Molecular Testing Research Articles

B-048 Proposal of a new monitoring algorythm for patients with a HIV positive result with the Elecsys HIV DUO test

Abstract Background Worldwide HIV infections remain a public health problem, contributing significantly to morbidity. In Mexico we have had a progressive adaptation to the HIV epidemic providing free therapy and testing (4th generation tests) for the whole population in anbulatory centers for HIV/AIDS prevention and medical care. During 2022 Mexico reported 12,374 new cases. In the last decade there has been an increasing interest in the identification of patients HIV positives subgroups, based on disease progression and serological features. To date, 6 generations of tests for HIV detection have been developed, strongly reducing the window period for a positive result. Elecsys HIV Duo is a 5th generation immunological test that provides in a separate manner an antibody and antigen results for HIV detection. These results show a better insight of the serologycal status reducing the window period post infection. By using these tests we want to provide an early detection of new cases that gives a better prognosis for the patient and propose a new monitoring for patients with a positive antigen result but that have not yet produced antibodies. Such algorythm is currently lacking in the Mexican public health services. Methods A retrospective statystical analysis of HIV results of samples procesed with the Elecsys HIV DUO test during the january-april 2023 period in the National Reference Center of Salud Digna correlated with western blot results. Results The study population was 6405 patients, 6340 (98.98%) had a negative result in the test and 65 (1.02%) a positive test. Based in antibody/antigen results we categorized the positives results in three grupos: Group 1 Ab positive/Ag negative (16), group 2 Ab positive/Ag positive (32) and group 3 Ab negative/Ag positive (7). When correlated with the WB results all the patients from group 1 and 2 had a positive result while all patients in group 3 had a negative result. Conclusions Actually Mexican public health services do not have access to 5th generation HIV tests like the Elecsys HIV DUO test, therefore, public health profesional are not qualified to interprete these results and do not have a stated algorythm for patientes belonging to group 3. Therefore and based in our results we suggest 5th generation test (or superior if available) and propose a new patient monitoring algorythm with a molecular confirmatory test for viral detection. This proposal is strongly supported by the fact the we have a population that have not generated antibodys during the first weeks of post infection and will test negative in a serologycal confirmatory test like WB. Screening for patients in early infection stages is important because if we provide early therapy which may lead to infection reversal or a less impact in C4+ T cells numbers. Studies like this provide information for the generation of public politics in benefit of the population.

A-301 Evaluation of Second-Generation Visby Medical Sexual Health Point-of-Care Test: Clinical Concordance, Analytical Error Rates, and Result Turnaround Time

Abstract Background Rapid testing for Neisseria gonorrhoeae, Chlamydia trachomatis, and Trichomonas vaginalis may be useful for antibiotic stewardship initiatives. Our institution recently implemented the second-generation Visby Medical Sexual Health Test (Visby Gen2) for rapid diagnosis of STIs in our emergency department. Here we (1) compared result concordance of the (Visby Gen2) to the first-generation Visby Medical Sexual Health Click Test (Visby Gen1), (2) compared assay failure rates of the Visby Gen1 to Gen2 tests, and (3) compared result turnaround time (TAT) for clinically ordered rapid STI tests to central laboratory STI results. Methods Accuracy was assessed using residual clinical samples in Aptima buffer submitted for routine molecular STI testing (C. trachomatis, N. gonorrhoeae, and T. vaginalis) in the central laboratory on the Panther platform (Hologic). Aptima samples were diluted 1:33 in Visby collection buffer prior to testing on the Visby cartridge. Clinically reported results were used as reference results. Diluted samples with discordant results were re-tested on the reference method and the result from the dilution was used in calculations. Assay failure rates were calculated as the number of failed assays compared to the total assays performed. TAT for rapid and central lab testing was calculated as time of sample received in laboratory to time verified in laboratory information system. Results For Visby Gen1 we observed negative concordance of 100% (41/41) for C. trachomatis, 97.5% (39/40) for N. gonorrhoeae, and 97.1% (34/35) for T. vaginalis. Positive concordance was 91.7% (11/12) for C. trachomatis, 100% (11/11) for N. gonorrhoeae, and 100% (17/17) for T. vaginalis. For Visby Gen1 we observed a 10.5% (12/114) cartridge failure rate. For Visby Gen2, we observed negative concordance of 100% (59/59) for C. trachomatis, 100% (63/63) for N. gonorrhoeae, and 100% (55/55) for T. vaginalis while positive concordance was 100% (10/10) for C. trachomatis, 100% (6/6) for N. gonorrhoeae, and 90.9% (10/11) for T. vaginalis. The Visby Gen2 assay displayed a 4.9% (4/81) cartridge failure rate. Six weeks after implementing the Visby Gen2 assay in our ED, rapid STI panel TAT was 0.48 hours on average (n=20). In the central laboratory the average TAT was 22.31 hours (n=7892). Conclusions Assay concordance to reference method was similar for Visby Gen1 and Gen2 assays. The cartridge failure rate improved by 46.7% with the Gen2 assay which should decrease the need to repeat testing due to assay failure. Result TAT decreased by 97.8% when comparing rapid Visby results to central laboratory. Therefore, Visby STI testing using the Gen2 assay can provide accuracy and rapid results likely to facilitate more rapid patient management.

B-201 Clinical Performance Evaluation of IRON-qPCR™ RV, a Novel Molecular POCT system, for the Qualitative Detection of Respiratory Viruses in Nasopharyngeal Swab

Abstract Background The availability of Point-of-Care testing (POCT) based on molecular diagnostics to test simultaneously for multiple respiratory viruses is very limited though significant progress has been made in molecular testing for COVID-19 during the pandemic. Considering the similar symptoms presented by patients infected with various respiratory pathogens, it is crucial to have multiple POCT systems capable of detecting multiple respiratory pathogens while distinguishing SARS-CoV-2 from other pathogens. To meet the growing demand for multiplex testing for respiratory pathogens, a molecular POCT, IRON-qPCR™ RV has been developed. IRfON-qPCR™ RV is a multiplex real-time RT-PCR assay designed for the qualitative detection and differentiation of SARS-CoV-2, Influenza A, Influenza B, RSV-A, and RSV-B RNA from human nasopharyngeal swab specimens. The IRON-qPCR™ proceeds the entire process automatically from nucleic acid extraction to real-time RT-PCR within 40 minutes. The main goal of this study is to evaluate the clinical performance of IRON-qPCR™ RV in comparison with other assays and kits using nasopharyngeal swab samples. Methods To assess the clinical performance of the IRON-qPCR™ RV, specimen collection and evaluation were conducted at a clinical institution in France, utilizing a total of 980 nasopharyngeal swab samples. The comparators used were the Xpert® Xpress CoV-2/Flu/RSV plus Kit and the RealStar® RSV RT-PCR Kit 3.0. Since RSV subtypes are not distinguished by the Xpert kit, all RSV without subtype distinction were compared. Additionally, RealStar kit was used to compare the results of IRON-qPCR™ RV for RSV subtypes A and B. Clinical samples showing discrepancies between Xpert and RealStart, and the IRON-qPCR™ RV were further analyzed using Allplex™ SARS-CoV-2/FuA/FluB/RSV Assay and sequencing. Results Through the comparison of clinical performance of the IRON-qPCR™ RV with Xpert for SARS-CoV-2, Influenza A, and Influenza B in nasopharyngeal swab samples, the clinical sensitivity was analyzed to be over 95.5%, and the clinical specificity was over 99.6%. For RSV, compared to Xpert, the clinical sensitivity was analyzed to be 96.9%, and the clinical specificity was 98.9%. Furthermore, in comparison with RealStar, the clinical sensitivity and specificity of IRON-qPCR™ RV for RSV-A were determined to be 96.2% and 100%, respectively, and the clinical sensitivity and specificity for RSV-B were 96.0% and 100%. Additionally, discrepant samples in comparison with Xpert were further tested using the Allplex as a resolver kit. The result showed that the clinical sensitivity and specificity of IRON-qPCR™ RV for SARS-CoV-2, Influenza A, and Influenza B were over 98.3% and 100%. For RSV, the clinical sensitivity and specificity were 99.5% and 99.1%. Conclusions The clinical performance of IRON-qPCR™ RV was analyzed with the clinical sensitivity of over 95% and the clinical specificity of over 99%. Upon analysis including the results of the resolver kit for discrepant samples, increased clinical sensitivity and specificity were determined. The results of this study strongly support that the IRON-qPCR™ RV is a reliable POCT system for the simultaneous detection and differentiation of multiple respiratory viruses. Furthermore, it is applicable to district hospitals as well as clinical laboratories for accurate and timely testing.

A-251 Simplification of Molecular Diagnostics for Sexually Transmitted Infection Point-of-Care Testing

Abstract Background HPV-caused cancers contribute to a large disease burden, accounting for 5% of all cancers. It is estimated that over 700,000 people develop HPV-related cancers each year with the majority being cervical cancer. The burden of this disease is disproportionately carried by low-income countries with the highest rates of HPV cervical infections primarily found in sub-Saharan Africa, Latin America, Eastern Europe, and South-East Asia. Many regions in low-resource countries lack adequate access to sensitive point-of-care screening tools, preventing timely diagnosis and treatment. Current low-cost methods, such as Pap smears and visual inspection using acetic acid suffer from low sensitivity, specificity, and reproducibility which limit their effectiveness as a screening modality. Many countries use nucleic acid amplification tests (NAATs) to identify key HPV infections which may progress towards cervical cancer. However, the expenditure for NAAT-capable equipment and reagents are cost-prohibitive for rural and underserved communities. To reduce screening barriers, we developed an isothermal HPV molecular test that can detect all 14 cancer-causing HPV strains using a novel amplification methodology combined with G-quadruplex DNAzyme colorimetric detection. Methods We developed a novel isothermal amplification technique that is related to loop-mediated isothermal amplification (LAMP) but uses modified looped primers to enable exponential amplification at 60°C for 1 hour. The modified primers only require two binding sites compared to 4-6 in LAMP. To detect the amplified products, we used G-quadruplex peroxidase-like DNAzyme probes which reduce ABTS to produce a visually interpreted result. Analytical validation evaluated the method’s limit of detection, specificity, and accuracy. As proof of concept in a relevant matrix, clinical cervical brushings collected ThinPrep Pap media were tested with the new method and compared to an FDA-approved reference qPCR test. Results Repeated experiments demonstrate that the lowest detectable HPV DNA concentration was approximately 1000 genomic copies/µL with no amplification with other pathogens. As proof of concept, the comparison to the reference standard demonstrated high accuracy. Conclusions The application of our assay is intended as a near-patient screening tool with further evaluation by a clinician for confirmation. With an accurate and rapid screening tool, we envision low-resource regions across the world will have the tools to rapidly detect and treat cervical cancers in their early stages.

B-206 Tick-borne disease molecular testing positivity and coinfection incidence in the northeastern united states: 2021-2023

Abstract Background The CDC estimates that Lyme disease affects hundreds of thousands of people each year in the United States. Tick-borne diseases caused by pathogens such as Anaplasma phagocytophilum, Babesia microti, Ehrlichia chaffeensis, and species of Borrelia follow a seasonal pattern due to the life cycle of disease-carrying ticks. In endemic areas, like the northeastern United States, the risk of coinfection by multiple tick-borne disease pathogens is higher and can complicate patient treatment. For example, while Anaplasma and Borrelia can be treated with doxycycline a Babesia coinfection would not be resolved with this medication. In this study, we performed a retrospective analysis of tick-borne disease molecular testing results to monitor positivity rates and incidence of coinfection. Methods This retrospective analysis included whole blood specimens submitted to a regional clinical laboratory in the northeastern United States for tick-borne disease molecular testing. Test results from 2021-2023 were analyzed for positivity rate trends and coinfection incidence. DNA was isolated from patient specimens and tested using laboratory developed real-time Taq polymerase PCR assays. Results Positivity rates for all tick-borne disease pathogens studied followed typical seasonal patterns (Table). Beginning in the early spring, as nymphs ended their dormancy and began to feed, infection rates of tick-borne disease climbed. Infections peaked in mid-summer and remained elevated through late autumn. For Anaplasma, a biphasic pattern was observed, with a smaller peak in late autumn when adult ticks are most active. Coinfections with Anaplasma and Babesia were observed in 136 specimens, while coinfections with Borrelia and Babesia were observed in 145 specimens. Conclusions Positivity rates for tick-borne disease pathogens followed expected seasonal patterns in the northeastern US. The incidence of coinfections involving Babesia microti highlights the importance of properly identifying tick-borne infections given the different treatment regimens indicated.

B-353 High risk HPV genotypes prevalence in Mexico

Abstract Background The greatest risk factor for the development of cervical cancer is infection by human papillomavirus (HPV). To date, more than 200 genotypes have been described, 14 of them considered by the WHO as high risk genotypes (HR) due to their high oncogenic capacity, with special attention given to genotypes 16 and 18. In Mexico, cervical cancer is the third cause of cancer-associated death in women, therefore, the timely detection of HR genotypes in women becomes imperative for the reduction of the burden of this disease. The detection of high-risk HPV genotypes through the PCR molecular test is part of primary cervical cancer screening, however, this practice is not common in Mexico. Here, we analyzed the results of HPV genotyping studies in women attending cervical cancer screening studies at Salud Digna with the objective of determining the prevalence and dsitribution of HR-HPV in Mexico. Methods Retrospective analysis of the results obtained for the detection of HPV in cervical samples from patients who were attended at Salud Digna clinics from june to august 2023. The samples were processed by automated RT-PCR (ROCHE COBAS PRIME-Cobas 6800). The kit used was the COBASHPV which detects the 14 HR genotypes and generates 4 types of results: negative, positive for HPV16, positive for HPV18 and positive for POOL (which includes the remaining 12 genotypes). For the analysis, Mexico was divided into 7 regions which share sociocultural factors (Northwest, North, West, Center, Gulf, South, Southeast). Results The study population was 95,934 patients (mean age of 41y). At the national level, 18.93% (18,159) of patients are positive for HPV POOL, 3.54% (3,399) for HPV 16 and 1.78% (1709) for HPV 18. The regions with the highest positivity are the southeast region for HPV POOL (22.32%), the south region for HPV 16 (3.77%) and HPV 18 (2.44%) while the region with the lowest percentage is the Northwest region (HPV POOL 17.86%, HPV16 3.39%, HPV18 1.57%). The age range with the highest percentage of positivity is 14-29y for HPV POOL, 30-39y for HPV 16, and 30-39y for HPV 18. Conclusions We found that Mexican patients are becoming infected at an early age with the genotypes that are part of the pool, however, we observe a marked trend towards a decrease in cases as the age of the population advances.The regions of the country with a higher percentage of HPV positive patients are the south and the southeast, regions that also concentrate most of the extreme poverty in Mexico. These numbers should be taken with caution given that in absolute values these are also are the regions of the country where the least people go for a cervical cancer screening study, emphasizing the need to promote these studies in these regions. In the case of genotypes with a greater oncogenic capacity, both HPV16 and HPV18 show a greater prevalence in economically productive age ranges. Retrospective studies like provide information that allow governments to generate public policies focused on the most affected regions.

A Rare Case Of Desmoid Tumor In The Lower Mandibular Sector Of An Adolescent: Surgical Intervention And Outcomes

Introduction: Desmoid tumors are rare, benign neoplasms known for their locally aggressive behavior and high recurrence rates. They arise from fibroblasts and are characterized by their infiltrative growth, making surgical management challenging. This report presents a case of a desmoid tumor in the lower mandibular sector of a 16-year-old male, focusing on surgical intervention and molecular insights. Case Report: A 16-year-old male presented with a growing mass in the lower right mandible, causing pain and mobility of tooth 47. Imaging revealed an infiltrative lesion eroding the mandibular bone. Histopathological analysis confirmed a desmoid tumor with spindle-shaped fibroblasts and nuclear β-caténine expression. Molecular testing identified a CTNNB1 gene mutation, confirming the diagnosis. Discussion: Desmoid tumors, despite being benign, are challenging due to their aggressive local behavior. Surgical excision with clear margins is the primary treatment, as these tumors are resistant to chemotherapy and radiotherapy. This case highlights the importance of precise surgical planning and the role of β-caténine and CTNNB1 mutations in diagnosis and prognosis. Conclusion: Effective management of desmoid tumors in adolescents requires thorough surgical intervention and comprehensive diagnostic analysis. Long-term follow-up is crucial to monitor for recurrence. The molecular characteristics of the tumor, such as CTNNB1 mutations, play a significant role in guiding treatment and predicting outcomes.

A-279 Performance Evaluation of the Respiratory Viral for BD MAX™ System in Geriatric Population

Abstract Background Respiratory Viral Infection is one of the most common infection in the geriatric population and cause major concern in the Long-Term Care Facilities. Influenza A and B, SARS-CoV-2, and respiratory syncytial virus (RSV) are responsible for most of the hospitalization and deaths among elderly patients. Rapid identification, treatment, and isolation are among the most important steps to fight the spreading of the infection. Methods The BD Respiratory Viral Panel for BD MAX™ System is an automated multiplexed real-time reverse transcriptase polymerase chain reaction (RT- PCR) test intended for the simultaneous, qualitative detection and differentiation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B, and/or respiratory syncytial virus (RSV) nucleic acid in nasopharyngeal swab (NPS) and anterior nasal swab (ANS) specimens from individuals with signs and symptoms of respiratory tract infection. The assay is targeting RNA from the nucleocapsid phosphoprotein gene (N1 and N2 regions) of the SARS-CoV-2, a conserved region of the matrix protein M1 gene for influenza A, conserved regions of the matrix protein M1 gene and HA gene for influenza B, conserved regions of the N and M genes for RSV, and the human RNase P gene. The assay was evaluated for: precision, reproducibility, accuracy, and correlation with BioGx for SARS-CoV-2, Solana (Quidel) for influenza A, influenza B and RSV; the percentage agreement for the evaluation steps was calculated. We ran 86 samples collected from patients residing in Long-Term Care Facilities. Statistical analyses were done using Analyse-it. Results The percentage agreement for precision, reproducibility, and accuracy were 100%. The patients’ correlation was 100% when compared to the existing molecular testing in the laboratory. Female patients accounted for 62.8% (54 female and 32 male); 2 patients were positive for both influenza A and RSV, and one patient was positive for both influenza A and SAR-CoV-2. Conclusions The Respiratory Viral panel for BD MAX™ System gave the benefit of a fully automated, high precision, accuracy and acceptable sensitivity assay; in addition, it offers easier collection (one swabs versus multiple swabs), faster turnaround time for four targets in less than three hours which allow for earlier isolation to prevent the spreading of the infection and initiating treatment when needed. As with every molecular assay avoiding contamination is very important to eliminated false positive results.

B-227 Customized molecular tests for minimal residual disease: a tool for therapeutic decisions in follicular lymphoma patients

Abstract Background Monitoring of minimal residual disease (MRD) is based on accurate laboratory tests which can recognize a small fraction of malignant cells that survived the course of treatment. Several studies of the B-non-Hodgkin lymphoma group have been presented that MRD positivity at the end of treatment is a negative prognostic index. Follicular lymphoma (FL) is a chronic indolent malignancy, which response highly to immuno-chemotherapy followed by prolonged remissions but with inevitable relapse in most patients. The GALLIUM study showed that immuno-chemotherapy combinations, 6 cycles of bendamustine-obinutuzumab (BO), is the most efficacious treatment, but with severe side effects .In addition, 90% of patients achieved negative MRD from peripheral blood (PB) or bone marrow (BM) after only 3 BO cycles. These findings raise the possibility for MRD based treatment approach, where the duration of chemotherapy could be decided according to MRD status at mid-induction (MI). Identification of a marker in the PB and/or BM of each FL patient which will be use to the design of a sensitive RQ-PCR test for MRD detection for follow-up. Methods Qualitative PCR for translocation 14:18 and for the VDJ rearrangement sequence of the immunoglobulin heavy chain was used for marker identification. MRD monitoring was done by RQ-PCR. MRD monitoring for VDJ was designed specifically to each patients based on his VDJ sequence. MRD was assessed on PB and BM at MI. Results Marker for monitoring was identified at 11/21 patients in this study. After 3 combined therapy cycles, 7 patients were found to have MRD negativity by RQ-PCR therefore continue with immuno-therapy only. MRD positivity was assessed in BM of 3 patients (0.11%, 0.022%, and 0.133%). These 3 patients continued with the combined therapy. RQ-PCR sensitivity was 10-4-10-5. Conclusions This study will reveal the ability to use sensitive and specific MRD that has to be designed for each patient according to his marker and enable the establishment of a treatment with a high safety profile for FL patients. Correlation between MRD status and clinical and safety parameters will be assessed at the end of the study, 30 months after the first treatment, taking into account MRD status from different time point of the follow-up period.

B-212 Laboratory Performance in Molecular Detection of Mycobacterium tuberculosis Through Analysis of External Quality Assessment Program Results: WHO-Recommended Tests Outperform Others

Abstract Background In 2022, tuberculosis caused 11,200 deaths in Brazil and 1,300,000 globally. With 87,344 new cases, it remains a leading infectious cause of death, second only to COVID-19. Prompt detection is critical, particularly with the growing resistance to rifampicin and isoniazid, highlighting the need for molecular testing. External Quality Assessment Programs (EQAP) are essential to ensure the accuracy, reliability, and harmonization of laboratory results amid the complexities of M. tuberculosis infection. Here, we evaluate the overall performance of participating laboratories (labs) in three EQAP related to tuberculosis: M. tuberculosis molecular detection (MTB), Rifampicin resistance detection (RIF), and Isoniazid resistance detection (INH). All are organized by a Brazilian provider accredited according to the ABNT NBR ISO/IEC 17043:2011 standard. Methods The EQAP samples were suspensions containing human cells, with or without the addition of cultured, inactivated, and lyophilized M. tuberculosis. Labs received two samples quarterly for testing accuracy, sensitivity, and specificity. We computed these metrics along with participant and round numbers. The Mann-Kendall test assessed accuracy trends over time. Furthermore, kit type accuracies for in-vitro diagnostic (IVD) vs. laboratory-developed tests (LDT), World Health Organization recommended (WHO-recommended) vs. other kits (non-WHO), and methods (qPCR vs. PCR) were compared using chi-square tests and odds-ratio calculations. Results In the MTB EQAP (2018-2022), 63 labs participated over 20 rounds, with 22 (range: 6-48) labs per round on median, achieving 96.6% accuracy (853/883), 97.5% sensitivity (556/570), and 94.9% specificity (297/313). The Mann-Kendall test found no significant accuracy trends over time (τ = -0.91, p = 0.36). IVDs outperformed LDTs with 97.8% (751/768) vs. 87.9% (102/116) accuracy (OR=6.0, 95%CI 3.42-20.9, p<0.0001). WHO-recommended kits were more accurate than non-WHO kits, 98.2% (674/686) vs. 90.4% (179/198) (OR=5.96, 95%CI 1.05-12.7, p<0.0001). qPCR exceeded the accuracy of PCR, 97.2% (833/857) versus 74% (20/27) (OR=12.1, 95%CI 4.8-32.9, p<0.0001). For RIF EQAP (2020-2022), 49 laboratories in 9 rounds, with 25 (range: 18-42) laboratories per round on median, showed 97.4% accuracy (297/305), 97.2% sensitivity (176/181), and 97.6% specificity (121/124). In the INH EQAP (2021-2022), 7 laboratories over 7 rounds, with 4 (range: 2-5) laboratories per round on median, reached 95.2% accuracy (20/21), 100% sensitivity (4/4), and 94.1% specificity (16/17). Differences between types of kits and methods for RIF and INH, as well as trends over time, were not significant or could not be calculated due to the limited number of samples. Conclusions The MTB EQAP underscored the high participation and suitability of labs, along with excellent diagnostic performance; IVD kits were 6 times more likely to yield adequate results than LDTs. WHO-recommended kits were 5.9 times more likely to produce adequate results than non-WHO kits. qPCR was 12.6 times more likely to achieve adequate results than PCR. Despite fewer participants in RIF and INH, their performance rates were high; more data are needed for conclusive results on kit and method types. This study affirms the quality of molecular diagnostics for tuberculosis in Brazil, informs on kit and method selection, and underscores the critical role of EQAPs in combating a significant global health issue.

Molecular Markers in Follicular and Oncocytic Thyroid Carcinomas: Clinical Application of Molecular Genetic Testing.

Oncocytic thyroid carcinoma (OTC) was previously considered a variant of follicular thyroid carcinoma (FTC) but has recently been reclassified as a separate form of thyroid cancer. This study aimed to demonstrate that FTC and OTC are fundamentally distinct entities that can potentially be differentiated preoperatively through cytology and/or molecular testing. A retrospective chart review of patients diagnosed with FTC and OTC operated upon at two university health centers from January 2016 to September 2023 (n = 3219) was conducted. Molecular testing results were correlated with histopathologic diagnosis. Fifty patients met the inclusion criteria. FTC was identified in 27 (54.0%) patients, and OTC in 23 (46.0%) patients. Patients with OTC were older (61.8 years) than FTC patients (51.2 years) (p = 0.013). Moreover, aggressive tumors were found in 39.1% (9/23) of OTCs compared to 11.1% (3/27) of FTCs (p = 0.021). Amongst Bethesda category III and IV nodules, 17 out of 20 (85.0%) OTC cytology reports demonstrated an oncocytic subtype compared to only 5 out of 24 FTC cytology reports (20.8%) (p = 0.002). On molecular testing, the EIF1AX alteration was exclusively present in OTCs while the PAX8/PPARy and PTEN alterations were exclusively found in FTCs. Copy number alterations (CNAs) were found to be more prevalent in OTC (66.7%) compared to FTC (33.3%), and they were not indicative of tumor aggressiveness. Within the OTC group, all three patients who had a TP53 alteration were diagnosed with aggressive cancer. Lastly, the OTCs exhibited a higher frequency of multiple alterations on molecular testing (66.7%) compared to FTCs (33.3%). To our knowledge, this is the largest study to date comparing the clinical application of abnormalities found on molecular testing for FTC and OTC. It further demonstrates the distinct clinicopathological and molecular characteristics of OTC.

Ensuring precision medicine for veterans with lung cancer: A randomized clinical trial.

178 Background: National guidelines recommend molecular testing for patients with non-small cell lung cancer, yet this is not routinely completed in practice. In prior work, we identified barriers to testing in the Veterans Affairs. First, physicians are unaware if and when testing has occurred. Second, patients are unaware of testing and the implications on treatment and clinical outcomes. In response, in collaboration with a Veteran and Caregiver Advisory Board, we created a multilevel intervention led by a peer volunteer who: 1) provides tailored education of molecular testing for 1 month for Veterans newly diagnosed with lung cancer and, 2) alerts clinicians via secure messaging if tumor samples have not been tested. We conducted this randomized clinical trial to assess whether the intervention improves patient knowledge of molecular testing and patient activation and increases receipt of molecular genomic testing compared with usual care. Methods: All veterans >18 years old with a new diagnosis of any stage non-small cell lung cancer were eligible. Exclusions included inability to consent. All participants completed baseline assessments at randomization and at 1-month follow-up comprised of a 3-question validated precision medicine knowledge questionnaire and a 13-question validated patient activation measure. Genomic testing was assessed by chart review at 6-months follow-up. We used regression models to assess differences in mean knowledge and activation scores over time between groups and compared rates of genomic testing. Results: 75 Veterans were screened with 46 eligible. All 46 consented to participate, with 23 in each group. All were male (100%), had mean age of 76.3+/-5.54 years; 31 (67.4%) were Latinx; 2 (4.4%) Asian; 11 (23.9%) Black; 1 (2.2%) Native Hawaiian; 32 (69.6%) White; 32 (69.6%) had Stage 4 disease. At 1 month follow-up mean knowledge scores increased over time in the intervention group and remained stable in the control group (mean score 2.30 +/- 0.97 versus 1.16 +/- 1.15, p=0.014). At 1-month follow-up, patient activation increased for the intervention group more than the control group (46.7 +/- 11.3 versus 37.6 +/- 9.26, p=0.002). There were no significant differences in tumor testing between groups (intervention: 95.6% versus control: 86.9%, p=0.62) or time to first treatment course from biopsy (intervention: 28.2 days versus control 36.2 days). Conclusions: A volunteer led effort improved patient education regarding precision medicine and patient activation among Veterans as compared with usual care alone. Interventions that include volunteers and other support can enhance care and clinical outcomes among veterans with lung cancer. Clinical trial information: NCT05795959 .

Health Disparities among Patients with Cancer Who Received Molecular Testing for Biomarker-Directed Therapy.

Health disparities present a barrier to successful oncology treatment. The potential for precision oncology to reduce health disparities has not previously been analyzed. We performed a retrospective analysis of 12,627 patients from six major cancer centers whose tumors underwent molecular testing at Caris Life Sciences between 2010 and 2020. Kaplan-Meier and Cox regression were used to describe and analyze overall survival. The molecular and demographic features of the cohort were analyzed by χ2 and ANOVA tests. Black patients composed 25% of the cohort and White patients 63%. Among this molecularly-tested cohort, there were minimal outcome differences based on race, geographic location, or poverty level. When analyzing the interaction of age, race, and sex, racial-based disparities were noted primarily for young non-White women in the study cohort but were more pronounced for men and women of all ages in the broader patient population within the Surveillance, Epidemiology, and End Results database. Mutations in five genes-APC, EGFR, STK11, TP53, and KRAS-were found to affect overall survival among our cohort, and their prevalence varied by race in specific tumor types. Real-world outcomes data in mutation-defined cohorts also provided additional context to previously reported therapeutic response trends. Our study shows that patients who undergo molecular testing display reduced racial health disparities compared with the general population, whereas persistent racial disparities are influenced by age and sex. Genomic-driven racial disparities should be examined at a tumor lineage-specific level. Increased access to molecular testing for all eligible patients may play a role in improving health equity. Significance: This study is the largest of its kind to analyze health disparities and genomic features among a diverse multiinstitutional cohort of patients who underwent molecular testing. Continuing to increase awareness of and access to molecular testing approaches may help to reduce cancer health disparities and improve outcomes for all patients.

Real-world molecular testing patterns in primary advanced or recurrent endometrial cancer (pA/rEC) in the US.

395 Background: Targeted therapy can improve outcomes in women with pA/rEC, but real-world biomarker testing rates are unknown. This study estimated the real-world proportion of patients receiving biomarker testing (within ≤6 months of advanced/recurrent diagnosis) and characterized testing according to sociodemographic and clinical characteristics. Methods: We used the US Flatiron Health electronic health record–derived deidentified database. Records from 1/1/2013 to 8/31/2023 for women ≥18 years old with advanced/recurrent EC were searched to identify testing for DNA mismatch repair/microsatellite instability (MMR/MSI), HER2, and estrogen or progesterone receptors (ER/PR); a subsample dataset from 4/1/2013 to 11/30/2022 was analyzed for additional biomarkers. The subsample has information on additional biomarker testing and was used to evaluate the frequency of testing for these biomarkers. Testing rates were evaluated using descriptive statistics; characteristics associated with testing were identified by multivariate logistic regression. Results: Among persons meeting eligibility criteria (n=2982), the mean age was 65 years; the majority were non-Hispanic White (56%), had commercial insurance (79%), and received care in a community setting (73%). The subsample (n=509) had similar characteristics to the full cohort. Between 2013-2022, 73% (n=2165) of patients received testing for any biomarker. Testing rates for individual biomarkers are shown in the Table. From 2013 to 2021, testing increased for MMR/MSI (17% to 81%), ER/PR (45% to 62%), and HER2 (15% to 43%). The likelihood of testing was higher among patients with primary advanced EC (OR, 1.45; 95% CI, 1.03-2.06), endometrioid carcinoma histology (1.39; 1.01-1.93), commercial insurance (1.51; 1.18-1.93), at an academic facility (1.70; 1.37-2.11), and with no prior surgery (2.29; 1.83-2.86) relative to other attributes. Conclusions: Molecular testing has increased over time, indicating a continuous trend toward personalized treatment decisions. Several factors associated with an increased likelihood of biomarker testing were identified. Understanding these factors can inform approaches to increase access to molecular testing and increase testing rates. Biomarker testing rates, 2013-2022. Biomarker, n (%) 2013 2021 Overall MMR/MSI a 35 (15) 238 (80) 1604 (54) HER2 a 31 (14) 121 (41) 612 (21) ER/PR a 99 (43) 177 (59) 1465 (49) p53/ TP53 b 13 (36) 31 (74) 260 (51) TMB b 3 (8) 14 (33) 91 (18) CTNNB1 b 4 (11) 12 (29) 88 (17) ARID1A b 4 (11) 15 (36) 91 (18) CDK4/6 b 5 (14) 14 (33) 110 (22) POLE b 4 (11) 17 (40) 110 (22) ARID1A, AT-rich interactive domain-containing protein 1A; CDK4/6, cyclin-dependent kinases 4 and 6; CTNNB1, catenin beta-1; POLE, polymerase-epsilon; TMB, tumor mutation burden. a 2013, n=228; 2021, n=298; overall, n=2982. b Rates from subsample dataset (4/1/2013 to 11/30/2022); 2013, n=36; 2021, n=42; overall, n=509.

Nouveautés en pathologie thyroïdienne : classification OMS 2022, système Bethesda 2023, biologie moléculaire et testing moléculaire

WHO CLASSIFICATION 2022, BETHESDA SYSTEM 2023, MOLECULAR BIOLOGY AND MOLECULAR TESTING: Thyroid pathology has experienced significant advances with the publication of the 5th edition of the World Health Organization classification of endocrine tumors in 2022 and the third edition of the Bethesda system for thyroid cytopathology in 2023. At the same time, the availability of next-generation sequencing data coupled with numerous translational research projects have considerably increased our knowledge of the genomics and mechanics of thyroid cancers, enabling us to refine prognosis and propose new targeted therapies. In this review, we will take up the main new features of the WHO 2022 and Bethesda 2023 classifications, as well as molecular biology findings, with an emphasis on the practical implications for clinicians.

Microbiological profile and prevalence of histamine-producing bacteria in fresh sardines stored at different temperatures

Background and Aim: The European pilchard (Sardina pilchardus) is an important fish species for the Moroccan economy in terms of production and export. Biogenic amine histamine is a metabolite produced in the flesh of some fish species after death due to the decarboxylation of free histidine by histaminogenic bacteria. Failure to control the histamine risk in European pilchard may lead to public health and socioeconomic issues. This study aimed to estimate the prevalence of histaminogenic bacteria in association with histamine levels and the growth of microflora in Moroccan sardines (European pilchard). Materials and Methods: We conducted the study by monitoring Moroccan sardines of histamine content and microbiological profile (aerobic plate count [APC], coliforms, and thermo-tolerant coliforms [TTC]) during 6 days of storage at three different temperatures (0°C, 10°C, and ambient temperature [22°C]). The histamine assay was performed using a spectrofluorometric method, and the microbiological identification of histamine-producing bacteria was performed using a combination of biochemical and molecular tests. Results: The histamine content in European pilchard stored at 0°C was negligible. However, high concentrations were observed at 10°C and 22°C. The microbiological profile showed a positive association between microflora counts and histamine content according to storage time. At 0°C, a moderate increase in the APC, a decrease in coliforms, and an absence of TTC were observed. The rapid proliferation of all microflora was observed at 10°C, whereas at 22°C, the proliferation was almost exponential. Bacterial identification revealed the exclusive presence of species belonging to the Enterobacteriaceae family at varying frequencies depending on storage temperature. Morganella morganii and Proteus mirabilis had the highest histamine induction rates in L-histidine-supplemented broth, with 1600 and 255 parts per million (ppm), respectively, after 48-h incubation at 35°C. Klebsiella ozaenae could produce 136 ppm and Serratia plymuthica 115 ppm. Reverse transcription polymerase chain reaction showed positive results for the presence of genes associated with histidine decarboxylase. The hdc genes of M. morganii, P. mirabilis, and K. ozaenae were successfully amplified and exhibited strong similarity with the reference gene of M. morganii. Conclusion: This study describes for the first time the hdc gene in bacteria that form histamine in Moroccan sardines. The results also confirm that respect for the cold chain integrity is a crucial factor in histamine management. This information should help stakeholders in the implementation of sound strategies for managing the hazards associated with seafood and their products. Keywords: Enterobacteriaceae, histamine, Histaminogenic bacteria, polymerase chain reaction, sardine, seafood.

Nosocomial cluster of patients infected with imipenemase-1-producing Enterobacter ludwigii.

Introduction. Imipenemase (IMI) enzymes are an uncommon class A carbapenemases that have been isolated from aquatic environments and, occasionally, from clinical isolates of Enterobacterales.Aim. We describe a cluster of three patients infected by IMI-1 carbapenemase-producing Enterobacter ludwigii (IMI-1-Elud) in a tertiary university hospital in Gran Canaria, Spain.Methodology. Antimicrobial susceptibility was determined using the Vitek2 AST-N355 card and antibiotic gradient strips. The modified carbapenem inactivation method (CIM) test was performed in cases where the ertapenem MIC value was higher than 0.125 mg l-1. The carbapenemase was identified by PCR and DNA microarray and later characterized by whole-genome next-generation sequencing (NGS) with Illumina.Results. Three patients presented thoracic or abdominal infections caused by IMI-1-Elud ST1677 from 14 June 2022 to 14 July 2022. All patients underwent at least one gastroscopy during their admission, and two of them were located in adjoining rooms. Isolates were resistant to carbapenems, colistin and fosfomycin but susceptible to ciprofloxacin. IMI/NMC-A carbapenemase was detected by PCR and hybridization test and confirmed by NGS as IMI-1. All patients underwent at least one gastroscopy, and two of them were in nearby rooms. Patients showed microbiological and clinical improvement following focus drainage and targeted antibiotic treatment with a fluoroquinolone.Conclusions. This study reports the first documented global outbreak of patients infected with IMI-1-Elud. The source appeared to be related to endoscopes. Contact transmission may also have played a role. A screening method such as the modified CIM test is crucial for detecting less common carbapenemases that might not be identified by rapid molecular or immunochromatographic tests, as these often do not include bla IMI genes, which could lead to the undetected dissemination of carbapenemase-producing Enterobacterales. Effective infection source control and targeted treatment are essential for achieving a favourable clinical outcome.

Microscopic impacts of ultrasonic vibration on interfacial strength of SiCp/Al composites

SiCp/Al composites are used in aerospace and deep-space exploration equipment because of their extremely high strength and thrust-to-weight ratios; however, the differences in the properties of the reinforcement and matrix materials in this type of composites have restricted their applications. The ultrahigh-frequency vibration characteristics of ultrasonic vibration processing technology can effectively solve the above bottlenecks, but the effect of high-frequency vibration on the interfacial properties of SiCp/Al composites is still unclear. The effects of ultrasonic vibration on the interface strength of composites were analyzed from a microscale perspective by means of single particle push-out Molecular Dynamics (MD) simulations and tests under different conditions. The results show that the interface strength is negatively correlated with particle size but positively correlated with ultrasonic amplitude, with a maximum increase of about 51% relative to no ultrasound. Brittle-plastic transition was observed on the surface of particles with high interface strength, and lateral microcracks due to stress concentration were present on the surface of particles with low interface strength. Higher strains and grain refinement were obtained for larger amplitudes, and stacking faults and tangle dislocations appeared on the side of the interface layer close to the Al matrix. The results provide potential insights to improve the micromechanical and mechanical properties of SiCp/Al composites, enhance the longevity of the materials, and realize the sustainable use of resources by expanding the efficient, precise, and clean machining of such materials.

Examining Impact of Insurance Type on Genetic Testing in Pediatric Neurology

ObjectiveStudies that examine the impact of insurance type on the ease of obtaining genetic testing are scarce. Therefore, we aim to analyze how different types of insurance influence the time taken to obtain genetic test results among pediatric neurology patients. MethodsThis was a retrospective cohort study from Dayton Children’s Hospital. Patients who had at least one neurologic genetic result found in the electronic medical record from 01/01/2014 to 03/01/2023 were included in the study. Variables collected include demographics, health insurance data, and genetic testing results. Results141 patients were included. Most patients were male (51.8%), white (78.0%), and not Hispanic/Latino (96.5%). The mean age at time of genetic testing was 7.9 years. Most patients had Medicaid as their primary insurance (60.3%) as compared to private insurance (39.7%). 215 genetic reports were examined (137 Medicaid charts and 78 private insurance charts). There was no statistically significant difference from mean time lapse between test order date to results date for Medicaid patients (27.3 days) versus private insurance (31.5 days, p=0.40). Molecular genetics testing and epilepsy gene panel order were the most common tests ordered for both Medicaid (86.1%, 37.2%) and private insurance (88.5%, 39.7%, respectively). ConclusionsThe mean time between test order date to results date was comparable between private and Medicaid insured patients. Our results suggest that there is no significant difference for time to result between pediatric neurology patients who carry public versus private insurance for genetic testing.

Relative exchangeable copper, a high-quality biomarker for differentiation of Traditional Chinese Medicine syndrome in Wilson's disease.

To investigate the value of relative exchangeable copper (REC) in diagnosing Wilson's disease (WD) and to determine its significance in the differentiation of Traditional Chinese Medicine (TCM) syndrome. A total of 78 patients with WD were recruited on the same day of the medical visit, and among them, 32 were suffering from non-WD (N-WD) and 37 were heterozygous ATP7B carriers (HC) enrolled as controls. Molecular genetic testing was performed for diagnosing WD and HC. Additionally, REC levels in different TCM syndromes were investigated. The correlation between REC and serum ceruloplasmin (Cp), serum copper oxidase (CO), and 24-h urinary copper was analyzed using the Global Assessment Scale and Unified Wilson's Disease Rating Scale and the significance of REC in WD diagnosis was investigated. Resting-state functional magnetic resonance imaging was used to assess the clinical symptoms of WD and analyze its severity in different TCM syndromes. REC determination helped in significantly distinguishing patients with N-WD or HC from those with WD with a cut-off of 21.15%. Furthermore, the comparative analysis of REC ratios among different TCM syndromes showed markedly high REC levels in the dampness-heat internal accumulation syndrome group. Additionally, the seed-based functional connectivity value from the putamen to the cerebellum was significantly correlated with TCM syndromes. REC level is a high-quality biomarker for diagnosing WD that effectively reflects disease severity and plays an essential role in deciding on treatment strategies and prognosis. Furthermore, REC levels are closely related to TCM syndromes in WD; thus, it is a potential objective quantitative indicator for distinguishing TCM syndromes in WD.