Browsing by Author "Lavik, John-Paul"

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    Introduction to the Laboratory and Blood Bank: Creation of a Resource for Third-Year Medical Students
    (2024-04-26) Merritt, Emily; Harmon, Joseph; Lavik, John-Paul
    The transition between the pre-clinical and clinical years is an important and challenging step for medical students. Students must apply the knowledge learned during their preclinical years to novel situations while learning to interact with patients, families, and team members and how to utilize the resources and support systems available in the clinical environment. Despite being vital components of clinical care, exposure to the microbiology and pathology labs and blood bank is frequently limited prior to and during clerkships, thereby decreasing students’ opportunities to understand their role in a clinical setting and how to most appropriately utilize them in patient care. The purpose of this study was to evaluate the effectiveness of focused education on the role of the microbiology lab, pathology lab, and blood bank in preparing medical students for clerkships. A pre-recorded module was created consisting of a video lecture that was delivered via Kaltura. The lecture covered information about the pathology and microbiology labs and the blood bank relevant to students entering the clinical environment, including what broadly occurs in the lab, when the lab may call providers, and when and how providers should call the lab. Medical students in the Indiana University School of Medicine rising third-year class (n = 336) completed the module as a component of the Transitions 2 course in the latter half of April 2024, which introduces students to the clinical environment prior to clerkships and bridges the gap between pre-clinical and clinical education. The module was required pre-work before students completed a clinical case embedded within the Transitions 2 course. Students completed a pre- and post-quiz consisting of clinical scenarios commonly encountered in the clinical setting on clerkships. The effectiveness of the module was evaluated by comparing students’ pre- and post-quiz scores with Wilcoxon signed rank tests. Our results demonstrate that education on the microbiology and pathology labs and blood banks give students a foundation for their clerkships to better understand these resources and how to use them, which will hopefully facilitate their learning and functioning as team members and learners in the clinical environment.
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    Serum from COVID-19 patients early in the pandemic shows limited evidence of cross-neutralization against variants of concern
    (Nature, 2022-03) Griffin, Amanda J.; O'Donnell, Kyle L.; Shifflet, Kyle; Lavik, John-Paul; Russell, Patrick M.; Zimmerman, Michelle K.; Relich, Ryan F.; Marzi, Andrea; Pathology and Laboratory Medicine, School of Medicine
    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in a variety of clinical symptoms ranging from no or mild to severe disease. Currently, there are multiple postulated mechanisms that may push a moderate to severe disease into a critical state. Human serum contains abundant evidence of the immune status following infection. Cytokines, chemokines, and antibodies can be assayed to determine the extent to which a patient responded to a pathogen. We examined serum and plasma from a cohort of patients infected with SARS-CoV-2 early in the pandemic and compared them to negative-control sera. Cytokine and chemokine concentrations varied depending on the severity of infection, and antibody responses were significantly increased in severe cases compared to mild to moderate infections. Neutralization data revealed that patients with high titers against an early 2020 SARS-CoV-2 isolate had detectable but limited neutralizing antibodies against the emerging SARS-CoV-2 Alpha, Beta and Delta variants. This study highlights the potential of re-infection for recovered COVID-19 patients.
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    Serum from COVID-19 patients early in the pandemic shows limited evidence of cross-neutralization against variants of concern
    (Springer Nature, 2022-03-10) Griffin, Amanda J.; O’Donnell, Kyle L.; Shifflett, Kyle; Lavik, John-Paul; Russell, Patrick M.; Zimmerman, Michelle K.; Relich, Ryan F.; Marzi, Andrea; Pathology and Laboratory Medicine, School of Medicine
    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in a variety of clinical symptoms ranging from no or mild to severe disease. Currently, there are multiple postulated mechanisms that may push a moderate to severe disease into a critical state. Human serum contains abundant evidence of the immune status following infection. Cytokines, chemokines, and antibodies can be assayed to determine the extent to which a patient responded to a pathogen. We examined serum and plasma from a cohort of patients infected with SARS-CoV-2 early in the pandemic and compared them to negative-control sera. Cytokine and chemokine concentrations varied depending on the severity of infection, and antibody responses were significantly increased in severe cases compared to mild to moderate infections. Neutralization data revealed that patients with high titers against an early 2020 SARS-CoV-2 isolate had detectable but limited neutralizing antibodies against the emerging SARS-CoV-2 Alpha, Beta and Delta variants. This study highlights the potential of re-infection for recovered COVID-19 patients.
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    Standardization of SARS-CoV-2 Cycle Threshold Values: Multisite Investigation Evaluating Viral Quantitation across Multiple Commercial COVID-19 Detection Platforms
    (ASM, 2023-01) Gavina, Kenneth; Franco, Lauren C.; Robinson, Christopher M.; Hymas, Weston; Lei, Guang-Sheng; Sinclair, Will; Hall, Tara; Carlquist, John; Lavik, John-Paul; Emery, Christopher L.; Heaton, Phillip R.; Hillyard, David; Lopransi, Bert K.; Relich, Ryan F.; Pathology and Laboratory Medicine, School of Medicine
    The demand for testing during the coronavirus disease 2019 (COVID-19) pandemic has resulted in the production of several different commercial platforms and laboratory-developed assays for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This has created several challenges, including, but not limited to, the standardization of diagnostic testing, utilization of cycle threshold (CT) values for quantitation and clinical interpretation, and data harmonization. Using reference standards consisting of a linear range of SARS-CoV-2 concentrations quantitated by viral culture-based methods and droplet digital PCR, we investigated the commutability and standardization of SARS-CoV-2 quantitation across different laboratories in the United States. We assessed SARS-CoV-2 CT values generated on multiple reverse transcription-PCR (RT-PCR) platforms and analyzed PCR efficiencies, linearity, gene targets, and CT value agreement. Our results demonstrate the inappropriateness of using SARS-CoV-2 CT values without established standards for viral quantitation. Further, we emphasize the importance of using reference standards and controls validated to independent assays, to compare results across different testing platforms and move toward better harmonization of COVID-19 quantitative test results.
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    The Brief Case: Suspicious Gram-Negative Coccobacilli-Francisella tularensis subsp. novicida Isolated from an Immunocompromised Patient
    (American Society for Microbiology, 2023) Gavina, Kenneth; Whitacre, Brynne E.; Meyer, Thomas L.; Van Benten, Kayla; Glazier, Mark; Emery, Christopher L.; Lavik, John-Paul; Relich, Ryan F.; Pathology and Laboratory Medicine, School of Medicine
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    Validation of a qualitative real-time PCR assay for the detection of Candida auris in hospital inpatient screening
    (American Society for Microbiology, 2024) Franco, Lauren C.; Ahmed, Mahmoud; Kendra, Christopher G.; Sperling, R. Matthew; Van Benten, Kayla; Lavik, John-Paul; Emery, Christopher L.; Relich, Ryan F.; Gavina, Kenneth; Pathology and Laboratory Medicine, School of Medicine
    Candida auris is a multidrug-resistant opportunistic fungal pathogen capable of causing serious infections and healthcare-associated outbreaks. Screening for colonization with C. auris has become routine and is recommended in many hospitals and healthcare facilities as an infection control and prevention strategy. Subsequently, and since there are currently no FDA-approved tests for this purpose, clinical microbiology laboratories have become responsible for developing protocols to detect C. auris using axial and inguinal screening swabs. In a College of American Pathologists-accredited large academic healthcare center setting, we implemented a laboratory-developed nucleic-acid amplification test for the detection of C. auris DNA. Our test validation evaluated the performance of the DiaSorin C. auris primer set used in a real-time qualitative PCR assay on the LIAISON MDX thermocycler with the Simplexa Universal Disc. The assay was highly sensitive and specific, with a limit of detection of 1-2 CFU/reaction, with no observed cross-reactivity with other Candida spp., bacterial skin commensal organisms or commonly encountered viruses. When run in parallel with a culture-based detection method, the PCR assay was 100% sensitive and specific. The assay was precise, with low variability between replicates within and between runs. Lastly, pre-analytical factors, including swab storage time, temperature, and transport media, were assessed and found to have no significant effect on the detection of C. auris at variable concentrations. Taken together, this study expands the available options for nucleic acid detection of C. auris and characterizes pre-analytical factors for implementation in both high- and low-volume laboratory settings. Importance: This study overviews the validation and implementation of a molecular screening tool for the detection of Candida auris in a College of American Pathologist-accredited clinical laboratory. This molecular laboratory-developed test is both highly sensitive and specific and has significant health-system cost-savings associated with significantly reduced turn-around-time compared to traditional standard-of-care culture-based work up. This method and workflow is of interest to support clinical microbiology diagnostics and to help aid in hospital inpatient, and infection prevention control screening.