bluuebunny/crossref_metadata_2025 huggingface dataset:
Zoonotic transmission risk of Acinetobacter baumannii from Alaskan wildlife
Authors: Leu-Burke G , Edwards E , Jones H
Published: November 2023

Introduction/Objective

Acinetobacter baumannii is a multi-drug resistant gram-negative bacterium often isolated in water and soil. A challenge in both human and veterinary nosocomial infections, Acinetobacter is adaptable, forming biofilms and carbapenem resistance (CRAB). As an opportunistic infection, Acinetobacter is an emerging pathogen especially in immunocompromised individuals which include marginalized housing insecure populations. Anchorage dedicates large areas for urban park environments providing high impact of human and moose wildlife interaction.

Previous studies link zoonotic transmission of bacteria through direct fecal contact or water contamination. The significant number of vulnerable unsheltered individuals in Anchorage using public green belts presents a potential risk for Acinetobacter baumannii colonization.

Methods/Case Report

To assess environmental Acinetobacter exposure from urban wildlife, we ground collected 150 moose fecal samples between 2019-2022. Samples were placed into support medium, cultured onto MacConkey agar and incubated at 37C. Biochemical identification and antibiotic susceptibility testing were performed using MicroScan™ (Beckman/Coulter Brea, CA) conventional panels with antimicrobial interpretation along clinical laboratory standards (CLSI).

Results (if a Case Study enter NA)

Acinetobacter baumannii was isolated in moose feces, with proportion of positive samples increasing annually: 7.5% (2019), 12.5% (2020), and 14.2% (2021). Antimicrobial analysis found 100% of samples resistant to cefpodoxime, cefazolin, ceftriaxone, cefuroxime, ampicillin, and ampicillin-sulbactam, with 72% resistant to ertapenem and imipenem. Aztreonam resistance was 22%, cefepime 17%, with only 5% resistant to ciprofloxacin.

Conclusion

The increasing colonization of moose feces with multi-drug resistant Acinetobacter baumannii potentially poses a significant public health risk in Anchorage, Alaska. With moose inhabiting areas used by the vulnerable homeless and outdoor enthusiasts, there exists a high risk for exposure potential towards opportunistic infection, and colonization. The multi-drug resistance pattern on observed on several of A. baumannii isolates suggests the possibility of CRAB. As one of the five pathogens listed as an urgent threat by the CDC, it is imperative to study potential sources of carbapenem resistant A. baumannii, including environmental exposure. Finding moose fecal samples positive for A. baumannii indicates a need for continued surveillance and risk assessment for community acquired infection.
Characterization of innate immune response to hepatitis B virus genotype F acute infection in tree shrew (Tupaia belangeri) model
Authors: Or Rashid M
Published: November 2023

Introduction/Objective

Hepatitis B virus (HBV) infection is a global public health problem. The clinical outcomes of HBV infections are influenced by the host as well as viral factors, including viral genotypes and subgenotypes. The interplay between HBV and host innate immunity remains unclear because of the lack of a suitable small animal model. Tree shrews (Tupaia belangeri) have been utilized as a useful animal model for hepatitis viruses such as hepatitis B and C viruses.

Methods/Case Report

In this study, we characterized acute infections by HBV genotype F (HBV-F) wild type (Wt) and mutant type (Mt) viruses in adult tree shrews. Serum alanine aminotransferase levels were measured before and post-infection 7 and 14 dpi. Both HBV-F-Wt and Mt were detected in the HBV-F-infected tree shrew serum and liver tissue at 7 and 14 dpi.

Results (if a Case Study enter NA)

We examined the intrahepatic expression patterns of Toll-like receptors (TLRs) (TLR1–9 mRNAs), cGAS, several transcription factors such as STAT1, STAT2, IRF7, HNF4, PD-L1, and cytokines, including IFN-β, IFN-γ, IL-6, and TNF-α in HBV-F Wt/Mt-infected tree shrews. When compared with an uninfected animal group, significant suppression of TLR8 in HBV-F-Wt infected animals and significant suppression of PD-L1 in both HBV-F-Wt and Mt infected animals were observed.

Conclusion

Thus, tree shrew can be a useful animal model to characterize HBV-F pathogenesis.
Association between asymptomatic Plasmodium falciparum malaria infection, anemia and mean corpuscular volume of school children in the Volta Region of Ghana
Authors: Sanyaolu A , Orish V , Kwadzokpu P , Lokpo S , Marinkovic A , Prakash S , Okorie C
Published: November 2023

Introduction/Objective

Although several studies have reported abnormal MCV values and anemia associated with malaria infections with a focus on P. falciparum among patients with complicated and uncomplicated malaria. This study assessed the association between asymptomatic P. falciparum malaria infection, anemia, and the MCV values of school children in Ghana.

Methods/Case Report

We conducted a cross-sectional study using 3 ml of blood samples from 549 children aged 5- 17 years attending 5 schools selected in the Volta Region. Semi-structured questionnaires were administered to the children to obtain demographic data. Blood samples were collected into a K2EDTA tube and then used to estimate the children’s automated full blood count (FBC) and malaria status using microscopy. MCV was classified into low, normal, and high. Data obtained were analyzed using STATA 15 software. P-values less than 0.05 were considered statistically significant.

Results (if a Case Study enter NA)

Most of the children in this study (49.9%) had normal MCV (81.3-91.3 fL) with an overall malaria prevalence of 55.6 % (95% CI: 51.3-59.8) and anemia prevalence of 48.6% (95% CI 44.4-52.9). The majority of the anemic children had normal MCV (81.3-91.3 fL) (49.8, 95% CI 43.7-56.0). The predicted probability of malaria was highly likely among children whose MCV fell within the first and third quartiles.

Conclusion

This study shows a reduced predicted probability of malaria among children with low and high MCV, playing a protective function against malaria. Further studies are required to elucidate the association and interaction between MCV, anemia, and asymptomatic Plasmodium falciparum infection.
COVID-19 Pandemic: Total Testing Cost Impact on Neisseria Gonorrhoeae and Chlamydia Trachomatis Testing and Positivity Rate in the Veteran Population
Authors: Petersen J M , Jhala A
Published: November 2023

Introduction/Objective

The College of American Pathologists (CAP) checklist includes the quality assurance (QA) monitoring of the rate of diagnosis of Neisseria Gonorrhoeae (NG) and/or Chlamydia trachomatis (CT) by the molecular laboratory. Recently, the societal impacts of the economic lockdowns of the COVID-19 pandemic had a significant effect on the number of tests. However, the impact on the total testing costs as well as the positivity rate has not been well studied in the Veteran population.

Methods/Case Report

Quarterly quality assurance data from October 1st, 2018, to December 31st, 2022, was reviewed to obtain both the test volume for CT/NG and the number of positive test results at a Veterans Affairs Medical Center (VAMC). In addition, the cost to perform each test in reagents and consumables was also noted. Quarter 1 at the VAMC begins in October of the prior calendar year. The quarters in the period of April 1st, 2020, to December 31st, 2020 (corresponding to Quarter 3 2020 to Quarter 1 2021), was analyzed and compared to both the quarterly data prior to and after this period to note the impact of the COVID-19 pandemic on the quality assurance data. Testing had been performed using the Abbott m2000 RealTime System (Abbott Park, Illinois).

Results (if a Case Study enter NA)

A total of 18,904 tests for CT/NG had been performed on the Veteran population during the study period. Of these 18,904 tests, 385 were positive for NG and 515 were positive for CT. Quarterly percentage rates on a quarterly basis ranged from 1.58% to 4.53% (CT) and 1.16% to 4.53% (NG) with average rates of 2.78% and 2.13%, for Chlamydia and Gonorrhea respectively. The total reagent and consumable cost for each test was $28.84 per test. The period of Quarter 3 2020 to Quarter 1 2021 was marked by a decrease in total tests (331, 713 and 781 tests respectively compared with 1,049 tests in the quarter just before this period) with a corresponding decreased total test cost expenditure ($9,546.04, $20,592,92, and $22,524.04 respectively compared with $30,253.16 in the quarter just before this period) for performed tests. There was also an increase in the positivity rate (the highest positivity rate for both CT and NG of 4.53% was noted in quarter 3 2020) in this period of Quarter 3 2020 to Quarter 1 2021.

Conclusion

The initial period of the COVID-19 pandemic was marred by widespread economic lockdowns that impacted the total number of CT and NG tests performed, total test expenditures for tests performed, as well as the positivity rate.
Liquid Biopsy: A Highly Useful Tool to Decide Personalized Therapy in Veteran Patients with Metastatic Pancreaticobiliary Cancer
Authors: Dalal S , Petersen J M , Jhala D , Allbee A
Published: November 2023

Introduction/Objective

Pancreatic cancer is one of the leading causes of death in Veteran patients. Early detection and treatment of the pancreatic cancers are key to the successful management of pancreatic cancer with good patient outcome. The National Comprehensive Cancer Network (NCCN) recommends tumor molecular profiling in all patient cases of unresectable or metastatic pancreatic adenocarcinomas and biliary tract cancers who are candidates for chemotherapy. This testing can be performed using liquid biopsy to obtain this molecular profiling from circulating tumor cells (CTC) to obtain information that may impact treatment. However, the literature of metastatic pancreaticobiliary cancers targeted by liquid biopsies and the mutations found is sparse, particularly for the veteran population.

Methods/Case Report

A retrospective review was performed of all patients with a submitted liquid biopsy specimen at a Veteran Affairs Medical Center (VAMC) from April 2020 to March 3rd, 2023, to examine those patients with

metastatic pancreaticobiliary cancers, specifically pancreatic adenocarcinoma, and cholangiocarcinoma. Information on mutations detected was collected.

Results (if a Case Study enter NA)

There were a total of 5 patient specimens with a history of metastatic pancreatic

adenocarcinoma (4 cases/5) and cholangiocarcinoma (1 case/5). The first liquid biopsy from a patient with a history of metastatic pancreaticobiliary cancer was sent on April 14th, 2020, and the last was sent on November 12th, 2021.

TP53 was detected on all the successfully tested pancreatic adenocarcinoma cases. Other mutations detected in the individual pancreatic adenocarcinoma cases were KRAS, TET2 BCOR, DNMT3A, FUBP1, RAD21, and STAG2. The mutations found on the single cholangiocarcinoma case included DNMT3A and TP53. 1 of the 4 cases sent on a patient with pancreatic adenocarcinoma resulted in a sample failure.

Conclusion

Liquid biopsies provided comprehensive molecular profiling in cases of metastatic pancreatic adenocarcinoma and biliary tract cancer in the veteran population treated at a local VAMC to help decide on personalized therapy, in compliance with the recommendations of the NCCN. The results of this pilot quality assurance study help highlight the potential of liquid biopsies to detect most commonly mutated genes such as KRAS and T53 in pancreatic cancer.
MYC amplifications are a common event in urothelial bladder carcinomas associated with an aggressive tumor phenotype
Authors: Kluth M , Hitzschke M , Lennartz M , Blessin N C , Sauter G , Plage H , Klatte T , Schlomm T , Marx A H , Rink M , Slojewski M , Ecke T , Koch S , Horst D , Zecha H
Published: November 2023

Introduction/Objective

Gene amplifications of the proto-oncogen MYC are common events in carcinomas. In this study, we analyzed the impact of MYC amplifications on tumor aggressiveness and patient prognosis in urothelial bladder carcinomas.

Methods/Case Report

MYC copy number status was analyzed on more than 2,500 urothelial bladder carcinomas in a tissue microarray format by using dual-labeling fluorescence in-situ hybridization (FISH) with probes for centromere 8 and MYC (8q24). The results were compared with tumor phenotype and patient outcome.

Results (if a Case Study enter NA)

MYC amplification (ratio MYC/centromere 8 ≥2) occurred in 10% of 2,052 analyzable urothelial bladder carcinomas. Of these, 141 (6.8%) had a low level MYC copy number gain (MYC/centromere 8 ratio ≥2 and ≤ 3) and 68 (3.3%) had high-level MYC amplifications (MYC/centromere 8 ratio >3) . The rate of MYC gain and MYC amplification increased from pTa G2 low (0.6%), to pTa G2 high (7.7%), and pTa G3 (8.2%) carcinomas, and were highest in muscle-invasive pT2-4 (13.2%) carcinomas (p<0.0001). In muscle-invasive urothelial carcinomas, the MYC amplification rate increased from pT2 (13.1%), to pT3 (14.7%), and pT4 (19.8%) but these differences failed to reach statistical significance (p=0.0902). MYC amplification was also unrelated to patient survival in 526 patients with pT2-4 urothelial carcinomas who had undergone cystectomy (p=0.5526).

Conclusion

MYC amplification is a common event in urothelial bladder carcinoma - especially in case of pTa G3 and muscle-invasive carcinoma. The association of MYC amplification with advanced stage may reflect increasing genomic instability going along with tumor progression.
Pleomorphic Adenoma with a Novel Rearrangement - LINC01606::PLAG1
Authors: Naik U , Bellman A , Elsayad M , Saluja K , Zeybek A
Published: November 2023

Introduction/Objective

Pleomorphic adenoma (PA) is characterized by presence of three components including bi- layered ducts, myoepithelial cells, and chondromyxoid/fibrous stroma in varying proportions. Evaluation of molecular aberrations helps recognizing challenging cases. Pleomorphic adenoma gene 1 (PLAG1) and high-mobility group AT- hook 2 (HMGA2) are hallmark genes showing rearrangement with various partner genes. Here, we present a case of myoepithelial cell rich PA, showing PLAG1 rearrangement with a novel partner gene.

Methods/Case Report

A 77-year-old male with history of slow-growing, right post-auricular mass over 5-year duration, now presented with overlying skin ulceration and bleeding/intermittent oozing. CT scan showed a complex, lobular, enhancing 8.7 x 8.4 x 7.0 cm mass, arising from the right parotid gland. Fine needle aspiration was performed and reported inconclusive with blood and fibrin only. The patient elected to undergo total parotidectomy with cervical lymph node dissection. Histology revealed a circumscribed, cellular salivary neoplasm with extensive hemorrhage/infarction and cystic degeneration. The viable neoplastic cells composed of sheet of spindle and epithelioid/plasmacytoid cells, with focal glandular and cribriform areas. Very focally chondromyxoid change is noted. The tumor cells stained with CK7, S100, and SOX10, few scattered cells positive for SMA, p63, and p40, with Ki67 labeling index of 5-10%. None of the cervical lymph nodes showed metastatic tumor. Overall, the features were compatible with myoepithelial cell rich salivary neoplasm with working diagnosis of cellular pleomorphic adenoma.

Next generation RNA sequencing showed a LINC01606::PLAG1 [inv(8;8)(8q12.1;8q12.1)] fusion alteration.

Results (if a Case Study enter NA)

NA

Conclusion

PLAG1 is located at 8q12.1 and have been reported to be involved in chromosome rearrangements in various tumors including salivary gland tumors, mainly pleomorphic adenoma. Many fusion partners of PLAG1 have been reported. This report presents LINC01606 gene as a novel fusion partner of PLAG1 in a case of myoepithelial rich PA. This fusion leads to in-frame fusion of exons 1-2 of the LINC01606 gene to exons 3-5 of the PLAG1 gene.
Association of SARS-CoV-2 infection with Age and Gender deduced by RT PCR amplification of ORF1ab, E and N Genes Cycle Threshold (Ct)
Authors: Ullah R , Yousaf M , Rashid Z , Sajjad Naqvi S , Ur Rehman M , Ul Ain Q , Ammad M , Arshad N , Al Yafei Z , Noorul Hasan T , Hussain A
Published: November 2023

Introduction/Objective

COVID-19 pandemic caused by SARS-CoV-2 has significantly impacted public health globally. Accurate and rapid detection of the infectious agent is essential for disease control and management. RT-PCR amplifies the specific targets in viral genome. The amplification signals and the cycle threshold (Ct) value gives the idea of presence of the virus and their loads. Understanding the association between Ct values, age, and gender could provide insights into the viral load and could also shed light on the potential alterations in disease transmission, severity, clinical outcomes, and dynamics among different populations and age groups. The current study aims to elaborate the correlation between Ct values of (ORF1ab, E, and N) with age and gender.

Methods/Case Report

11,108 samples were tested for COVID-19 RT-PCR assay in the current study at PureLab Pure Health, Abu Dhabi, UAE.

Results (if a Case Study enter NA)

1009/11,108 (9.08 %) positivity was observed in the studied population. COVID- 19 was more prevalent in females (53.51%) as compared to males (46.48%). Significantly higher positivity was observed in age group (31-40 years) in both males (24.09%, 113/469) and females (24.44%, 132/540). The Ct values for all the three (03) targets were ranged from 11.37 to 39.39. Longitudinal analysis showed significant increased during the study period from starting to end as were hypothesized. Interestingly, all the three (03) targets (ORF1ab, E, and N) were present in all age groups. This may indicate the existing clade can infect all the age groups even children less than 01 years old.

Conclusion

In conclusion, between age groups, there was no significant difference in viral loads. In general, females had a larger viral burden than males. Studying the association between Ct values of SARS-CoV-2 genes age and gender is essential for understanding the viral load dynamics and potential variations in disease characteristics among different population groups. Such investigations could contribute to disease prognosis, risk stratification and the development of targeted interventions based on demographic characteristics. However, further research is essential to establish reliable patterns and unravel the complex interplay between viral load, gender, age, and clinical outcomes in COVID-19 patients.
Myeloid/Lymphoid Neoplasms With Fibroblast Growth Factor Receptor 1 Rearrangement: A US Real-World Chart Review
Authors: Parasuraman S , Saverno K , Colucci P , Kish J , Zimmerman-Savill K
Published: November 2023

Introduction/Objective

Myeloid/lymphoid neoplasms (MLN) with fibroblast growth factor receptor 1 gene (FGFR1) rearrangement (MLNFGFR1) is a rare and aggressive hematologic malignancy characterized by molecular disruption of FGFR1 at the 8p11 locus. This real-world study describes demographic and clinical characteristics, diagnostic testing, and clinical outcomes in patients with MLNFGFR1 in the US.

Methods/Case Report

Probable MLNFGFR1 cases (n=51) were identified from a retrospective, physician-abstracted (5/29/2020-6/23/2020) chart review of patients within the US Cardinal Health Oncology Provider Extended Network (feasibility survey). In a subsequent full chart review (12/29/2020-3/4/2021), 33 of these probable MLNFGFR1 cases were considered to be confirmed based on additional 8p11/FGFR1 testing result data collected. Descriptive analyses of demographic/clinical characteristics, diagnostic testing, and clinical outcomes of patients with confirmed MLN FGFR1 were performed.

Results (if a Case Study enter NA)

The mean age at initial MLNFGFR1 diagnosis was 65.9 (SD 13.5) years, 60.6% patients were male, and 63.6% were white. Patients were managed by 12 physicians,10 in community practices.

FGFR1 translocations were identified by karyotyping in 72.7% of patients. Rearrangements in FGFR1 were detected by fluorescence in situ hybridization, next generation sequencing, and/or real-time polymerase chain reaction in 66.7%, 21.2% and 6.1% of patients, respectively. FGFR1 rearrangement was detected in bone marrow aspirate and peripheral blood in 90.9% and 9.1% of patients, respectively. Fusion partners ZMYM2 and CPSF6 were reported in 46.2% and 15.4% of patients, respectively, and BCR, CUX1, RANBP2, TPR, and MYO18A were reported in 7.7% of patients each.

Conclusion

Although rare, patients with MLNFGFR1 do present in US community practice settings. Conventional cytogenetics can identify FGFR1 translocations which can be confirmed by FISH with FGFR1 break-apart probes. NGS can be used to identify cryptic rearrangements when clinical suspicion is high but no rearrangement is present on FISH. In addition to diagnosis, RT-PCR is also useful to assess molecular response.
Nine-Gene Prognostic Signature for Myelodysplastic Syndrome
Authors: Lyapichev K , Kazacheuskaya L , Memon M D , Ong M , Cotelingam J , Beedupalli K , Centeno L , Patil A
Published: November 2023

Introduction/Objective

Myelodysplastic Syndrome (MDS) is a family of clonal hematopoietic malignancies found frequently in the seventh and eight decades, supporting that aging and acquired somatic mutations drive development of the disease. Without a cure, the prognosis is poor. Patient consideration for bone marrow transplantation remains low (<5%), and enrollment in clinical trials is slightly better (25%). Information regarding MDS-specific whole genome sequencing, a prognostic prediction system, and overall survival is limited and may be beneficial in developing curative therapies. Hence, we aimed to analyze the genomic profile, epidemiology, and overall survival of MDS.

Methods/Case Report

We utilized cBioPortal cancer genomics [The Cancer Genome Atlas (TCGA) PanCancer Atlas, TCGA Firehose Legacy, and TCGA Nature 2013] to study the mutations associated with MDS. Epidemiological characteristics and genetic profiles available on cBioportal were evaluated. Gene mutations with the most statistically significant, shortest overall survival and survival in days were used for the gene query, and survival rate with the common mutations was calculated. Logrank test and Kaplan–Meier estimators were used in analyzing the survival function. Patients with two or more overlapping mutations were excluded.

Results (if a Case Study enter NA)

We identified 7,554 patients with MDS out of which 2,852 had a primary MDS. There were 3,323 patients who had gender and age data available. 26.5% were male, and most patients (600) were between the ages of 70-75 years. 1573 (20.8%) were alive and 1600 (21.2%) were deceased. The common mutations associated with reduced survival were ASXL1, NPM1, FLT3, TET2, SF3B1, SRSF2, STAG2, RUNX1, TP53. Median survival of patients with these mutations was 32.02, 27.32, 25.97, 64.21, 80.94, 46.82, 44.28, 16.21, and 10.52 months respectively in comparison with the unaltered mutation group (68.68) (p < 0.0001). Survival was lowest amongst TP53 10.52 months and RUNX1 16.21 months. Leukemia free survival with ASXL1, NPM1, FLT3, TET2, SF3B1, SRSF2, STAG2, RUNX1, and TP53 mutations was 27.88, 13.02, 23.44, 56.52, 79.96, 37.32, 24.89, 14.86,

and 9.44 months respectfully in comparison to the unaltered mutation group (68.68) (p < 0.0001).

Conclusion

Our study found that TP53 and RUNX1 genes were associated with the worst prognosis in MDS with median survival of 10.52 and 16.21 months, respectively. This study may provide insight for genetic predictors and targeted therapies for MDS, as well as provide better understanding of patient prognosis.
Validating Recorded EHR and Actual Weight: Single Institution Study
Authors: Yeon S , Turcios Escobar S E , Janiszewski S , Lauridsen L , Campbell-Lee S , Allison D
Published: November 2023

Introduction/Objective

Our hemapheresis clinic performs outpatient and inpatient therapeutic apheresis procedures including red blood cell exchange and therapeutic plasma exchange. Accurate height, weight, and hematocrit are required for calculating replacement fluid volumes for both procedures. Our practice has been using the patient’s most recent weight recorded in the EHR. The purpose of this quality improvement project is to validate concordance between patients’ actual body weight and documented body weight.

Methods/Case Report

STUDY DESIGN AND DATA COLLECTION

We performed this quality improvement project in our hemapheresis clinic. The study focused on weight variations impacting calculations for apheresis volume requirements. Data were collected from March 20th, 2023 – April 20th, 2023. Patients receiving red blood cell exchange or therapeutic plasma exchange were randomly selected and weighed prior to the procedure on a calibrated scale. The most recently recorded weight in the EHR was also collected. Non-ambulatory patients or patients receiving phlebotomy or stem cell collection were excluded from the study.

Statistical Analysis:

Statistical analyses were performed using R Statistical Software (Foundation for Statistical Computing, Vienna, Austria). We compared means of two observations using a paired t-test. P values less than 0.05 were considered to be statistically significant to test null hypothesis.

Results (if a Case Study enter NA)

A total of 40 patient data were collected. Seventeen male and 23 female patients were weighed and recorded. The mean value of EHR weight is 70.56kg and that of clinic weight is 71.41kg (P=0.08701). The weight discrepancy was calculated in comparison with EHR recorded weight and it was transformed to weight discrepancy by percentage using d(clinic weight -EHR weight)/clinic weight*100. Out of 40 patients, 33 patients had weight discrepancy by percentage between 0 to 4%.

Conclusion

Patient body weight is an important factor in calculating the replacement volume requirements in therapeutic apheresis. It is often prescribed based on the recorded EHR weight. In our data, we have shown that the weight discrepancy is not significant and therefore EHR recorded weight is reliable in replacement volume calculation. Our study is subject to several limitations that it was conducted for one month in a single institution and the sample size is not large. However, our study is novel in describing the relationship between recorded patient data and the actual patient data.
Unpredictable Blood Product Usage in Orthotropic Liver Transplantation: A Foregone Conclusion or A Problem Solved by Artificial Intelligence?
Authors: Gosnell H L , Barouqa M , Rashidi H , Reyes Gil M
Published: November 2023

Introduction/Objective

Orthotropic liver transplantation (OLT) is a complex procedure requiring coordination between operative and transfusion medicine staff. Unanticipated blood product demands during these surgeries strain blood bank inventory, especially when units are needed for patients with significant alloantibodies. Currently, transfusion medicine services issue set numbers of crossmatched red blood cell (RBC) units for these procedures. At our institution, 10 units are issued for each OLT. This project categorized OLT patients into three groups by RBC unit requirements: <5 units, 5-9 units and >10 units. Furthermore, we identified pre-operative clinical and lab factors predicting placement into each category. From this data, we developed an artificial intelligence platform (CCBBAI-1).

Methods/Case Report

We collected data from 474 adults (>18 years old) that underwent OLT from Jan. 1, 2021, to Dec. 31, 2022. Demographic, anticoagulant, and lab testing data generated within 24 hours of admission were obtained. Data analysis was performed in R-studio. CCBBAI-1 was built using machine intelligence learning optimizer platform (MILO).

Results (if a Case Study enter NA)

Based on univariate regression analysis (p-value<0.05, 95% confidence interval (CI)), the following lab variables were predictive of >10 RBC units issued: high INR (OR 3.48 [CI 2.35-5.26]), admission heparin dosage (2.61 [1.56-4.31]), total bilirubin (1.06 [1.04-1.08]), conjugated bilirubin (1.08 [1.04-1.11]), PTT (1.04 [1.03-1.06]), BUN (1.03 [1.02-1.04]), and creatinine (1.55 [1.33-1.83]). Low albumin (1.50 [1.13-2.22]) and MCV (1.04 [1.02-1.07]) also projected a 10 RBC unit procedural requirement. The univariate regression analysis variables predictive in categorizing patients requiring 5-9 units vs < 5 units were as follows: decreased albumin (2.17 [1.42-3.33]), decreased serum calcium level (1.72 [1.13-2.63]) and elevated INR (2.14 [1.36-3.40]). The mean number of units issued for each patient group including those requiring >10, 5-9, and <5 units were 22, 7, and 2 units, respectively. CCBBAI-1 achieved a sensitivity of 87.0% and specificity of 70.0% in classifying patients requiring >10 RBC units. Patients needing <10 units were analyzed in a second module to determine if they needed 5-9 units, achieving a sensitivity of 64.7% and a specificity of 62.4%.

Conclusion

Our study divided OLT patients into three categories and identified predictive laboratory values characterizing each group, a step towards improving transfusion medicine efficacy in this context.
Blood Shortage Monitoring: Comparison of the Supply Situation During the Omicron Surge and at the Tail End of the COVID-19 Pandemic this Year
Authors: Petersen J M , Jhala D
Published: November 2023

Introduction/Objective

The COVID-19 pandemic was marked by the first-ever declaration of a severe blood crisis by the American Red Cross in 2022. During this blood crisis, the, there were significant shortages of blood products that required precise monitoring of the current stock for communication and collaboration with the clinical team to ensure uninterrupted patient care. The blood supply gradually improved since 2022’s blood crisis, particularly as the public health emergency related to COVID-19 ended on May 11th, 2023. However, published literature on the comparison of the blood supply in the last calendar months of the public health emergency versus during the blood shortage is sparse.

Methods/Case Report

From January 28th, 2022, to February 28th, 2022, the amount of red blood cell (RBC) inventory was noted along with the percentage reduction from usual pre-crisis inventory level. This inventory information was communicated with the clinical services to coordinate clinical care during the blood supply crisis. Additionally, a separate inventory comparison to cover the last 5 calendar months (including May) until the end of the Public Health Emergency on May 11th, 2023, was performed from January 1st, 2023, to May 11th, 2023.

Results (if a Case Study enter NA)

During the crisis from January 28th, 2022, to February 28th, 2022, there were significant reductions in red blood cell inventory (up to 67% reduction in O+ units and 75% for A+ units). Collaboration with the clinical team and efforts to procure and conserve blood products enabled continuity of clinical care. On the other hand, there was documented improvement in the blood inventory at the tail end of the pandemic (January 1st, 2023, to May 11th, 2023) with average inventory reductions of only 19% in O+ units and 43% in A+ units.

Conclusion

There was a significant blood shortage during the Omicron surge of 2022 that required inventory monitoring, collaboration with the clinical team, and efforts to procure and conserve blood products to ensure continued successful clinical care. As the pandemic’s public health emergency neared its end, the blood supply situation has been improving substantially.
Trends in hematopoietic stem cell utilization and cost of cryopreservation
Authors: Jebackumar Travis , Soundar Esther
Published: November 2023

Autologous stem cell transplantation (ASCT) is the standard of care treatment for multiple myeloma. Standard ASCT procedures collect hematopoietic stem cells (HPSC) in excess for multiple transplants due to reports of high mobilization failure and unsuccessful ASCT collections following myeloablative treatments. Cost analysis studies estimate that one year of cryopreservation and one day of HPSC collection would each cost $5000 per patient. Limited data is available on the usage of the second transplant and the storage costs of non-transplanted products. This study evaluates the utilization of cryopreserved HPSC products and calculates the cost of cryopreservation. A retrospective chart review study of a cohort of 240 deceased MM patients, who received ASCT between January 2010 to December 2015. Demographic and clinical data were obtained from the laboratory and electronic medical record. The cohort was categorized into two groups, with 130 patients in Group 1 (≤60 years) and 110 patients in Group 2 (>60 years). Cumulative incidence of a second transplant was computed from the life table using the Kaplan Meier method. The cost of cryopreservation was calculated based on the time HPSC products remained in the freezers before disposal. PBSC was mobilized using Granulocyte Colony Stimulating Factor (GCSF), or GCSF and Mozobil. The average age of patients at first collection is 61 (IQR: 54-66) years and the average age of death is 64 (IQR: 58 -70) years. The average life span of patients after receiving the first transplant is 3 (IQR: 2-5) years. The average number of collection days is 2 (IQR: 1-3). 65 patients had 1-day collections, 105 had 2-day collections and 70 had ≥3-day collections. 175 patients (73%) had >1 day collection. Only 22 patients (9%) received a second transplant and 18 of them (82%) were in Group 1 (≤60). The cumulative incidence of a second transplant by 5 years is 23% for Group 1 and 4% for Group 2. Two-transplant collections required 492 days of apheresis with an overall cost of $2,500,000; however, one-transplant collections would cost $1,400,000 for 279 apheresis days. The median cost of cryopreservation for each patient who did not receive the second transplant is $15,000 (IQR: $8000 - $25,000). Therefore, the estimated cost for all patients in the study is $3,600,000 until the disposal of HPSC products. The incidence of a second transplant is low across all patients and significantly lower in patients greater than 60 years of age. Cryopreserved stem cell products remain under-utilized, leading to substantial financial burden. The duration of HPSC collection and cryopreservation must be re-evaluated for future treatment plans. Institutional policies should be revised based on the utilization trend to lower the operational cost of storage.
Lorazepam Detection with Urine Benzodiazepines Screening Tests: Not all Tests are Created Equal
Authors: Akter Tanjina , Babic Nikolina
Published: November 2023

Lorazepam belongs to the benzodiazepines family of drugs and is one of the commonly used anti-anxiety medications in the US. In clinical practice, immunoassay screening tests are used to monitor compliance, detect abuse and in cases of drug overdose. Many clinicians rely on benzodiazepine immunoassay screening tests to detect lorazepam due to the test availability on automated clinical analyzers, short turnaround time and cost efficiency. However, compromised test sensitivity often leads to erroneous results. In this study, we used mass spectrometry to establish the lorazepam cross-reactivity threshold in two commonly used benzodiazepine screening tests: the Abbott ARCHITECT cSystem 16000 and NexScreen Drug Screen Cup.

Methods: Mass spectrometry testing was performed at a major reference laboratory. Lorazepam-positive patient urine at concentrations of 320 ng/mL and 4,895 ng/mL were tested concurrently by two immunoassay methods. The Abbott ARCHITECT is a semi-quantitative assay with a positivity cut-off of 200 ng/mL. According to the manufacturer’s instructions for use (IFUs), the cross-reactivity threshold of the test is equivalent to a lorazepam concentration of 650 ng/mL. The NexScreen Drug Screen Cup is a lateral flow immunoassay used as a point-of-care (POC) test. The positivity cut-off of this test is 300 ng/mL; per IFUs, the cross-reactivity threshold of this test to lorazepam is 3,900 ng/mL, and 5,000 ng/mL for lorazepam-glucuronide, a drug metabolite. To determine the test sensitivity of the NexScreen test, patient specimen (4,895 ng/mL) was diluted at 1:5, 1:10, 1:20, 1:50, and 1:100, targeting the lorazepam concentrations of 979, 490, 245, 98 and 49 ng/mL respectively. To determine the sensitivity of the immunoassays to the parent molecule vs the metabolite, pre-screened negative urine was spiked with lorazepam or lorazepam-glucuronide at a concentration of 650 ng/mL, 5000 ng/mL, and 10000 ng/mL.

Results: Abbott ARCHITECT failed to detect lorazepam in both patients, while the NexScreen resulted in positive benzodiazepine screen results for both patient specimens. All lorazepam-spiked specimens tested positive on both methods. However, all lorazepam glucuronide-spiked specimens tested negative on Abbott ARCHITECT and positive on NexScreen cup. The highest dilution detected by NexScreen was 1: 20, equivalent to approximately 245 ng/mL of lorazepam.

Conclusion: Our findings suggest that the ARCHITECT benzodiazepine assay should not be used to screen patients on lorazepam, given its inability to detect the major metabolite, lorazepam glucuronide. Whenever available, a mass spectrometry method is always preferred. The results of our study demonstrated that in a specific patient population, where the likelihood of positive lorazepam test is high, the NexScreen cup is a viable, cost-effective alternative due to its excellent sensitivity.
Performance of a Modified ALLType NGS HLA Typing Assay with the Ion Chef/Ion S5/TypeStream Visual System
Authors: Shen Manli , Duffy Brian , Jennemann Jo-ellen , Willey Patricia , Tang Mei San , Brescia Peter , Lee Jar How , Liu Chang
Published: November 2023

OBJECTIVE

S: The commercial ALLType assay (One Lambda, West Hills, CA) enables accurate, high-resolution typing of 11 HLA genes using the Ion Chef/Ion S5/TypeStream Visual (TSV) system. The assay features a multiplexed PCR to enrich all target HLA genes in a sample, and up to 48 samples can be indexed and sequenced in a run. The assay is laborious due to the late pooling of indexed libraries. Early pooling significantly simplifies the workflow but may increase the background noise and typing errors. This project aims to examine the feasibility of early pooling immediately after the indexing step and evaluate the performance of such a modified ALLType protocol.

METHODS

A total of 75 unique samples with diverse HLA genotypes were included in this study, which comprised 52 proficiency testing samples of three different sources, 10 stem cell recipients, 7 stem cell donors (including 2 buccal swabs), and 6 deceased organ donors. Genomic DNA extracted from these samples was tested in four sequencing runs, with 15-31 samples per run, using the modified ALLType procedure (reagent lot: 15). The results were compared with the reference typings generated by the manufacturer-established protocol. All data were analyzed using TSV (version 3.0) and the IPD-IMGT/HLA library (version 3.47); the default analysis parameters were applied. The primary endpoint of the study was the concordance of 3-field typing results. The secondary endpoint was key health metrics, including allele balance, key-exon coverage, and background noise. We also evaluated the saving on hands-on time and reagents with the modified protocol.

RESULTS

The concordance rates of 3-field typing results were 100% for HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, and HLA-DRB1, and 96.2% for HLA-DRB3/4/5. The three discrepant HLA-DRB3/4/5 results with the modified protocol were false positive allele calls due to a small number of contaminating reads, which were corrected by increasing the threshold for HLA-DRB3/4/5 in TSV. The allele balance and exon 2 coverage across all samples and genes were comparable between the modified and reference protocols, with R-squared values of 0.83 and 0.81, respectively. High background signals in exons were observed in only 0.6% of all samples with both protocols. The modified protocol reduced the hands-on time by 15%, from 6.5 to 5.5 hours, and reduced the use of library preparation reagents by 30%.

CONCLUSION

It is feasible to pool indexed libraries early during the library preparation process without increasing the background noise in the sequencing data. The modified ALLType protocol showed typing accuracy and health metrics comparable to the original protocol, with significant savings on time and reagents.
Analytical Performance Evaluation of BioRad’s Unassayed Multiqual, Immunoassay Plus and Assayed Multiqual InteliQ Tube-Based Quality Control Materials
Authors: Laryea Erving T , Mitchell Kelsey , Standford Eric , Hernandez Julia , Wiencek Joesph R
Published: November 2023

Introduction

Quality control (QC) practices commonly require aliquoting of liquid material into sample cups prior to analysis. Recently, newer tube-based QC has become available that can be scanned directly onto the analyzer without additional aliquoting. In this study, we evaluate the performance of the BioRad’s Unassayed Multiqual (Mutiqual), Immunoassay (IA) Plus and Assayed InteliQ Muliqual (InteliQ) tube-based QC material. Materials and

Methods

The analytical performance of Multiqual, IA Plus and InteliQ materials were compared over 14 days at three concentrations on an Abbott Alinity ci analyzer system. The analysis included 20 unique clinical chemistry and 4 immunoassay analytes. For an applied comparison, all QC materials were analyzed using the same lot on multiple days, times, and by various laboratory team members (n=10). The means, standard deviations (SD) and coefficient of variation (CV) were calculated for each analyte. Minimum acceptable allowable imprecision (I) specifications were set using the biological variation (BV) database from European Federation for Laboratory Medicine (EFLM), which was calculated for each analyte using the equation I = 0.75*CV within-subject. Sample cups used for Multiqual and IA plus were also calculated to determine consumable waste for these materials over the study period and extrapolated for a year.

Results

Multiqual, IA Plus and InteliQ CVs for each analyte were compared to the EFLM BV database and showed comparable results for most analytes studied. Most analytes demonstrated < 5% CV over the 14-day period for InteliQ except alkaline phosphatase, bicarbonate, total bilirubin, and triiodothyronine for either 1, 2 or 3 levels. Total bilirubin and free thyroxine were outside this CV for Multiqual and IA Plus. In addition, minimum acceptable allowable imprecision goals from EFLM were not met for several analytes that were included in InteliQ such as albumin, alkaline phosphatase, aspartate aminotransferase, calcium, bicarbonate, chloride, and sodium. Multiqual and IA plus analytes that did not meet imprecision goals were bicarbonate, chloride, sodium, and free thyroxine, respectively. A total of 84 sample cups were needed to perform Multiqual and IA plus QC analysis over the study period or approximately 2184 over a year.

Conclusion

Multiqual, IA Plus and InteliQ QC materials provide similar analytical performance although each material had some analytes that did not meet acceptable imprecision limits defined by EFLM. Implementation of new tube-based QC materials can reduce sample cup consumables and may reduce technologist time required to aliquot Multiqual and IA Plus.
A rare case of compound Hemoglobin Lansing/Hemoglobin S coinherited with alpha thalassemia trait (-alpha3.7) presented with spurious hypoxemia and moderate hemolytic anemia
Authors: Marhatta Adwait , Fang Yanan , Mulvey Joseph , Campbell Sean , Choudhuri Jui
Published: November 2023

We present a case of a 27-year-old female at 27 weeks of gestation, who presented at the emergency department for vaginal spotting. She was also found to have low oxygenation on pulse oximetry of approximately 82% at room air. Her SpO2 did not improve with O2 supplement. She had a similar presentation a month before, with mild light-headedness and low oxygenation. However, two repeated air blood gas (ABG) findings were normal for oxygen saturation. Hemoglobinopathy was suspected due to the disparity. She was anemic during her presentation, with hemoglobin 8.3 g/dl, RBC count 3.36 million/ul, MCV 81 fl and MCH 24.7 pg. Additional workup showed increased reticulocyte count, decreased haptoglobin, negative direct Coombs test, negative G6PD test, and no evidence of a PNH clone. Capillary hemoglobin electrophoresis showed HbA 59.8%, HbS 34.5%, HbA2 3.6% and a small peak (2.1%) in the Z8 zone with a trailing edge at HbF window. HPLC revealed an “unknown peak” of 8.2% with a retention time of 1.93 minutes as well as the HbS peak. There was also a tiny additional A2 peak unresolved from the main A2 peak. Alpha globin gene sequencing revealed one copy of the -alpha3.7 alpha-globin deletion and one copy of Hb Lansing variant in the alpha2-globin gene. This is consistent with the compound Hemoglobin Lansing/Hemoglobin S coinherited with alpha thalassemia trait. Hemoglobin Lansing is a rare unstable alpha hemoglobin variant with mutation of c.264C>G resulting with a substitution of His by Gln at codon 87. The mutation was first discovered in the alpha 2 gene. Then the same mutation was found in alpha 1 gene later and named as Hemoglobin Lansing-Ramathibodi. To the best of our knowledge, this is the first reported case of Hemoglobin Lansing with alpha thalassemia trait (-alpha3.7) and HbS. Spuriously low pulse oximetry measurements have previously been reported in Hb Lansing variants. It was speculated to be due to different absorption spectra of Hb Lansing which is under study now. The patient also presented with hemolytic anemia. The exact cause was undetermined yet although it might be related to her hemoglobinopathy. Mild hemolytic anemia was reported in two cases of co-inheritance of Lansing-Ramathibodi and Hb Pakse (a non-deletional alpha thalassemia) but not in the members of the same family with Hb Lansing alone. It was also reported that some unstable alpha chain variants, when associated with another alpha thalassemia defect, present with a more severe phenotype including hemolytic anemia even though essentially asymptomatic in a heterozygous state.