Education & Certifications


  • PhD, Bharathidasan University, Microbiology (2016)
  • Diploma in Molecular Diagnosis, Alagappa University (2009)
  • MS, Bharathidasan University, Microbiology (2008)
  • BS, Bharathidasan University, Microbiology (2006)

All Publications


  • Sequential Treatment Failure With Aztreonam-Ceftazidime-Avibactam Followed by Cefiderocol Due to Preexisting and Acquired Mechanisms in a New Delhi Metallo-β-lactamase-Producing Escherichia coli Causing Fatal Bloodstream Infection. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Senchyna, F., Murugesan, K., Rotunno, W., Nadimpalli, S. S., Deresinski, S., Banaei, N. 2024

    Abstract

    We report a fatal case of New Delhi metallo-β-lactamase (NDM)-producing Escherichia coli in a bacteremic patient with sequential failure of aztreonam plus ceftazidime-avibactam followed by cefiderocol. Acquired resistance was documented phenotypically and mediated through preexisting and acquired mutations. This case highlights the need to rethink optimal treatment for NDM-producing organisms.

    View details for DOI 10.1093/cid/ciad759

    View details for PubMedID 38289725

  • Accuracy of QuantiFERON in active tuberculosis suspects with comorbidities and nontuberculous mycobacterial infection in Northern California. Journal of clinical microbiology Lu, J., Murugesan, K., Senchyna, F., Budvytiene, I., Banaei, N. 2023: e0077523

    Abstract

    The QuantiFERON-TB Gold (QFT) is routinely utilized in North American health systems to detect a cellular immune response to Mycobacterium tuberculosis antigens in symptomatic and asymptomatic patients. The sensitivity of QFT in tuberculosis (TB) patients with comorbidities is not well established and the specificity of QFT in patients with nontuberculous mycobacteria (NTM) infections is incompletely understood. Between 2012 and 2023, all patients with culture-positive TB and patients with NTM infection per the expert diagnostic guidelines or biopsy-proven NTM infection who had a concurrent QFT test were included in this study. The sensitivity and specificity of QFT were measured in TB and NTM patients, respectively. In 109 patients with active TB, the overall sensitivity of QFT was 78.0% (85/109; 95% CI: 70.1, 85.7). The sensitivity was 86.0% (49/57; 95% CI: 76.6, 94.8) and 69.2% (36/52; 95% CI: 56.7, 81.8) in immunocompetent and immunocompromised patients, respectively. The overall specificity of QFT in 88 patients with NTM infection was 76.1% (67/88; 95% CI: 67.2, 85.0). After the exclusion of 17 NTM patients with risk factors for latent TB infection, the specificity was 94.4% (67/71; 95% CI: 89.1, 99.7). Two patients had NTM species known to cross-react with QFT. In two NTM patients infected with species (Mycobacterium intracellulare subsp. intracellulare and Mycobacterium intracellulare subsp. chimaera) not known to cross-react, whole genome sequencing did not detect ESAT-6 or CFP-10. In Northern California, the QFT assay demonstrated moderately low to moderately high sensitivity in TB patients and very high specificity in NTM patients, thus ruling out concerns for cross-reactivity with NTM.

    View details for DOI 10.1128/jcm.00775-23

    View details for PubMedID 37843251

  • Superior accuracy of Aspergillus plasma cell-free DNA PCR over serum galactomannan for the diagnosis of invasive aspergillosis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Mah, J., Nicholas, V., Tayyar, R., Moreno, A., Murugesan, K., Budvytiene, I., Banaei, N. 2023

    Abstract

    Invasive aspergillosis (IA) in immunocompromised hosts carries a high morbidity and mortality. Diagnosis is often delayed as definitive diagnosis requires invasive specimen collection while non-invasive testing with galactomannan is moderately accurate. Plasma cell-free DNA PCR represents a novel testing modality for the non-invasive diagnosis of invasive fungal disease (IFD). We directly compared the performance of Aspergillus plasma cfDNA PCR to serum galactomannan for the diagnosis of IFA during routine clinical practice.We conducted a retrospective study of all patients with suspected IFD who had Aspergillus plasma cfDNA PCR testing at Stanford Health Care from September 1st, 2020 - October 30th, 2022. Patients were categorized into proven, probable, possible and no IA based on the EORTC/MSG 2020 definitions. Primary outcomes included the clinical sensitivity and specificity for Aspergillus plasma cfDNA PCR and galactomannan.Overall, 238 unique patients with Aspergillus plasma cfDNA PCRs test results, including 63 positives and 175 non-consecutive negatives, were included in this study. Majority were immunosuppressed (89.9%) with a 22.3% 30-day all-cause mortality. The overall sensitivity and specificity of Aspergillus plasma cfDNA PCR was 86.0% (37/43; 95% CI, 72.7-95.7) and 93.1% (121/130; 95% CI, 87.4-96.3). The sensitivity and specificity of serum galactomannan in hematologic malignancies/stem cell transplants was 67.9% (19/28; 95% CI, 49.3-82.1) and 89.8% (53/59; 95% CI, 79.5-95.3), respectively. The sensitivity of cfDNA PCR was 93.0% (40/43; 95% CI, 80.9-98.5) in patients with a new diagnosis of IA.Aspergillus plasma cfDNA PCR represents a more sensitive alternative to serum galactomannan for non-invasive diagnosis of IA.

    View details for DOI 10.1093/cid/ciad420

    View details for PubMedID 37450614

  • Enkurin: A novel marker for myeloproliferative neoplasms from platelet, megakaryocyte, and whole blood specimens. Blood advances Mosale Seetharam, S., Liu, Y., Wu, J., Fechter, L., Murugesan, K., Maecker, H. T., Gotlib, J., Zehnder, J. L., Paulmurugan, R., Krishnan, A. 2023

    Abstract

    Impaired protein homeostasis, though well established in age-related disorders, has been linked in recent research with the pathogenesis of myeloproliferative neoplasms (MPNs). As yet, however, little is known about MPN-specific modulators of proteostasis, thus impeding our ability for increased mechanistic understanding and discovery of additional therapeutic targets. Loss of proteostasis, in itself, is traced to dysregulated mechanisms in protein folding and intracellular calcium signaling at the endoplasmic reticulum (ER). Here, using ex vivo and in vitro systems (including CD34+ cultures from patient bone marrow, and healthy cord/peripheral blood specimens), we extend our prior data from MPN patient platelet RNA sequencing, and discover select proteostasis-associated markers at RNA and/or protein levels in each of platelets, parent megakaryocytes, and whole blood specimens. Importantly, we identify a novel role in MPNs for enkurin (ENKUR), a calcium mediator protein, implicated originally only in spermatogenesis. Our data reveal consistent ENKUR downregulation at both RNA and protein levels across MPN patient specimens and experimental models, with a concomitant upregulation of a cell cycle marker, CDC20. Silencing of ENKUR by shRNA in CD34+ derived megakaryocytes further confirm this association with CDC20 at both RNA and protein levels; and indicate a likely role for the PI3K/Akt pathway. The inverse association of ENKUR and CDC20 expression was further confirmed upon treatment with thapsigargin (an agent that causes protein misfolding in the ER by selective loss of calcium) in both megakaryocyte and platelet fractions at RNA and protein levels. Together, our work sheds light on enkurin as a novel marker of MPN pathogenesis beyond the genetic alterations; and indicates further mechanistic investigation into a role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation.

    View details for DOI 10.1182/bloodadvances.2022008939

    View details for PubMedID 37315179

  • Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13. Nature communications Thakku, S. G., Lirette, J., Murugesan, K., Chen, J., Theron, G., Banaei, N., Blainey, P. C., Gomez, J., Wong, S. Y., Hung, D. T. 2023; 14 (1): 1803

    Abstract

    Detection of microbial cell-free DNA (cfDNA) circulating in the bloodstream has emerged as a promising new approach for diagnosing infection. Microbial diagnostics based on cfDNA require assays that can detect rare and highly fragmented pathogen nucleic acids. We now report WATSON (Whole-genome Assay using Tiled Surveillance Of Nucleic acids), a method to detect low amounts of pathogen cfDNA that couples pooled amplification of genomic targets tiled across the genome with pooled CRISPR/Cas13-based detection of these targets. We demonstrate that this strategy of tiling improves cfDNA detection compared to amplification and detection of a single targeted locus. WATSON can detect cfDNA from Mycobacterium tuberculosis in plasma of patients with active pulmonary tuberculosis, a disease that urgently needs accurate, minimally-invasive, field-deployable diagnostics. We thus demonstrate the potential for translating WATSON to a lateral flow platform. WATSON demonstrates the ability to capitalize on the strengths of targeting microbial cfDNA to address the need for point-of-care diagnostic tests for infectious diseases.

    View details for DOI 10.1038/s41467-023-37183-8

    View details for PubMedID 37002219

    View details for PubMedCentralID PMC10064635

  • Enkurin: A novel marker for myeloproliferative neoplasms from platelet, megakaryocyte, and whole blood specimens. bioRxiv : the preprint server for biology Seetharam, S. M., Liu, Y., Wu, J., Fechter, L., Murugesan, K., Maecker, H., Gotlib, J., Zehnder, J., Paulmurugan, R., Krishnan, A. 2023

    Abstract

    Impaired protein homeostasis, though well established in age-related disorders, has been linked in recent research with the pathogenesis of myeloproliferative neoplasms (MPNs). As yet, however, little is known about MPN-specific modulators of proteostasis, thus impeding our ability for increased mechanistic understanding and discovery of additional therapeutic targets. Loss of proteostasis, in itself, is traced to dysregulated mechanisms in protein folding and intracellular calcium signaling at the endoplasmic reticulum (ER). Here, using ex vivo and in vitro systems (including CD34 + cultures from patient bone marrow, and healthy cord/peripheral blood specimens), we extend our prior data from MPN patient platelet RNA sequencing, and discover select proteostasis-associated markers at RNA and/or protein levels in each of platelets, parent megakaryocytes, and whole blood specimens. Importantly, we identify a novel role in MPNs for enkurin ( ENKUR ), a calcium mediator protein, implicated originally only in spermatogenesis. Our data reveal consistent ENKUR downregulation at both RNA and protein levels across MPN patient specimens and experimental models, with a concomitant upregulation of a cell cycle marker, CDC20 . Silencing of ENKUR by shRNA in CD34 + derived megakaryocytes further confirm this association with CDC20 at both RNA and protein levels; and indicate a likely role for the PI3K/Akt pathway. The inverse association of ENKUR and CDC20 expression was further confirmed upon treatment with thapsigargin (an agent that causes protein misfolding in the ER by selective loss of calcium) in both megakaryocyte and platelet fractions at RNA and protein levels. Together, our work sheds light on enkurin as a novel marker of MPN pathogenesis beyond the genetic alterations; and indicates further mechanistic investigation into a role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation.VISUAL ABSTRACT: Key Points: Enkurin, a calcium adaptor protein, is identified as a novel marker of pathogenesis in MPNs.MPN megakaryocyte and platelet expression of enkurin at RNA and protein levels is inversely associated with a cell differentiation cycle gene, CDC20.Likely role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation.

    View details for DOI 10.1101/2023.01.07.523111

    View details for PubMedID 36712071

  • Cellular and humoral immune response to SARS-CoV-2 vaccination and booster dose in immunosuppressed patients: An observational cohort study. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology Yang, L. M., Costales, C., Ramanathan, M., Bulterys, P. L., Murugesan, K., Schroers-Martin, J., Alizadeh, A. A., Boyd, S. D., Brown, J. M., Nadeau, K. C., Nadimpalli, S. S., Wang, A. X., Busque, S., Pinsky, B. A., Banaei, N. 2022; 153: 105217

    Abstract

    BACKGROUND: Humoral and cellular immune responses to SARS-CoV-2 vaccination among immunosuppressed patients remain poorly defined, as well as variables associated with poor response.METHODS: We performed a retrospective observational cohort study at a large Northern California healthcare system of infection-naive individuals fully vaccinated against SARS-CoV-2 (mRNA-1273, BNT162b2, or Ad26.COV2.S) with clinical SARS-CoV-2 interferon gamma release assay (IGRA) ordered between January through November 2021. Humoral and cellular immune responses were measured by anti-SARS-CoV-2 S1 IgG ELISA (anti-S1 IgG) and IGRA, respectively, following primary and/or booster vaccination.RESULTS: 496 immunosuppressed patients (54% female; median age 50 years) were included. 62% (261/419) of patients had positive anti-S1 IgG and 71% (277/389) had positive IGRA after primary vaccination, with 20% of patients having a positive IGRA only. Following booster, 69% (81/118) had positive anti-S1 IgG and 73% (91/124) had positive IGRA. Factors associated with low humoral response rates after primary vaccination included anti-CD20 monoclonal antibodies (P<0.001), sphingosine 1-phsophate (S1P) receptor modulators (P<0.001), mycophenolate (P=0.002), and B cell lymphoma (P=0.004); those associated with low cellular response rates included S1P receptor modulators (P<0.001) and mycophenolate (P<0.001). Of patients who had poor humoral response to primary vaccination, 35% (18/52) developed a significantly higher response after the booster. Only 5% (2/42) of patients developed a significantly higher cellular response to the booster dose compared to primary vaccination.CONCLUSIONS: Humoral and cellular response rates to primary and booster SARS-CoV-2 vaccination differ among immunosuppressed patient groups. Clinical testing of cellular immunity is important in monitoring vaccine response in vulnerable populations.

    View details for DOI 10.1016/j.jcv.2022.105217

    View details for PubMedID 35714462

  • A modular and reconfigurable open-channel gated device for the electrokinetic extraction of cell-free DNA assays. Analytica chimica acta Futai, N., Fukazawa, Y., Kashiwagi, T., Tamaki, S., Sakai, R., Hogan, C. A., Murugesan, K., Ramachandran, A., Banaei, N., Santiago, J. G. 2022; 1200: 339435

    Abstract

    The high-efficiency separation and extraction of short fragments of cell-free DNA (cfDNA) remain challenging due to their low abundance and short lengths. This study presents a method for separating short cfDNA fragments, with lengths ranging from about 100 to 200 base pairs, from liquid human plasma samples into separable and extractable bands as solid agarose gel slabs. To achieve this, a novel millimeter-scale fluidic device is used for sample handling, transient isotachophoresis, and extraction. The device features open-to-atmosphere liquid chambers that define and manually actuated (i.e., movable) agarose-made gate valve structures. The agarose gates then define discrete zones for buffers, sample injection, DNA pre-concentration via isotachophoresis, size-based gel separation, and DNA-band extraction. As a demonstration of its efficacy, the device is applied to the enrichment and purification of M.tuberculosis genomic DNA fragments spiked in human plasma samples. This purified cfDNA is analyzed using the quantitative polymerase chain reaction (qPCR) of the IS6110 repetitive sequence in the M.tuberculosis genome. The data from this study demonstrates that high sensitivity can be achieved in cfDNA detection, as shown by the comparison with a typical solid-phase extraction method and buffer spiked with cfDNA. Evidence is presented that suggests plasma peptides generated by treatment of the sample with proteinase K acts as endogenous spacer molecules, which improve the resolution and purification of DNA relative to the marker dye and other contaminants that decrease the signal level in qPCR.

    View details for DOI 10.1016/j.aca.2022.339435

    View details for PubMedID 35256135

  • Long Term Accuracy of SARS-CoV-2 Interferon-γ Release Assay and its Application in Household Investigation. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Murugesan, K., Jagannathan, P., Altamirano, J., Maldonado, Y. A., Bonilla, H. F., Jacobson, K. B., Parsonnet, J., Andrews, J. R., Shi, R. Z., Boyd, S., Pinsky, B. A., Singh, U., Banaei, N. 2022

    Abstract

    An immunodiagnostic assay that sensitively detects a cell-mediated immune response to SARS-CoV-2 is needed for epidemiological investigation and for clinical assessment of T cell-mediated immune response to vaccines, particularly in the context of emerging variants that might escape antibody responses.The performance of a whole blood interferon-gamma (IFN-γ) release assay (IGRA) for the detection of SARS-CoV-2 antigen-specific T cells was evaluated in COVID-19 convalescents tested serially up to 10 months post-infection and in healthy blood donors. SARS-CoV-2 IGRA was applied in contacts of households with index cases. Freshly collected blood in the lithium heparin tube was left unstimulated, stimulated with a SARS-CoV-2 peptide pool, and stimulated with mitogen.The overall sensitivity and specificity of IGRA were 84.5% (153/181; 95% confidence interval [CI] 79.0-89.0) and 86.6% (123/142; 95% CI;80.0-91.2), respectively. The sensitivity declined from 100% (16/16; 95% CI 80.6-100) at 0.5-month post-infection to 79.5% (31/39; 95% CI 64.4-89.2) at 10 months post-infection (P<0.01). The IFN-γ response remained relatively robust at 10 months post-infection (3.8 vs. 1.3 IU/mL, respectively). In 14 households, IGRA showed a positivity rate of 100% (12/12) and 65.2% (15/23), and IgG of 50.0% (6/12) and 43.5% (10/23) in index cases and contacts, respectively, exhibiting a difference of +50% (95% CI +25.4-+74.6) and +21.7% (95% CI, +9.23-+42.3), respectively. Either IGRA or IgG was positive in 100% (12/12) of index cases and 73.9% (17/23) of contacts.The SARS-CoV-2 IGRA is a useful clinical diagnostic tool for assessing cell-mediated immune response to SARS-CoV-2.

    View details for DOI 10.1093/cid/ciac045

    View details for PubMedID 35079772

  • Immunogenicity of a Third COVID-19 mRNA Vaccine Dose in PID Patients with Functional B-cell Defects. The journal of allergy and clinical immunology. In practice Gernez, Y., Murugesan, K., Cortales, C. R., Banaei, N., Hoyte, L., Pinsky, B. A., Lewis, D. B., Pham, M. 2022

    View details for DOI 10.1016/j.jaip.2022.02.030

    View details for PubMedID 35259538

  • Immunogenicity and Tolerability of COVID-19 mRNA Vaccines in PID patients with functional B-cell defects. The Journal of allergy and clinical immunology Pham, M. N., Murugesan, K., Banaei, N., Pinsky, B. A., Tang, M., Hoyte, E., Lewis, D. B., Gernez, Y. 1800

    Abstract

    BACKGROUND: Data on the safety and efficacy of COVID-19 vaccination in people with a range of primary immune deficiencies are lacking since these patients were excluded from COVID-19 vaccine trials. This information may help in clinical management of this vulnerable patient group.OBJECTIVE: To assess humoral and T-cell immune responses after two doses of SARS-CoV-2 mRNA vaccines in patients with PIDs and functional B-cell defects.METHODS: A double-center retrospective review of patients with PID who completed COVID-19 mRNA vaccination and who had humoral responses assessed through SARS-CoV-2 spike protein receptor binding domain (RBD) IgG antibody levels with reflex assessment of the antibody to block RBD binding to ACE2 (hereafter referred to as ACE2 receptor blocking activity, as a surrogate test for neutralization) and T-cell response evaluated by an interferon-gamma release assay (IGRA). Immunization reactogenicity was also reviewed.RESULTS: A total of 33 patients with humoral defect were evaluated. 69.6% received BNT162b2 vaccine (Pfizer-BioNTech) and 30.3% received mRNA-1273 (Moderna). The mRNA vaccines were generally well tolerated without severe reactions. The IGRA was positive in 77.4% of our patients (24 of 31). About half of our subjects (16 of 33) had detectable RBD-specific IgG responses but only two of these 16 subjects had an ACE2 receptor blocking activity level of >50%.CONCLUSION: Vaccination of this cohort of PID patients with COVID-19 mRNA vaccines was safe and cellular immunity was stimulated in a majority. However, antibody responses to the spike protein RBD were less consistent, and, when detected, was not effective at ACE2 blocking.CLINICAL IMPLICATION: mRNA vaccination may be less effective at preventing acquisition of SARS-CoV-2 in our cohort of PID patients with functional B-cell defects. The Induction of SARS-CoV-2 spike protein-specific T-cell immunity by vaccination might help reduce the severity of disease in these patients.

    View details for DOI 10.1016/j.jaci.2021.11.022

    View details for PubMedID 34952033

  • Clinical Accuracy and Impact of Plasma Cell-Free DNA Fungal PCR Panel for Non-Invasive Diagnosis of Fungal Infection. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Senchyna, F. n., Hogan, C. A., Murugesan, K. n., Moreno, A. n., Ho, D. Y., Subramanian, A. n., Schwenk, H. T., Budvytiene, I. n., Costa, H. A., Gombar, S. n., Banaei, N. n. 2021

    Abstract

    Invasive fungal infection (IFI) is a growing cause of morbidity and mortality in oncology and transplant patients. Diagnosis of IFI is often delayed due to need for invasive biopsy and low sensitivity of conventional diagnostic methods. Fungal cell-free DNA (cfDNA) detection in plasma is a novel testing modality for the non-invasive diagnosis of IFI.A novel bioinformatic pipeline was created to interrogate fungal genomes and identify multicopy sequences for cfDNA PCR targeting. A real-time PCR panel was developed for 12 genera and species most commonly causing IFI. Sensitivity and specificity of the fungal PCR panel were determined using plasma samples from patients with IFI and non-IFI controls. Clinical impact of fungal PCR panel was evaluated prospectively based on the treating team's interpretation of the results.Overall, the sensitivity and specificity were 56.5% (65/115, 95% confidence interval [CI], 47.4%-65.2%) and 99.5% (2064/2075; 95% CI, 99.0%-99.7%), respectively. In the subset of patients with an optimized plasma volume (2mL), sensitivity was 69.6% (48/69; 95% CI, 57.9%-79.2%). Sensitivity was 91.7% (11/12; 95% CI, 62.5%-100%) for detection of Mucorales agents, 56.3% (9/16; 95% CI, 33.2%-76.9%) for Aspergillus species, and 84.6% (11/13; 95% CI, 56.5%-96.9%) for Candida albicans. In a prospective evaluation of 226 patients with suspected IFI, cfDNA testing was positive in 47 (20.8%) patients and resulted in a positive impact on clinical management in 20/47 (42.6%).The fungal cfDNA PCR panel offers a non-invasive approach to early diagnosis of IFI, providing actionable results for personalized care.

    View details for DOI 10.1093/cid/ciab158

    View details for PubMedID 33606010

  • Comparative genomics of Enterobacter cloacae complex before and after acquired clinical resistance to Ceftazidime-Avibactam. Diagnostic microbiology and infectious disease Senchyna, F., Tamburini, F. B., Murugesan, K., Watz, N., Bhatt, A. S., Banaei, N. 2021; 101 (4): 115511

    Abstract

    Resistance to Ceftazidime-Avibactam in Enterobacter cloacae is poorly understood. Whole genome sequencing identified 6 variants in isolates collected from a patient before and after acquiring Ceftazidime-Avibactam resistance. This included a Phe396Leu mutation in acrB, a component of the AcrAB-TolC efflux pump, possibly mediating enhanced efflux of Ceftazidime and/ or Avibactam.

    View details for DOI 10.1016/j.diagmicrobio.2021.115511

    View details for PubMedID 34418822

  • Interferon-gamma release assay testing to assess COVID-19 vaccination response in a SARS-CoV-2 seronegative patient on rituximab: a case report. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases Ferguson, J., Murugesan, K., Banaei, N., Liu, A. 2021

    Abstract

    We describe the case of a 44-year-old female on Rituximab for treatment of multiple sclerosis with undetectable SARS-CoV-2 IgG specific antibodies eighteen days after second dose of SARS-CoV-2 vaccine. Interferon-gamma release assay testing for SARS-CoV-2 was positive on day nineteen, demonstrating robust T-cell mediated response despite lack of antibody-mediated response.

    View details for DOI 10.1016/j.ijid.2021.06.054

    View details for PubMedID 34216738

  • SARS-CoV-2 infection and COVID-19 severity in individuals with prior seasonal coronavirus infection. Diagnostic microbiology and infectious disease Gombar, S. n., Bergquist, T. n., Pejaver, V. n., Hammarlund, N. E., Murugesan, K. n., Mooney, S. n., Shah, N. n., Pinsky, B. A., Banaei, N. n. 2021; 100 (2): 115338

    Abstract

    We show that individuals with documented history of seasonal coronavirus have a similar SARS-CoV-2 infection rate and COVID-19 severity as those with no prior history of seasonal coronavirus. Our findings suggest prior infection with seasonal coronavirus does not provide immunity to subsequent infection with SARS-CoV-2.

    View details for DOI 10.1016/j.diagmicrobio.2021.115338

    View details for PubMedID 33610036

  • High Frequency of SARS-CoV-2 RNAemia and Association With Severe Disease. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Hogan, C. A., Stevens, B. A., Sahoo, M. K., Huang, C., Garamani, N., Gombar, S., Yamamoto, F., Murugesan, K., Kurzer, J., Zehnder, J., Pinsky, B. A. 2020

    Abstract

    BACKGROUND: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in blood, also known as RNAemia, has been reported, but its prognostic implications are poorly understood. This study aimed to determine the frequency of SARS-CoV-2 RNA in plasma and its association with coronavirus disease 2019 (COVID-19) clinical severity.METHODS: An analytical cross-sectional study was performed in a single-center tertiary care institution and included consecutive inpatients and outpatients with confirmed COVID-19. The prevalence of SARS CoV-2 RNAemia and the strength of its association with clinical severity variables were examined and included intensive care unit (ICU) admission, invasive mechanical ventilation, and 30-day all-cause mortality.RESULTS: Paired nasopharyngeal and plasma samples were included from 85 patients. The median age was 55 years, and individuals with RNAemia were older than those with undetectable SARS-CoV-2 RNA in plasma (63 vs 50 years; P = .04). Comorbidities were frequent including obesity (37.6%), hypertension (30.6%), and diabetes mellitus (22.4%). RNAemia was detected in 28/85 (32.9%) of patients, including 22/28 (78.6%) who required hospitalization. In models adjusted for age, RNAemia was detected more frequently in individuals who developed severe disease including ICU admission (32.1 vs 14.0%; P = .04) and invasive mechanical ventilation (21.4% vs 3.5%; P = .02). All 4 deaths occurred in individuals with detectable RNAemia. An additional 121 plasma samples from 28 individuals with RNAemia were assessed longitudinally, and RNA was detected for a maximum duration of 10 days.CONCLUSIONS: This study demonstrated a high proportion of SARS-CoV-2 RNAemia, and an association between RNAemia and clinical severity suggesting the potential utility of plasma viral testing as a prognostic indicator for COVID-19.

    View details for DOI 10.1093/cid/ciaa1054

    View details for PubMedID 32965474

  • Interferon-gamma release assay for accurate detection of SARS-CoV-2 T cell response. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Murugesan, K. n., Jagannathan, P. n., Pham, T. D., Pandey, S. n., Bonilla, H. F., Jacobson, K. n., Parsonnet, J. n., Andrews, J. R., Weiskopf, D. n., Sette, A. n., Pinsky, B. A., Singh, U. n., Banaei, N. n. 2020

    Abstract

    We investigated feasibility and accuracy of an interferon-gamma release assay (IGRA) for detection of T cell responses to SARS-CoV-2. Whole blood IGRA accurately distinguished between convalescents and uninfected healthy blood donors with a predominantly CD4+ T cell response. SARS-CoV-2 IGRA may serve as a useful diagnostic tool in managing the COVID-19 pandemic.

    View details for DOI 10.1093/cid/ciaa1537

    View details for PubMedID 33035306

  • Investigation of preanalytical variables impacting pathogen cell-free DNA in blood and urine. Journal of clinical microbiology Murugesan, K. n., Hogan, C. A., Palmer, Z. n., Reeve, B. n., Theron, G. n., Andama, A. n., Somoskovi, A. n., Steadman, A. n., Madan, D. n., Andrews, J. n., Croda, J. n., Sahoo, M. K., Cattamanchi, A. n., Pinsky, B. A., Banaei, N. n. 2019

    Abstract

    Pathogen cell-free DNA (pcfDNA) in blood and urine is an attractive biomarker; however, the impact of preanalytical factors is not well understood.Blood and urine samples from healthy donors spiked with cfDNA from Mycobacterium tuberculosis, Salmonella enterica, Aspergillus fumigatus and EBV, and samples from tuberculosis patients were used to evaluate the impact of blood collection tube, urine preservative, processing delay, processing method, freezing and thawing, and sample volume on pcfDNA. PCR cycle threshold (CT) was used to measure amplifiable cfDNA.In spiked samples, median CT for M. tuberculosis, S. enterica, and EBV cfDNA was significantly lower in blood collected in K2EDTA than Streck and PAXgene blood collection tubes, and significantly lower in EDTA-urine than Streck-urine. Blood and urine samples from TB patients preserved with K2EDTA and Tris-EDTA, respectively, showed significantly lower median M. tuberculosis CT compared with Streck blood collection tube and urine preservative. Processing delay increased median pathogen CT for Streck and PAXgene but not K2EDTA blood samples, and for urine preserved with Streck reagent but not EDTA. Double spin compared with single spin plasma separation increased median pathogen CT regardless of blood collection tube. No differences were observed between whole urine and supernatant, and between fresh and thawed plasma and urine after 24 weeks at -80 °C. Larger plasma and urine volume in contrived and patient samples showed a significantly lower median M. tuberculosis CT. These findings suggest large volume single spin K2EDTA-plasma and EDTA-whole urine with up to 24-hour processing delay may optimize pcfDNA detection.

    View details for DOI 10.1128/JCM.00782-19

    View details for PubMedID 31511335