRNA analysis by the real- time quantitative polymerase chain reaction (RT-qPCR) using a stem-loop primer. The main purpose of this approach was to improve sensitivity and convenience.

Methods/Case Report

We conducted studies on miR-21, miR-30a and miR-200c. To assess the relationship between the sequence interval and reactivity between the miRNA-specific sequence on the stem-loop primer and detection probe, various sequence patterns were examined using miRNA from K562 cells. The sensitivity and reactivity of the designed primers and probes were examined using each synthetic miRNA and transurethral resection of bladder tumor (TURBT) samples. The synthetic RNA was serially diluted in 10% increments. Twenty-seven TURBT cases were examined. The prepared samples were extracted with the FastGene RNA Basic Kit and FastGene miRNA Enhancer. After extraction, cDNA was prepared using FastGene Scriptase II. We performed quantitative analysis by the RT-qPCR using a ZEN double quencher probe. The samples were analyzed with the Taq Man miRNA assay.

Results (if a Case Study enter NA)

The probe and miRNA-specific sequences of the stem-loop primer showed better reactivity when the design contained less space within the sequences. Serial dilution of the samples using synthetic miRNA showed that linearity depended on the addition amount, and occurred at a concentration of log 7 or more. In the TURBT samples, the Δ of the mean Cp value, and the correlation coefficients of miR-21, miR-30a, and miR-200c, were 3.13 and 0.966; 1.10 and 0.991; and 0.39 and 0.997, respectively, compared with the TaqMan miRNA assay.

Conclusion

This demonstrates that our method has the same or higher sensitivity than the TaqMan miRNA assay. Overall, these findings suggest that the analysis of miRNA with a stem-loop primer using the double quencher probe is useful.
Homologous Recombination Deficiency and Tumor Mutational Burden as Clinical Biomarkers for Melanoma
Authors: Yip J , Lum C , Halford Z , Pon J , Woron A
Published: November 2022

Introduction/Objective

Homologous recombination deficiency (HRD) cancers have high levels of genetic instability, potentially being targets for platinum agents or poly-ADP ribose polymerase inhibitors. Tumor mutational burden (TMB), which is used to guide immunotherapy, is thought to be associated with HRD. This study aimed to evaluate the frequency of HRD and its correlation with other genomic parameters in melanoma.

Methods/Case Report

A total of 14 cases with the diagnosis of melanoma were found in the genomic database between March 1, 2021 to July 30, 2021. One case had an EWSR1-ATF1 translocation and was excluded. Copy number variations and absence of heterozygosity detection were analyzed by the NxClinical software (BioDiscovery, El Segundo, CA). HRD was scored by three DNA-based measures of genomic instability (loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale transitions (LST)). HRD-LOH is the number of LOH regions > 15 Mb and do not cross the centromere. HRD-TAI is the number of regions > 10 Mb with allelic imbalance that extend to one of the subtelomeres and do not cross the centromere. HRD-LST is the number of break points between regions > 10 Mb. A high HRD score and LOH percentage were defined as ≥ 42 and ≥ 16%, respectively.

Results (if a Case Study enter NA)

Of the 13 cases, 10 had a high TMB and 3 had a low TMB. A high HRD score was found in 3 cases; high LOH percentage was found in 4 cases. PDL-1 was expressed in 8 of the 11 cases tested. A high HRD score correlated with high LOH percentage by Pearson’s chi-squared test (p < 0.01). No significant association was found between TMB and HRD score or LOH percentage. Common alterations among cases with high TMB included mutations in NRAS (3/13; 23.1%), CDKN2A (2/13; 15.4%), BRAF (2/13; 15.4%), BRCA2 (2/13; 15.4%), RAF1 (2/13; 15.4%), RET (1/13; 7.7%), IDH1 (1/13; 7.7%), PALB2 (1/13; 7.7%), BRCA1 (1/13; 7.7%), ERBB2 (1/13; 7.7%), NF1 (1/13; 7.7%), MLH1 (1/13; 7.7%), ATM (1/13; 7.7%) and MET (1/13; 7.7%). One case had amplifications in CCND1, FGF 3/4/19 and MET. Among cases with low TMB, alterations included MYC amplification (1/3; 33.3%) and BRAF mutations (2/3; 66.6%).

Conclusion

In our study, HRD score is not associated with TMB status. There is a strong correlation between HRD score and LOH percentage, suggesting that LOH is a major component in the genomic scarring seen in HRD. HRD may be an independent biomarker of immunogenicity to guide immunotherapy.
Enhancing Coordination Around Cancer Biomarker and Hereditary Genetic Testing Among Members of the Multidisciplinary Care Team
Authors: Kim J , Boehmer L , Plotkin E , Allen T , Gutman P , Shiller M , Brown S , Pan V
Published: November 2022

Introduction/Objective

Advances in precision medicine necessitate a closer integration across pathologists, genetic counselors, and other members of the multidisciplinary cancer care team (MDT). Recognizing that physical distancing and fragmented communication may hinder care delivery, the Association of Community Cancer Centers (ACCC) ran a multi-year initiative to explore ways to improve MDT care coordination.

Methods/Case Report

ACCC held a multistakeholder leadership summit to identify and discuss critical issues regarding biomarker and hereditary genetic testing and the ways in which pathology and genetic counseling professionals interface with the cancer MDT. Through a consensus-driven process, participants identified key opportunities for achieving optimal integration. ACCC also conducted a national survey to explore barriers around biomarker and hereditary genetic testing. Building off these insights, ACCC conducted virtual workshops at three community cancer programs to improve processes around biomarker testing and targeted treatment planning.

Results (if a Case Study enter NA)

The pathology leadership summit identified the following priorities: 1) streamline and standardize the biomarker test ordering process; 2) improve tissue handling to optimize timely biomarker testing; 3) strengthen communication between pathologists and genetic counselors; 4) empower pathologists with leadership opportunities. In the ACCC survey (n=659), 57% indicated that some or most of their pathologists were generalists. 21% only held one general tumor board. 6% indicated that pathologists often do not attend tumor boards or cancer committee meetings. 64% indicated that pathologists can directly access some or all medical oncology patient records. 67% sent some or most biopsy samples out for biomarker testing. In the ACCC workshops, cancer programs in KS, NC, and NV identified ways to improve the timeliness of genetic counseling referrals and coordinate biomarker testing. Following the workshops, 64% indicated they planned to make moderate or significant changes in their processes.

Conclusion

Improving collaboration across pathologists, genetic counselors, and the rest of the cancer MDT may lead to more timely and comprehensive biomarker and hereditary genetic testing. These findings may help cancer programs refine processes of care.
Clinico-pathological and Molecular Features of Pancreatic Acinar Cell Carcinoma: Association with BRCA2 Mutation
Authors: Goyal G , Reusner J V , Haye K K , Tondon R
Published: November 2022

Introduction/Objective

Pancreatic acinar cell carcinoma (ACC) is a rare neoplasm of exocrine epithelial origin and accounts to <1% of primary neoplasms of pancreas.

Methods/Case Report

The cases diagnosed as ACC were retrieved from Pathology data base between January 2010 to July 2021. A retrospective review of clinical, pathological, molecular findings along with follow up was performed.

Results (if a Case Study enter NA)

Eight patients with resection specimens were identified over a period of 11 years. Median age of diagnosis was 74.5 yrs with M: F ratio of 3:1 and size range of 1.8 to 10.9 cm. The tumor was located in body/tail (5) and head of pancreas (3). Immunohistochemical stains for BCL10 and trypsin were utilized in 4 cases. One patient had lymph node metastasis and two patients had liver metastasis at the time of presentation. One patient presented with lipase hypersecretion syndrome. Four cases (50%) had pT3 stage. Follow-up period was available in 7 patients and ranged from 1-3 yrs, of which 3 died within 2 yrs of surgery while 4 patients were disease free. Three patients (35%) were found to have germline (1) and somatic BRCA2 mutations (2). These patients received platinum- based chemotherapy and were free from recurrence upon follow-up of 3 yrs.

Conclusion

Pancreatic ACC is a rare entity. In our study, 35% (3/8) cases were associated with somatic/germline BRCA2 mutations. Our results suggest that patients with ACC should undergo genetic testing for BRCA 1/2 mutations. This would not only enable treatment of these patients with specific targeted therapies, but also aid in screening of their families.
Do we need Diagnostic Decision Support For Pathologists in Anatomic Pathology Laboratory Information System (APLIS)?
Authors: Sonawane S S
Published: November 2022

Introduction/Objective

On a typical day, pathologists spend time not just looking at the slides but have various information needs in order to facilitate the sign-out. This study was performed to find out various resources utilized by pathologists to facilitate the sign-out and if having the diagnostic decision support in APLIS will improve the sign-out experience? To answer these questions a survey was created.

Methods/Case Report

An anonymous Google survey of 10 questions inquiring about practice setting, training level, work experience, various resources utilized to facilitate daily sign-out, time spent to find the information, and ways the sign-out experience can be enhanced was created and distributed among the pathologists via a social media platform.

Results (if a Case Study enter NA)

85 pathologists participated in the survey, and the results showed that 66% of respondents worked in an academic setting while 34% worked in a community practice setting. 37% of respondents had work experience >5 years while 23% had work experience < 5 years and the remainder of them were in training. 44% of them had a subspecialty sign-out system. EPICBeaker (27.3%) was the most commonly utilized APLIS system, followed by Cerner (22%) and Copath(16%), and reminder used Novopath, soft path, Med-tech, and Power path. The pathologists use various resources to facilitate daily sign out which include textbooks, ebooks, PubMed, CAP protocols, WHO books, own notes, and internet searches. Reasons to refer to these resources include finding the grossing guidelines, differential diagnosis, special or immunohistochemical stains, practices guidelines, correct tumor stage, and grade or molecular tests. On a typical day, 41% of the respondents spend 1-2 hours/day, and 25% of the respondents spend 2-3hrs/day finding the correct information to sign out their cases. 81% of the pathologists responded that if all the resources are available in APLIS will increase their productivity.

Conclusion

Having all the resources in one place in APLIS in the form of diagnostic decision support will enhance the sign-out experience for pathologists and will increase productivity.
Digital Pathology, A Cognitively Efficient Teaching Strategy: Current Application and a Glimpse into Future
Authors: Saxena R , Moore N , Johnson J
Published: November 2022

Introduction/Objective

If pathology education is to be efficacious, it must embrace the ramifications of cognitive load of the learners, to optimize the capacity of the working memory. When undergraduate students commence their learning of pathology, they encounter a heap of new data and classifications. Simplifying these intricate systems into assimilable subschemas and items is key for effective transfer of knowledge. The minimization of the profundity of intrinsic cognitive load is essential, considering that its impact on pathology beginners is often left unaccounted, both in active learning as well as in traditional methods of instruction. In today’s digital generation, digital pathology plays a key role by intertwining disease morphology with clinical presentation and fortifying its pathophysiologic basis. We designed a teaching methodology utilizing digital pathology to evaluate its effect on cognitive load.

Methods/Case Report

Active learning was implemented online using digital pathology, molecular pathology, and laboratory data in case-based setting with question-answer sessions. In small groups, students were encouraged to analyze digital pathology slides with the help of annotations and identify areas of histopathological significance. They utilized this information further to make an accurate diagnosis and answer corresponding questions, with access to answers available later, complemented with algorithms and concept maps. A 14-item structured questionnaire was delivered afterwards to evaluate the efficacy and popularity of the exercise.

Results (if a Case Study enter NA)

End-of-term examination results showed that learners developed higher-order comprehension skills along with a greater potential in interpreting histopathological data towards solving case studies. Feedback revealed a higher degree of overall satisfaction and increased ability to retain information.

Conclusion

Digital transformation of pathology education provides the kind of framework where learning happens naturally - developing in small boosts of progress until expertise is achieved, and students appreciate the value of the ‘learned thing’ along with the real utility of that knowledge. The innovative approach utilizing digitization and integration offers the opportunity of decrement in intrinsic cognitive load by invoking students to build better, reliable, long-lasting, supportable and inclusive schemata while correlating the relevant incoming information with previously stabilized knowledge and consolidating the entirety of understanding.