157 results on '"Asim A, Ahmed"'
Search Results
2. Isotretinoin's Effect on Fasting Lipid Profile in Acne Patients.
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Sajid, Madiha, Asim, Sadaf Ahmed, Iqbal, Tayyaba, Bhatti, Sadia, Zahir, Ayesha, and Imtiaz, Sania
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- 2024
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3. Plasma microbial cell-free DNA load is associated with mortality in patients with COVID-19
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Georgios D. Kitsios, William Bain, Nameer Al-Yousif, Radha Duttagupta, Asim A. Ahmed, Bryan J. McVerry, and Alison Morris
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Diseases of the respiratory system ,RC705-779 - Published
- 2021
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4. Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis
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Anne Piantadosi, Shibani S. Mukerji, Simon Ye, Michael J. Leone, Lisa M. Freimark, Daniel Park, Gordon Adams, Jacob Lemieux, Sanjat Kanjilal, Isaac H. Solomon, Asim A. Ahmed, Robert Goldstein, Vijay Ganesh, Bridget Ostrem, Kaelyn C. Cummins, Jesse M. Thon, Cormac M. Kinsella, Eric Rosenberg, Matthew P. Frosch, Marcia B. Goldberg, Tracey A. Cho, and Pardis Sabeti
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encephalitis ,metagenomic sequencing ,next-generation sequencing (NGS) ,meningitis ,virus ,hybrid capture ,Microbiology ,QR1-502 - Abstract
ABSTRACT Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections.
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- 2021
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5. Rapid detection of bacille Calmette-Guérin-associated mycotic aortic aneurysm using novel cell-free DNA assay
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Vignesh Vudatha, BS, Mark Ranson, MD, Lily Blair, PhD, and Asim A. Ahmed, MD
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Surgery ,RD1-811 ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Intravesical instillation of bacille Calmette-Guérin (BCG), an attenuated strain of Mycobacterium bovis, is an adjuvant immunotherapy for bladder carcinoma. Typical complications include fever, malaise, and dysuria. However, more severe complications have been reported, including granulomatous pneumonitis, BCG sepsis, and vascular infections. We present a case of an infrarenal abdominal aortic aneurysm complicated by iliopsoas abscess 2 years after BCG treatment and discuss a novel diagnostic tool for mycobacterial strain identification. Keywords: Mycotic aortic aneurysm, Mycobacterium, BCG, Next-generation sequencing, Cell-free DNA
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- 2019
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6. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts [version 4; peer review: 3 approved]
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Jose F. Camargo, Asim A. Ahmed, Martin S. Lindner, Michele I. Morris, Shweta Anjan, Anthony D. Anderson, Clara E. Prado, Sudeb C. Dalai, Octavio V. Martinez, and Krishna V. Komanduri
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Research Article ,Articles ,Cell-free microbial DNA ,next generation sequencing ,infection ,immunocompromised host ,hematopoietic stem cell transplant - Abstract
Background: Cell-free DNA (cfDNA) sequencing has emerged as an effective laboratory method for rapid and noninvasive diagnosis in prenatal screening testing, organ transplant rejection screening, and oncology liquid biopsies but clinical experience for use of this technology in diagnostic evaluation of infections in immunocompromised hosts is limited. Methods: We conducted an exploratory study using next-generation sequencing (NGS) for detection of microbial cfDNA in a cohort of ten immunocompromised patients with febrile neutropenia, pneumonia or intra-abdominal infection. Results: Pathogen identification by cfDNA NGS demonstrated positive agreement with conventional diagnostic laboratory methods in 7 (70%) cases, including patients with proven/probable invasive aspergillosis, Pneumocystis jirovecii pneumonia, Stenotrophomonas maltophilia bacteremia, Cytomegalovirus and Adenovirus viremia. NGS results were discordant in 3 (30%) cases including two patients with culture negative sepsis who had undergone hematopoietic stem cell transplant in whom cfDNA testing identified the potential etiological agent of sepsis; and one kidney transplant recipient with invasive aspergillosis who had received >6 months of antifungal therapy prior to NGS testing. Conclusion: These observations support the clinical utility of measurement of microbial cfDNA sequencing from peripheral blood for rapid noninvasive diagnosis of infections in immunocompromised hosts. Larger studies are needed.
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- 2020
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7. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts [version 3; peer review: 2 approved, 1 approved with reservations]
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Jose F. Camargo, Asim A. Ahmed, Martin S. Lindner, Michele I. Morris, Shweta Anjan, Anthony D. Anderson, Clara E. Prado, Sudeb C. Dalai, Octavio V. Martinez, and Krishna V. Komanduri
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Research Article ,Articles ,Cell-free microbial DNA ,next generation sequencing ,infection ,immunocompromised host ,hematopoietic stem cell transplant - Abstract
Background: Cell-free DNA (cfDNA) sequencing has emerged as an effective laboratory method for rapid and noninvasive diagnosis in prenatal screening testing, organ transplant rejection screening, and oncology liquid biopsies but clinical experience for use of this technology in diagnostic evaluation of infections in immunocompromised hosts is limited. Methods: We conducted an exploratory study using next-generation sequencing (NGS) for detection of microbial cfDNA in a cohort of ten immunocompromised patients with febrile neutropenia, pneumonia or intra-abdominal infection. Results: Pathogen identification by cfDNA NGS demonstrated positive agreement with conventional diagnostic laboratory methods in 7 (70%) cases, including patients with proven/probable invasive aspergillosis, Pneumocystis jirovecii pneumonia, Stenotrophomonas maltophilia bacteremia, Cytomegalovirus and Adenovirus viremia. NGS results were discordant in 3 (30%) cases including two patients with culture negative sepsis who had undergone hematopoietic stem cell transplant in whom cfDNA testing identified the etiological agent of sepsis; and one kidney transplant recipient with invasive aspergillosis who had received >6 months of antifungal therapy prior to NGS testing. Conclusion: These observations support the clinical utility of measurement of microbial cfDNA sequencing from peripheral blood for rapid noninvasive diagnosis of infections in immunocompromised hosts. Larger studies are needed.
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- 2019
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8. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts [version 4; peer review: 2 approved, 1 approved with reservations]
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Jose F. Camargo, Asim A. Ahmed, Martin S. Lindner, Michele I. Morris, Shweta Anjan, Anthony D. Anderson, Clara E. Prado, Sudeb C. Dalai, Octavio V. Martinez, and Krishna V. Komanduri
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Medicine ,Science - Abstract
Background: Cell-free DNA (cfDNA) sequencing has emerged as an effective laboratory method for rapid and noninvasive diagnosis in prenatal screening testing, organ transplant rejection screening, and oncology liquid biopsies but clinical experience for use of this technology in diagnostic evaluation of infections in immunocompromised hosts is limited. Methods: We conducted an exploratory study using next-generation sequencing (NGS) for detection of microbial cfDNA in a cohort of ten immunocompromised patients with febrile neutropenia, pneumonia or intra-abdominal infection. Results: Pathogen identification by cfDNA NGS demonstrated positive agreement with conventional diagnostic laboratory methods in 7 (70%) cases, including patients with proven/probable invasive aspergillosis, Pneumocystis jirovecii pneumonia, Stenotrophomonas maltophilia bacteremia, Cytomegalovirus and Adenovirus viremia. NGS results were discordant in 3 (30%) cases including two patients with culture negative sepsis who had undergone hematopoietic stem cell transplant in whom cfDNA testing identified the potential etiological agent of sepsis; and one kidney transplant recipient with invasive aspergillosis who had received >6 months of antifungal therapy prior to NGS testing. Conclusion: These observations support the clinical utility of measurement of microbial cfDNA sequencing from peripheral blood for rapid noninvasive diagnosis of infections in immunocompromised hosts. Larger studies are needed.
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- 2020
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- View/download PDF
9. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts [version 2; peer review: 1 approved, 1 approved with reservations]
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Jose F. Camargo, Asim A. Ahmed, Martin S. Lindner, Michele I. Morris, Shweta Anjan, Anthony D. Anderson, Clara E. Prado, Sudeb C. Dalai, Octavio V. Martinez, and Krishna V. Komanduri
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Research Article ,Articles ,Cell-free microbial DNA ,next generation sequencing ,infection ,immunocompromised host ,hematopoietic stem cell transplant - Abstract
Background: Cell-free DNA (cfDNA) sequencing has emerged as an effective laboratory method for rapid and noninvasive diagnosis in prenatal screening testing, organ transplant rejection screening, and oncology liquid biopsies. Methods: Here we report our experience using next-generation sequencing (NGS) for detection of microbial cfDNA in a cohort of ten immunocompromised patients with febrile neutropenia, pneumonia or intra-abdominal infection. Results: Among five hematological malignancy patients, for whom a microbiological diagnosis was established, pathogen identification by cfDNA NGS demonstrated 100% positive agreement with conventional diagnostic laboratory methods. Further, cfDNA identified the etiological agent in two patients with culture negative sepsis who had undergone hematopoietic stem cell transplant. Conclusion: These data support the clinical utility of measurement of microbial cfDNA sequencing from peripheral blood for rapid noninvasive diagnosis of infections in immunocompromised hosts. Larger studies are needed.
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- 2019
- Full Text
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10. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts [version 1; peer review: 1 approved]
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Jose F. Camargo, Asim A. Ahmed, Martin S. Lindner, Michele I. Morris, Shweta Anjan, Anthony D. Anderson, Clara E. Prado, Sudeb C. Dalai, Octavio V. Martinez, and Krishna V. Komanduri
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Research Article ,Articles ,Cell-free microbial DNA ,next generation sequencing ,infection ,immunocompromised host ,hematopoietic stem cell transplant - Abstract
Background: Cell-free DNA (cfDNA) sequencing has emerged as an effective laboratory method for rapid and noninvasive diagnosis in prenatal screening testing, organ transplant rejection screening, and oncology liquid biopsies. Methods: Here we report our experience using next-generation sequencing (NGS) for detection of microbial cfDNA in a cohort of ten immunocompromised patients with febrile neutropenia or deep-seated infection. Results: Among five hematological malignancy patients, for whom a microbiological diagnosis was established, pathogen identification by cfDNA NGS demonstrated 100% positive agreement with conventional diagnostic laboratory methods. Further, cfDNA identified the etiological agent in two patients with culture negative sepsis who had undergone hematopoietic stem cell transplant. Conclusion: These data support the clinical utility of measurement of microbial cfDNA sequencing from peripheral blood for rapid noninvasive diagnosis of infections in immunocompromised hosts. Larger studies are needed.
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- 2019
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11. Idiosyncratic Mòjiāng virus attachment glycoprotein directs a host-cell entry pathway distinct from genetically related henipaviruses
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Ilona Rissanen, Asim A. Ahmed, Kristopher Azarm, Shannon Beaty, Patrick Hong, Sham Nambulli, W. Paul Duprex, Benhur Lee, and Thomas A. Bowden
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Science - Abstract
The attachment glycoprotein (HNV-G) of henipaviruses interacts with host receptors at the cell surface and is a major determinant of species tropism. Here the authors provide structural and functional evidence that the emergent henipavirus, Mòjiang virus, uses an entry mechanism that is independent of known paramyoxviral cellular receptors.
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- 2017
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12. Persistent 2-for-1 Atrioventricular Node Anterograde Conduction During a Supraventricular Tachycardia
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Ankur Shah, Brad A. Clark, Saarik Gupta, Jasen L. Gilge, Asim S. Ahmed, Parin J. Patel, Leonard A. Steinberg, and Benzy J. Padanilam
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Cardiology and Cardiovascular Medicine - Published
- 2022
13. Prophylactic Colchicine After Radiofrequency Ablation of Atrial Fibrillation
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Asim S. Ahmed, Jennifer Miller, Jason Foreman, Keith Golden, Ankur Shah, Justin Field, Jasen Gilge, Brad Clark, Sandeep Joshi, Girish Nair, Jeffrey Olson, Benzy J. Padanilam, Eric Prystowsky, and Parin J. Patel
- Published
- 2023
14. A Unique Coexistence of Rectal Adenocarcinoma and Gastric Antral Gastrointestinal Stromal Tumor: A Case Report and Minireview
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Mahmoud Rezk-Abdelwahed Hussein, Abdullah Saad Alqahtani, Ahmed Mostafa Mohamed, Yahia Ibraheem Assiri, Nasser Ibraheem Alqahtani, Saeed Ali Alqahtani, Hatim Mahgoub Ali, Asim Abdallah Ahmed Elyas, Mubarak Mohammed Al-Shraim, Syed Shamshad Hussain, and Eman E. Abu-Dief
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digestive, oral, and skin physiology ,Stomach ,Carcinoma ,Rectum ,Case Report ,KIT ,digestive system diseases ,GIST ,Stem cell factor - Abstract
Several studies have reported the coexistence of gastric gastrointestinal stromal tumors (GISTs) with many primary carcinomas such as gastric and renal cell carcinomas. However, to date reports about the coexistence of gastric GISTs and colorectal adenocarcinoma are limited. Herein we report a unique case of gastric GIST coexisting synchronously with rectal adenocarcinoma in a 36-year-old male patient who presented with weight loss, vomiting, and bleeding per rectum. Computed tomography (CT) revealed circumferential rectal mass coexistent with an irregular gastric soft tissue mass. The diagnosis of rectal adenocarcinoma and gastric GIST was established by immunohistological evaluation of the colonoscopic (rectum) and CT-guided (stomach) biopsies. The patient received concomitant chemoradiotherapy for the rectal adenocarcinoma and neoadjuvant imatinib for the gastric GIST. This was followed by low anterior resection with total mesorectal excision and wedge resection of the gastric mass. Follow-up of the patient for 1.5 years revealed no evidence of disease recurrence. We also present a minireview of the literature that provides insights into this subject as a separate section.
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- 2021
15. 546. Resolution of a Cluster of Travel-Associated Leptospira santarosai Infection in Four Adolescents by Plasma Microbial Cell-Free DNA Detection with the Karius Test®
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Hai D Nguyen-Tran, Guliz Erdem, Marcelo Laufer, Lori Patterson, Asim A Ahmed, William A Bower, Renee Galloway, and Sara Saporta-Keating
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Infectious Diseases ,Oncology - Abstract
Background Leptospira can cause severe infections but their diagnosis can be challenging. Diagnosis is limited by nonspecific, protean clinical symptoms; the fastidious nature of Leptospira; and poor specificity, sensitivity, and long turnaround times of serologic testing. Given these limitations, identifying epidemiological clusters of leptospirosis can be challenging. Rapid, non-invasive diagnosis of leptospirosis by microbial cell-free DNA (mcfDNA) next-generation sequencing (NGS) of plasma offers a means to overcome these limitations in individual diagnosis and public health epidemiological surveillance. Methods The Karius Test® (KT) detects and quantifies mcfDNA in molecules/µL (MPM) in plasma from a curated genomic database of >20,000 organisms reporting on >1000 pathogens through the Karius CLIA certified/CAP accredited lab (Redwood City, CA). Four KT detections of Leptospira santarosai were identified April - August 2021 across four independent United States institutions. Clinical review was performed by pediatric infectious diseases consultants. Results KT detected L. santarosai in four adolescents with travel to Costa Rica or Belize (Table). A broad work-up was performed in all patients. McfDNA NGS was the first test to identify L. santarosai as the diagnosis in all cases with an average time to diagnosis of 2.5+/- 0.58 days from sample collection, enabling narrowed, targeted antibiotic treatment. L. santarosai mcfDNA was positive in three patients despite pretreatment; average L. santarosai mcfDNA concentration was 173.5+/- 186.1 MPM. Leptospira serologies were confirmatory in three patients, potential epidemiological exposures were identified in all patients, and all recovered. Conclusion KT enabled rapid, non-invasive diagnosis of diverse manifestations of L. santarosai against a competing broad differential in four adolescent travelers returning from Costa Rica or Belize. The resolution of the etiology of this cluster of patients with leptospirosis demonstrates the potential utility of mcfDNA to quickly diagnose and support case definitions of reportable diseases and the potential importance of plasma mcfDNA NGS in public health and epidemiological surveillance. Disclosures Asim A. Ahmed, MD, Karius: Employee|Karius: Stocks/Bonds Sara Saporta-Keating, MS, MD, Pfizer: Co-investigator in investigator-driven study sponsored by Pfizer.
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- 2022
16. 544. PICKUP: Pneumonia in the Immunocompromised - Use of the Karius Test for Detection of Undiagnosed Pathogens
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Stephen P Bergin, Roy F Chemaly, Radha Duttagupta, Robert Bigelow, Sanjeet S Dadwal, Joshua A Hill, Yeon Joo Lee, Ghady Haidar, Alfred Luk, Alexander Christian Drelick, Peter V Chin-Hong, Esther Benamu, Thomas Davis, Olivia Wolf, Micah T McClain, Eileen K Maziarz, Deng Madut, Armando Bedoya, Daniel L Gilstrap, Jamie Todd, Christina Barkauskas, Alfredo Puing, Amy Spallone, Brittany J McDowell, Dayana Shariff, Elizabeth Salsgiver, Deepa D Nanayakkara, Fareed Khawaja, Genovefa Papanicolaou, Jack Spagnoletti, Marico English, Monica Fung, Patrick Russel, Sarah Ibrahimi, Shraddha Pandey, Suzanne Adams, Wendy Liang, Elena Nemirovich-Danchenko, Mona Mughar, Sudeb Dalai, Yuen Cho, Asim A Ahmed, Desiree Hollemon, David K Hong, Marla Lay Vaughn, Tim Blauwkamp, Zivjena Vucetic, Rina Romano, Vance G Fowler, and Thomas L Holland
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Infectious Diseases ,Oncology - Abstract
Background Pneumonia is the most common infectious cause of morbidity and excess mortality complicating hematopoietic cell transplantation (HCT) and treatment of hematologic malignancy. Standard bronchoscopic and noninvasive microbiologic testing identify causative pathogens in less than half of cases. The Karius Test, a plasma next-generation sequencing assay of microbial cell-free DNA, may improve diagnostic yield in these patients. Methods Patients with active hematologic malignancy or recent HCT undergoing bronchoscopy for suspected pneumonia were prospectively enrolled in this observational study conducted at 10 United States medical centers. A panel of expert clinicians blinded to Karius Test results reviewed a standardized panel of microbiologic and molecular testing from bronchoalveolar lavage and blood samples for bacterial and fungal testing, nasopharyngeal swab for respiratory viral testing, imaging results, clinical documentation, and any additional microbiologic or molecular testing collected per usual standard of care to adjudicate a probable cause of pneumonia. The panel then adjudicated whether a probable cause of pneumonia or other clinically relevant infection was identified by the Karius Test. Results Between January 3, 2020 and February 4, 2022, 257 patients were enrolled. A planned interim analysis of the first 69 sequentially enrolled patients in the per protocol population was conducted. An adjudicated probable cause of pneumonia was identified by standard care in 18/69 (26%) patients. The Karius Test identified an adjudicated probable cause of pneumonia in 10/51 (20%) patients when no cause of pneumonia was identified by standard care testing. The combination of standard care and the Karius Test together identified a probable cause of pneumonia in 28/69 (41%) patients. At least one additional pathogen adjudicated as a probable cause of pneumonia was identified by the Karius Test in 6/18 (33%) of patients with positive standard care testing. Conclusion The Karius Test notably increased the probability of identifying a pathogenic cause of pneumonia among immunocompromised patients undergoing bronchoscopy. The additive diagnostic value of the Karius Test may significantly enhance management of this common condition. Disclosures Roy F. Chemaly, MD/MPH, Karius: Advisor/Consultant|Karius: Grant/Research Support Radha Duttagupta, PhD, Karius Inc: Stocks/Bonds Sanjeet S. Dadwal, MD, FACP, FIDSA, AlloVir: Advisor/Consultant|AlloVir: Grant/Research Support|Ansun Biopharma: Grant/Research Support|Aseptiscope: Advisor/Consultant|Aseptiscope: Stocks/Bonds|Astellas: Speaker's Bureau|Cidara: Advisor/Consultant|Gilead: Grant/Research Support|Karius: Grant/Research Support|Merck: Advisor/Consultant|Merck: Grant/Research Support|Merck: Speaker's Bureau|Takeda: Speaker's Bureau Joshua A. Hill, MD, Allovir: Advisor/Consultant|Allovir: Grant/Research Support|Covance/CSL: Advisor/Consultant|CRISPR: Advisor/Consultant|Deverra: Grant/Research Support|Gilead: Grant/Research Support|Karius: Advisor/Consultant|Karius: Grant/Research Support|Merck: Grant/Research Support|Octapharma: Advisor/Consultant|OptumHealth: Advisor/Consultant|Oxford Immunotec: Grant/Research Support|Pfizer: Advisor/Consultant|Symbio: Advisor/Consultant|Takeda: Advisor/Consultant Ghady Haidar, MD, Karius, Allovir, and AstraZeneca: Grant/Research Support Alfred Luk, MD, Karius: Grant/Research Support Jamie Todd, MD, Altavant Sciences: Advisor/Consultant|AstraZeneca: Grant/Research Support|Boehringer Ingelheim: Grant/Research Support|CareDx: Grant/Research Support|Cellarity: Advisor/Consultant|Natera: Advisor/Consultant Genovefa Papanicolaou, MD, AlloVir: Board Member|AlloVir: Serve as member of DSMC|Amplyx: Board Member|Amplyx: Serve as member of DSMC|Astellas: Advisor/Consultant|Cidara: Advisor/Consultant|CSL Behring: Advisor/Consultant|Merck: Advisor/Consultant|Merck: Grant/Research Support|Merck: Investigator for Merck|MSD: Advisor/Consultant|Octapharma: Advisor/Consultant|Octapharma: Board Member|Octapharma: Serve as EAC member|Partners RX: Advisor/Consultant|SymBio: Advisor/Consultant|Takeda: Advisor/Consultant|Takeda: Grant/Research Support|Takeda: Investigator for Takeda|Vera: Board Member|Vera: Serve as member of DSMC Elena Nemirovich-Danchenko, MD PhD, Karius: Stocks/Bonds Mona Mughar, BS, Karius: Stocks/Bonds Sudeb Dalai, MD, Karius: Stocks/Bonds Sudeb Dalai, MD, Karius: Stocks/Bonds Yuen Cho, MS, CLS(CA-DPH), Karius: Stocks/Bonds Asim A. Ahmed, MD, Karius: Employee|Karius: Stocks/Bonds Desiree Hollemon, MSN, MPH, Karius: Stocks/Bonds David K. Hong, MD, Janssen Pharmaceutical Companies of Johnson & Johnson: Employee|Vir Biotechnology: Employee|Vir Biotechnology: Stocks/Bonds Marla Lay Vaughn, BS, MT(ASCP), Karius: Employee|Karius: Stocks/Bonds Tim Blauwkamp, PhD, Karius: Board Member|Karius: Ownership Interest Zivjena Vucetic, MD, Karius: Stocks/Bonds Rina Romano, BS, Karius Inc: Stocks/Bonds|Karius Inc: Stocks/Bonds Rina Romano, BS, Karius Inc: Stocks/Bonds|Karius Inc: Stocks/Bonds Rina Romano, BS, Karius Inc: Stocks/Bonds|Karius Inc: Stocks/Bonds Vance G. Fowler, Jr, MD, MHS, Affinergy: Grant/Research Support|Affinergy: Honoraria|Affinium: Honoraria|Amphliphi Biosciences: Honoraria|ArcBio: Stocks/Bonds|Basilea: Grant/Research Support|Basilea: Honoraria|Bayer: Honoraria|C3J: Honoraria|Cerexa/Forest/Actavis/Allergan: Grant/Research Support|Contrafect: Grant/Research Support|Contrafect: Honoraria|Cubist/Merck: Grant/Research Support|Debiopharm: Grant/Research Support|Deep Blue: Grant/Research Support|Destiny: Honoraria|Genentech: Grant/Research Support|Genentech: Honoraria|Integrated Biotherapeutics: Honoraria|Janssen: Grant/Research Support|Janssen: Honoraria|Karius: Grant/Research Support|Medicines Co.: Honoraria|MedImmune: Grant/Research Support|MedImmune: Honoraria|NIH: Grant/Research Support|Novartis: Grant/Research Support|Novartis: Honoraria|Pfizer: Grant/Research Support|Regeneron: Grant/Research Support|Regeneron: Honoraria|Sepsis diagnostics: Sepsis diagnostics patent pending|UpToDate: Royalties|Valanbio: Stocks/Bonds Thomas L. Holland, MD, Aridis: Advisor/Consultant|Lysovant: Advisor/Consultant.
- Published
- 2022
17. Noninvasive diagnosis of secondary infections in COVID-19 by sequencing of plasma microbial cell-free DNA
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Grace Lisius, Radha Duttagupta, Asim A. Ahmed, Matthew Hensley, Nameer Al-Yousif, Michael Lu, William Bain, Faraaz Shah, Caitlin Schaefer, Shulin Qin, Xiaohong Wang, Yingze Zhang, Kevin J. Mitchell, Ellen K. Hughes, Jana L. Jacobs, Asma Naqvi, Ghady Haidar, John W. Mellors, Barbara Methé, Bryan J. McVerry, Alison Morris, and Georgios D. Kitsios
- Abstract
BackgroundSecondary infection (SI) diagnosis in COVID-19 is challenging, due to overlapping clinical presentations, practical limitations in obtaining samples from the lower respiratory tract (LRT), and low sensitivity of microbiologic cultures.Research QuestionCan metagenomic sequencing of plasma microbial cell-free DNA (mcfDNA-Seq) help diagnose SIs complicating COVID-19?Study Design and MethodsWe enrolled 42 inpatients with COVID-19 classified as microbiologically-confirmed SI (Micro-SI, n=8), clinically-diagnosed SI (Clinical-SI, n=13, i.e. empiric antimicrobials), or no clinical suspicion for SI (No-Suspected-SI, n=21) at time of enrollment. From baseline and follow-up plasma samples (days 5 and 10 post-enrollment), we quantified mcfDNA for all detected microbes by mcfDNA sequencing and measured nine host-response biomarkers. From LRT samples among intubated subjects, we quantified bacterial burden with 16S rRNA gene quantitative PCR.ResultsWe performed mcfDNA-Seq in 82 plasma samples. Sequencing was successful in 60/82 (73.2%) samples, which had significantly lower levels of human cfDNA than failed samples (p10 mcfDNA, p=0.03).InterpretationHigh circulating levels of mcfDNA in a substantial proportion of patients with COVID-19 without clinical suspicion for SI suggest that SIs may often remain undiagnosed. McfDNA-Seq, when clinically available, can offer a non-invasive diagnostic tool for pathogen identification, with prognostic value on host inflammatory response and clinical outcomes.
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- 2022
18. PO-02-068 REAL WORLD COLCHICINE USE FOR PREVENTION OF PERICARDITIS AFTER ABLATION FOR ATRIAL FIBRILLATION
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Sandeep Gautam, Joshua R. Silverstein, Parin J. Patel, Asim S. Ahmed, Andrew C. Corsello, and Jose Osorio
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Physiology (medical) ,Cardiology and Cardiovascular Medicine - Published
- 2023
19. PO-05-156 DIFFERENTIATING RIGHT VENTRICULAR FROM LEFT VENTRICULAR OUTFLOW TRACT PREMATURE VENTRICULAR COMPLEXES WITH A NOVEL QS PATTERN IN LEAD V1
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Justin Arunthamakun, Justin B. Field, Saarik Gupta, Bradley C. Clark, Asim S. Ahmed, Ankur N. Shah, Sandeep A. Joshi, Girish V. Nair, Benzy J. Padanilam, Parin J. Patel, and JASEN L. GILGE
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Physiology (medical) ,Cardiology and Cardiovascular Medicine - Published
- 2023
20. Sequencing of Circulating Microbial Cell-Free DNA Can Identify Pathogens in Periprosthetic Joint Infections
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Timothy A. Blauwkamp, Desiree Hollemon, Lily Blair, Douglas E. Padgett, Andy O. Miller, Thomas W. Bauer, Peter K. Sculco, Barry D. Brause, Michael B. Cross, Alexandra Grizas, Laura T. Donlin, Ian S. Cohn, Christopher E. Mason, Geoffrey H. Westrich, Matthew S. Hepinstall, Lionel B. Ivashkiv, Adriana P. Echeverria, Susan M. Goodman, Alberto V Carli, Christine Mironenko, Mathias P.G. Bostrom, Carine Ho, Mark P. Figgie, David K. Hong, David Danko, Galit Meshulam-Simon, Sara Shanaj, Michael W. Henry, Asim A. Ahmed, and Thomas P. Sculco
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Male ,Prosthesis-Related Infections ,Venipuncture ,Joint replacement ,business.industry ,Arthroplasty, Replacement, Hip ,medicine.medical_treatment ,Periprosthetic ,General Medicine ,Joint infections ,Cell-free fetal DNA ,Immunology ,medicine ,Humans ,Effective treatment ,Synovial fluid ,Female ,Orthopedics and Sports Medicine ,Surgery ,Prospective Studies ,Arthroplasty, Replacement, Knee ,business ,Cell-Free Nucleic Acids ,Pathogen ,Aged - Abstract
Background Over 1 million Americans undergo joint replacement each year, and approximately 1 in 75 will incur a periprosthetic joint infection. Effective treatment necessitates pathogen identification, yet standard-of-care cultures fail to detect organisms in 10% to 20% of cases and require invasive sampling. We hypothesized that cell-free DNA (cfDNA) fragments from microorganisms in a periprosthetic joint infection can be found in the bloodstream and utilized to accurately identify pathogens via next-generation sequencing. Methods In this prospective observational study performed at a musculoskeletal specialty hospital in the U.S., we enrolled 53 adults with validated hip or knee periprosthetic joint infections. Participants had peripheral blood drawn immediately prior to surgical treatment. Microbial cfDNA from plasma was sequenced and aligned to a genome database with >1,000 microbial species. Intraoperative tissue and synovial fluid cultures were performed per the standard of care. The primary outcome was accuracy in organism identification with use of blood cfDNA sequencing, as measured by agreement with tissue-culture results. Results Intraoperative and preoperative joint cultures identified an organism in 46 (87%) of 53 patients. Microbial cfDNA sequencing identified the joint pathogen in 35 cases, including 4 of 7 culture-negative cases (57%). Thus, as an adjunct to cultures, cfDNA sequencing increased pathogen detection from 87% to 94%. The median time to species identification for cases with genus-only culture results was 3 days less than standard-of-care methods. Circulating cfDNA sequencing in 14 cases detected additional microorganisms not grown in cultures. At postoperative encounters, cfDNA sequencing demonstrated no detection or reduced levels of the infectious pathogen. Conclusions Microbial cfDNA from pathogens causing local periprosthetic joint infections can be detected in peripheral blood. These circulating biomarkers can be sequenced from noninvasive venipuncture, providing a novel source for joint pathogen identification. Further development as an adjunct to tissue cultures holds promise to increase the number of cases with accurate pathogen identification and improve time-to-speciation. This test may also offer a novel method to monitor infection clearance during the treatment period. Level of evidence Diagnostic Level II. See Instructions for Authors for a complete description of levels of evidence.
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- 2021
21. Isolation and identification of fungal species in patients of recalcitrant tinea corporis and/or tinea cruris attending tertiary care hospital in Karachi.
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Sajid, Madiha, Asim, Sadaf Ahmed, Sadia, Iqbal, Tayyaba, Saher, Najam-us, and Shaikh, Sabhita Shabbir
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TERTIARY care , *MYCOSES , *DISEASE relapse , *ORAL drug administration , *UNIVERSITY hospitals , *KLEBSIELLA pneumoniae , *CANDIDA , *TICK infestations - Abstract
Background Tinea corporis and Tinea cruris is one of the chief infection seen in dermatology clinics affecting every age and gender. The rapidly rising prevalence of superficial fungal infection in our population warrants mycological analysis to establish any change in the causative dermatophytic specie responsible for ticking up the number of the cases. Objective To isolate and identify the fungal species in patients of recalcitrant tinea corporis and/or tinea cruris attending tertiary care hospital in Karachi. Methods This Cross-sectional study was conducted in the Outpatient Department of Dermatology, Dow University Hospital, Karachi, Pakistan from 11th April 2022 till 10th October 2022. It comprised of 60 patients who had either received one complete course of oral antifungal treatment and had responded poorly to the therapy (identified on the basis of clinical response) and had a recurrence of disease after cure. The skin scrapings were collected from these patients and then microscopy and cultures were performed. Results Out was 60 patients of Recalcitrant Tinea Corporis and/or T. cruris KOH mount was positive in 43 (71.6%) patients and the culture isolated and identified the causative species in 53 (88.3%) patients. T. Tonsurans account for about 33.3% of the cases followed by T. Mentagrophytes accounting for 15% of the patients. In 11.6 % of the patients isolated specie was T. Rubrum. Conclusion Rise in the number of recalcitrant dermatophytosis could possibly due to change in the species causing dermatophytosis. Mycological analysis can help in identifying such species and facilitate in the treatment of these patients. [ABSTRACT FROM AUTHOR]
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- 2023
22. Association of Vitamin D with Moderate to Severe Acne Vulgaris.
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Iqbal, Tayyaba, Asim, Sadaf Ahmed, Bhatti, Sadia, Sajid, Madiha, Mirza, Reema, and Huma, Zille
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- 2023
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23. Diagnostic utility of early premature ventricular complexes in differentiating atrioventricular reentrant and atrioventricular nodal reentrant tachycardias
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Ankur N. Shah, Justin Field, Brad A. Clark, Jeffrey A. Olson, Saarik Gupta, Girish V. Nair, Sandeep A. Joshi, Asim S. Ahmed, Jasen L. Gilge, Leonard A. Steinberg, Eric N. Prystowsky, Parin J. Patel, and Benzy J. Padanilam
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Physiology (medical) ,Cardiology and Cardiovascular Medicine - Abstract
His-refractory premature ventricular complexes perturbing a supraventricular tachycardia (SVT) establish the presence of an accessory pathway (AP). Earlier premature ventricular complexes (ErPVCs) may perturb SVTs but are considered nondiagnostic.The purpose of this study was to test the hypothesis that an ErPVC will always show a difference35 ms in its advancement of the next atrial activation during atrioventricular nodal reentrant tachycardia (AVNRT). During atrioventricular reentrant tachycardia (AVRT), a PVC delivered close to the circuit can result in greater advancement of atrial activation due to retrograde conduction via an AP. Thus, an AP response, defined as ErPVC (HSixty-five consecutive patients with SVT were retrospectively evaluated. ErPVCs were defined when the ventricular pacing stimulus was35 ms ahead of the His during tachycardia.Among the 65 cases, 43 were AVNRT and 22 AVRT. Fourteen AVRT cases had an AP response with a mean HAn AP response to PVCs (A
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- 2022
24. Utility of Plasma Microbial Cell-Free DNA Decay Kinetics After Aortic Valve Replacement for Bartonella Endocarditis: Case Report
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Dipesh Solanky, Asim A. Ahmed, Joshua Fierer, Eugene Golts, Meghan Jones, and Sanjay R. Mehta
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BackgroundDetection and sequencing of circulating microbial cell-free DNA (mcfDNA) in plasma is an increasingly popular tool for diagnosing many infectious diseases, but could also be used to monitor the progress of infection. However, the decay of this microbial cell-free DNA in blood following treatment has not been previously characterized.Case PresentationA 53 year-old male was diagnosed withBartonella quintanabioprosthetic aortic valve endocarditis by sequencing of the mcfDNA in the blood (Karius, Redwood City, CA). We then monitored the kinetics of decay of mcfDNA after parenteral antibiotics and valve resection in this individual. We measured plasma mcfDNA (Karius) in serial samples obtained in the operating room to calculate mcfDNA half-life after valve resection. After four weeks of parenteral antibiotics,BartonellamcfDNA signal decreased by 78%. The signal subsequently rose during operative manipulation of the infected valve but dropped 81-fold over four hours following valve resection. The half-life of mcfDNA between the time shortly following resection of the infected valve and 24 to 48 hours post-operatively was between 35 and 115 minutes. The trend in mcfDNA signal was characterized by rapid and then slower phases of decay within 24 hours, and little change between 24 and 48 hours.ConclusionsThis study is one of the first to characterize decay kinetics of mcfDNA and highlights the potential of monitoring mcfDNA in addressing major challenges in infective endocarditis management, including monitoring the response to therapy, and as an early screen for recurrence.
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- 2022
25. Microbial Cell-Free DNA Identifies the Causative Pathogen in Infective Endocarditis and Remains Detectable Longer Than Conventional Blood Culture in Patients with Prior Antibiotic Therapy
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Emily M Eichenberger, Nicholas Degner, Erick R Scott, Felicia Ruffin, John Franzone, Batu Sharma-Kuinkel, Pratik Shah, David Hong, Sudeb C Dalai, Lily Blair, Desiree Hollemon, Eliza Chang, Carine Ho, Lisa Wanda, Christiaan R de Vries, Vance G Fowler, and Asim A Ahmed
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Microbiology (medical) ,Infectious Diseases ,Major Article - Abstract
Background The diagnosis of infective endocarditis (IE) can be difficult, particularly if blood cultures fail to yield a pathogen. This study evaluates the potential utility of microbial cell-free DNA (mcfDNA) as a tool to identify the microbial etiology of IE. Methods Blood samples from patients with suspected IE were serially collected. mcfDNA was extracted from plasma and underwent next-generation sequencing. Reads were aligned against a library containing DNA sequences belonging to >1400 different pathogens. mcfDNA from organisms present above a statistical threshold were reported and quantified in molecules per milliliter (MPM). Additional mcfDNA was collected on each subject every 2–3 days for a total of 7 collections or until discharge. Results Of 30 enrolled patients with suspected IE, 23 had definite IE, 2 had possible IE, and IE was rejected in 5 patients by modified Duke Criteria. Only the 23 patients with definite IE were included for analysis. Both mcfDNA and blood cultures achieved a sensitivity of 87%. The median duration of positivity from antibiotic treatment initiation was estimated to be approximately 38.1 days for mcfDNA versus 3.7 days for blood culture (proportional odds, 2.952; P = .02771), using a semiparametric survival analysis. mcfDNA (log10) levels significantly declined (−0.3 MPM log10 units, 95% credible interval −0.45 to −0.14) after surgical source control was performed (pre- vs postprocedure, posterior probability >0.99). Conclusion mcfDNA accurately identifies the microbial etiology of IE. Sequential mcfDNA levels may ultimately help to individualize therapy by estimating a patient’s burden of infection and response to treatment.
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- 2022
26. Eastern Equine Encephalitis in Children, Massachusetts and New Hampshire,USA, 1970–2010
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Michael A. Silverman, John Misasi, Sandra Smole, Henry A. Feldman, Adam B. Cohen, Sandro Santagata, Michael McManus, and Asim A. Ahmed
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Encephalitis ,arbovirus ,Eastern equine encephalitis ,Eastern equine encephalitis virus ,pediatric ,Massachusetts ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
We describe the clinical, laboratory, and radiographic characteristics of 15 cases of eastern equine encephalitis in children during 1970–2010. The most common clinical and laboratory features were fever, headache, seizures, peripheral leukocytosis, and cerebrospinal fluid neutrophilic pleocytosis. Radiographic lesions were found in the basal ganglia, thalami, and cerebral cortex. Clinical outcomes included severe neurologic deficits in 5 (33%) patients, death of 4 (27%), full recovery of 4 (27%), and mild neurologic deficits in 2 (13%). We identify an association between a short prodrome and an increased risk for death or for severe disease.
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- 2013
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27. Multiple linear and zosteriform eccrine spiradenoma: A rare case.
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Sajid, Madiha, Zahir, Ayesha, and Asim, Sadaf Ahmed
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SWEAT glands - Abstract
Eccrine Spiradenoma (ES) is an uncommon tumor of eccrine sweat gland. It usually presents as a solitary, painful nodule located over trunk and proximal limbs. Multiple ES is a rare phenomenon, comprising less than 2% of all cases. We report a case of middle-aged female presented with multiple, painless tumors of varying morphology located in linear and zosteriform distribution diagnosed as ES. Prompt diagnosis of ES is pivotal due to risk of life threatening malignant transformation. This article highlights the rare presentation of ES and a brief review of this disease. [ABSTRACT FROM AUTHOR]
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- 2023
28. Liquid Biopsy for Invasive Mold Infections in Hematopoietic Cell Transplant Recipients With Pneumonia Through Next-Generation Sequencing of Microbial Cell-Free DNA in Plasma
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Lily Blair, David K. Hong, Terry Stevens-Ayers, Joyce Maalouf, Michael Boeckh, Asim A. Ahmed, Joshua A. Hill, Sudeb C. Dalai, Carine Ho, Timothy A. Blauwkamp, Cynthia E. Fisher, Desiree Hollemon, and Jacob Keane-Candib
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Microbiology (medical) ,medicine.medical_specialty ,Gastroenterology ,DNA sequencing ,Internal medicine ,medicine ,Humans ,Liquid biopsy ,Online Only Articles ,Retrospective Studies ,Aspergillus ,Hematopoietic cell ,biology ,business.industry ,Fungi ,Hematopoietic Stem Cell Transplantation ,Liquid Biopsy ,High-Throughput Nucleotide Sequencing ,Pneumonia ,biology.organism_classification ,medicine.disease ,Predictive value ,Transplant Recipients ,Infectious Diseases ,Cell-free fetal DNA ,business ,Cell-Free Nucleic Acids - Abstract
Background Noninvasive diagnostic options are limited for invasive mold infections (IMIs). We evaluated the performance of a plasma microbial cell-free DNA sequencing (mcfDNA-Seq) test for diagnosing pulmonary IMI after hematopoietic cell transplant (HCT). Methods We retrospectively assessed the diagnostic performance of plasma mcfDNA-Seq next-generation sequencing in 114 HCT recipients with pneumonia after HCT who had stored plasma obtained within 14 days of diagnosis of proven/probable Aspergillus IMI (n = 51), proven/probable non-Aspergillus IMI (n = 24), possible IMI (n = 20), and non-IMI controls (n = 19). Sequences were aligned to a database including >400 fungi. Organisms above a fixed significance threshold were reported. Results Among 75 patients with proven/probable pulmonary IMI, mcfDNA-Seq detected ≥1 pathogenic mold in 38 patients (sensitivity, 51% [95% confidence interval {CI}, 39%–62%]). When restricted to samples obtained within 3 days of diagnosis, sensitivity increased to 61%. McfDNA-Seq had higher sensitivity for proven/probable non-Aspergillus IMI (sensitivity, 79% [95% CI, 56%–93%]) compared with Aspergillus IMI (sensitivity, 31% [95% CI, 19%–46%]). McfDNA-Seq also identified non-Aspergillus molds in an additional 7 patients in the Aspergillus subgroup and Aspergillus in 1 patient with possible IMI. Among 19 non-IMI pneumonia controls, mcfDNA-Seq was negative in all samples, suggesting a high specificity (95% CI, 82%–100%) and up to 100% positive predictive value (PPV) with estimated negative predictive values (NPVs) of 81%–99%. The mcfDNA-Seq assay was complementary to serum galactomannan index testing; in combination, they were positive in 84% of individuals with proven/probable pulmonary IMI. Conclusions Noninvasive mcfDNA-Seq had moderate sensitivity and high specificity, NPV, and PPV for pulmonary IMI after HCT, particularly for non-Aspergillus species.
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- 2020
29. Avoiding Bladder Catheters During Atrial Fibrillation Ablation
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Benzy J. Padanilam, Sandeep Joshi, Girish V. Nair, DO Jeffrey A. Olson, DO Brad A. Clark, DO Asim S. Ahmed, and Parin J. Patel
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Male ,medicine.medical_specialty ,medicine.medical_treatment ,Unnecessary Procedures ,030204 cardiovascular system & hematology ,urologic and male genital diseases ,law.invention ,03 medical and health sciences ,Postoperative Complications ,0302 clinical medicine ,Bladder catheters ,Randomized controlled trial ,law ,Atrial Fibrillation ,medicine ,Clinical endpoint ,Humans ,Dysuria ,In patient ,030212 general & internal medicine ,Aged ,business.industry ,Urinary retention ,Atrial fibrillation ,Middle Aged ,Urinary Retention ,medicine.disease ,Ablation ,Surgery ,Treatment Outcome ,Urinary Tract Infections ,Catheter Ablation ,Female ,medicine.symptom ,Urinary Catheterization ,business - Abstract
This study sought to determine if atrial fibrillation (AF) ablation can be performed safely without bladder catheterization.Patients undergoing AF ablation often receive bladder catheters. Catheterization is associated with potential complications. The ABCD-AF (Avoiding Bladder Catheters During Atrial Fibrillation) ablation study evaluates the advantages of performing AF ablation without routine catheterization.In this single-center, prospective, randomized controlled trial, 80 patients received bladder catheterization (group A), and 80 patients received only as-needed catheterization (group B). The primary endpoint was a composite of cystitis, urethral injury, hematuria, dysuria, or urinary retention.The mean patient age was 63 ± 13 years, and 33% of patients were female. The primary outcome was reached in 45 patients in group A and 11 patients in group B (p 0.001). Urinary tract infection occurred in 7 patients in group A and 2 patients in group B (p = 0.17). Urinary retention occurred in 12 patients in group A and 5 patients in group B (p = 0.07). Randomization to catheterization carried an odds ratio of 8.1 (95% confidence interval [CI]: 3.7 to 17.5; p 0.001), and male sex carried an odds ratio of 3.8 (95% CI: 1.7 to 8.6; p = 0.001) for the primary endpoint. On subgroup analysis, randomization to undergo catheterization had no association with the primary outcome in female patients but had an odds ratio of 14.6 (95% CI: 5.6 to 38.1; p 0.001) in male patients. In multivariable analysis, sex and catheter status remained independently associated with the primary outcome.Bladder catheterization can be safely avoided in patients undergoing AF ablation and is associated with a significant reduction in adverse outcomes, especially in men.
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- 2020
30. Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance
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Shaun Arevalo, Jean-Jacques Muyembe-Tamfum, Guixia Yu, Asim A. Ahmed, Steve Ahuka-Mundeke, Mary A. Rodgers, Mars Stone, César González-Bonilla, Nuno R. Faria, Carole McArthur, Xianding Deng, Charles Y. Chiu, Lazare Kaptue, Zoraima Neto, Jean L. Patterson, Vijay S. Ganesh, Sneha Somasekar, Kristina Hsieh, Carlos F. Arias, Jimmy Kapetshi, Manasi Tamhankar, Nuno Taveira, Asmeeta Achari, Oliver G. Pybus, Placide Mbala-Kingebeni, Scot Federman, Shigeo Yagi, Sharon Messenger, Inês Bártolo, Nicaise Ndembi, Michael P. Busch, Debra A. Wadford, Steve Miller, Dora Mbanya, John R. Hackett, Susana López, José Esteban Muñoz-Medina, Gavin Cloherty, Joana Morais, Julien Thézé, University of Oxford [Oxford], and Abbott Laboratories Appeared in article as Abbott Laboratories NIH from the NIAID R33-AI129455 United States Department of Health & Human Services National Institutes of Health (NIH) - USA NIH National Heart Lung & Blood Institute (NHLBI) Appeared in article as NIH from the National Heart, Lung, and Blood Institute R01-HL105704 California Initiative to Advance Precision Medicine Charles and Helen Schwab Foundation Steven and Alexandra Cohen Foundation United States Department of Defense Appeared in article as United States Department of Defense W81XWH-17-1-0681 Wellcome Trust Appeared in article as Wellcome Trust Royal Society/Sir Henry Dale Fellowship 204311/Z/16/Z Global Challenges Research Fund 005073 Oxford John Fell Research Fund 005166 Africa Oxford grant AfiOx-48
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[SDV]Life Sciences [q-bio] ,medicine.disease_cause ,Polymerase Chain Reaction ,Applied Microbiology and Biotechnology ,Genome ,law.invention ,Dengue fever ,Dengue ,law ,Chikungunya ,Pathogen ,Polymerase chain reaction ,0303 health sciences ,Zika Virus Infection ,Shotgun sequencing ,High-Throughput Nucleotide Sequencing ,Ebolavirus ,3. Good health ,Virus Diseases ,Viruses ,RNA, Viral ,Infectious diseases ,Chikungunya virus ,Microbial genetics ,Microbiology (medical) ,Immunology ,Genome, Viral ,Computational biology ,Biology ,Microbiology ,Article ,03 medical and health sciences ,Virology ,Yellow Fever ,Genetics ,medicine ,Humans ,Author Correction ,030304 developmental biology ,030306 microbiology ,Infectious-disease diagnostics ,Computational Biology ,Zika Virus ,Cell Biology ,Dengue Virus ,Hemorrhagic Fever, Ebola ,medicine.disease ,Metagenomics ,DNA, Viral ,Metagenome ,Primer (molecular biology) - Abstract
Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use., This study describes a new method that improves the sensitivity of viral detection compared with next-generation sequencing and enables the detection of emerging flaviviruses not specifically targeted a priori. Metagenomic sequencing with spiked primer enrichment is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making it applicable for diagnostic laboratory and field use.
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- 2020
31. A Rare Etiology for Ascending Paralysis in an Infant
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Keisuke Abe, Chanel Casamina, Natascha Ching, Keith K Abe, Marian Melish, Karen S Thompson, Asim A Ahmed, and Prashant J Purohit
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Male ,Infectious Diseases ,Pediatrics, Perinatology and Child Health ,Eosinophilia ,Infant ,Animals ,Humans ,Angiostrongylus cantonensis ,Paralysis ,General Medicine ,Cell-Free Nucleic Acids ,Strongylida Infections - Abstract
An 11-month-old male infant with ascending paralysis had an unremarkable initial cerebrospinal fluid (CSF) analysis and imaging. Progressive neurological symptoms resulted in repeated CSF sampling, microscopy, and plasma microbial cell-free DNA next-generation sequencing analysis, that in combination with epidemiology, confirmed the diagnosis.
- Published
- 2021
32. Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis
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Jacob E. Lemieux, Tracey A. Cho, Matthew P. Frosch, Daniel J. Park, Gordon Adams, Isaac H. Solomon, Pardis C. Sabeti, Eric S. Rosenberg, Asim A. Ahmed, Bridget Ostrem, Kaelyn C. Cummins, Marcia B. Goldberg, Robert B. Goldstein, Michael J. Leone, Sanjat Kanjilal, Jesse M. Thon, Vijay S. Ganesh, Cormac M. Kinsella, Shibani S. Mukerji, Lisa Freimark, Anne Piantadosi, and Simon Ye
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Adult ,Male ,encephalitis ,hybrid capture ,virus ,Disease ,Microbiology ,Virus ,Serology ,metagenomic sequencing ,Virology ,medicine ,Humans ,Prospective Studies ,Powassan virus ,Borrelia burgdorferi ,next-generation sequencing (NGS) ,Pathogen ,Aged ,biology ,business.industry ,High-Throughput Nucleotide Sequencing ,meningitis ,Middle Aged ,medicine.disease ,biology.organism_classification ,methylated DNA depletion ,QR1-502 ,Viruses ,Central Nervous System Viral Diseases ,Metagenome ,Female ,Metagenomics ,business ,Meningitis ,Encephalitis ,Research Article - Abstract
Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections.
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- 2021
33. Plasma Microbial Cell-Free DNA Is Associated with Intensified Host Inflammation and Can Reveal Secondary Infections in Patients with COVID-19
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Bryan J. McVerry, Asim A. Ahmed, G. Lisius, Nameer Al-Yousif, N. Bensen, Haopu Yang, Caitlin Schaefer, R. Duttagupta, Georgios D Kitsios, Alison Morris, William Bain, Barbara Methé, and M. Lu
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business.industry ,Secondary infection ,Inflammation ,medicine.disease ,Antimicrobial ,Molecular diagnostics ,Procalcitonin ,Pneumonia ,Cell-free fetal DNA ,Immunology ,medicine ,Biomarker (medicine) ,medicine.symptom ,business - Abstract
Rationale: Severe COVID-19 pneumonia can be complicated by secondary bacterial or fungal infections, but their clinical distinction from isolated SARS-CoV-2 infection is challenging, especially with the more restricted practices regarding invasive diagnostics in patients with COVID-19. We sought to comprehensively screen for secondary infections by DNA pathogens (bacterial, fungal or viral) with a non-invasive, culture-independent metagenomic approach (microbial cell-free DNA sequencing-mcfDNA-Seq), and also examine for the biologic impact of circulating mcfDNA on the host response in COVID-19. Methods: We prospectively enrolled 42 hospitalized patients with COVID-19 and compared them with a historical cohort of mechanically-ventilated patients with culture-positive (n=27) vs. culture-negative pneumonia (n=40) or no clinical infection (n=16 controls). From plasma samples, we performed mcfDNA-Seq with the Karius test (Karius, Inc) and measured 10 host-response biomarkers of innate immunity and epithelial/endothelial injury (IL-6, IL-8, IL-10, RAGE, TNFR1, Angiopoietin-2, Procalcitonin, Fractalkine, Pentraxin-3, ST2). We compared mcfDNA-Seq between clinical groups and examined associations of mcfDNA and biomarker levels with linear regression models. Results: McfDNA-Seq was successful in 33/42 (79%) baseline samples from patients with COVID-19, with nine samples failing QC requirements. McfDNA was detectable in 21/33 (64%) of COVID-19 samples, a proportion significantly lower to culture-positive pneumonia (96%), higher than uninfected controls (31%) and similar to culture-negative pneumonia (56%) (between-groups Fisher's exact p
- Published
- 2021
34. Hand, Foot, and Mouth Disease Caused by Coxsackievirus A6
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Kelly Flett, Ilan Youngster, Jennifer Huang, Alexander McAdam, Thomas J. Sandora, Marcus Rennick, Sandra Smole, Shannon L. Rogers, W. Allan Nix, M. Steven Oberste, Stephen Gellis, and Asim A. Ahmed
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Coxsackievirus A6 ,hand ,foot and mouth disease ,enterovirus ,viral exanthema ,viruses ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Published
- 2012
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35. 1030. Chasing the Long Tail of Infectious Diseases: Detecting Capnocytophaga canimorsus and Pasteurella multocida Infections with A Plasma-based Microbial Cell-Free DNA Next Generation Sequencing Test
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Nicholas R Degner, Ricardo Galvan-Castillo, Jose Alexander, Aparna Arun, Christiaan R de Vries, Ann Macintyre, Bradley Perkins, Asim A Ahmed, and Matthew Smollin
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Infectious Diseases ,AcademicSubjects/MED00290 ,Oncology ,Poster Abstracts - Abstract
Background Capnocytophaga canimorsus (Cc) and Pasteurella multocida (Pm) are gram negative bacterial commensal pathogens typically from dogs or cats that can cause severe infection in humans when spread through licks, scratches or bites. The diagnosis of these infections can be limited by: (1) their fastidious nature and difficulty to culture; (2) the nonspecific manifestations of the infections; and (3) the unreliability of dog or cat exposure history. Open-ended microbial cell free DNA (mcfDNA) next-generation sequencing (NGS) offers a potential solution to overcome these limitations. Methods The Karius TestTM (KT) developed and validated in Karius’s CLIA certified/CAP accredited lab in Redwood City, CA detects mcfDNA in plasma. After mcfDNA is extracted and NGS performed, human reads are removed, and remaining sequences are aligned to a curated database of > 1500 organisms. McfDNA from organisms present above a statistical threshold are reported and quantified in molecules/µL (MPM). KT detections of Cc and Pm were reviewed from August 2017 - present; clinical information was obtained with test requisition or consultation upon result reporting. Results KT detected 5 cases of Cc (25,039 MPM +/- 41,062) and 8 cases of Pm (33,264 MPM +/- 69,301) (Table 1). All detections of Cc were in adults (60% male) and included 2 cases of culture-negative endocarditis (one with known liver disease) and one case of sepsis with diffuse rash. Pm detections occurred in 6 adults and 2 children (75% male) and included 2 cases of culture-negative endocarditis, and single cases each of endovascular graft infection, pneumonia, fever of unknown origin, and a cranial dog bite complicated by an abscess. Two patients had immunocompromising conditions including neuroblastoma and aplastic anemia. Conclusion Unbiased, plasma-based mcfDNA NGS provides a rapid, non-invasive test to diagnose diverse clinical infections by Cc and Pm. These cases highlight the potential of the KT to diagnose infections caused by fastidious/unculturable pathogens with non-specific clinical manifestations and broad differential diagnoses. Disclosures Nicholas R. Degner, MD, MPH, MS, Karius Inc. (Employee, Shareholder) Ricardo Galvan-Castillo, MD, Karius Inc. (Employee, Shareholder) Jose Alexander, MD, D(ABMM), FCCM, CIC, SM, MB(ASCP), BCMAS, Karius (Employee) Aparna Arun, MD, Karius (Employee) Ann Macintyre, DO, Karius, Inc. (Employee) Bradley Perkins, MD, Karius, Inc. (Employee) Asim A. Ahmed, MD, Karius, Inc. (Employee) Matthew Smollin, PharmD, Karius, Inc. (Employee)
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- 2021
36. 673. Unbiased Microbial Cell-free DNA Next-Generation Sequencing Resolves HHV6 Variant Specificity and Demonstrates a Predominance of HHV6B over HHV6A in Real-World Clinical Experience
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Jose Alexander, Sivan Bercovici, Nicholas R Degner, Ricardo Castillo-Galvan, Aparna Arun, Christiaan R de Vries, Ann Macintyre, Bradley Perkins, Asim A Ahmed, and Matthew Smollin
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Infectious Diseases ,Oncology - Abstract
Background Human herpesvirus 6 (HHV6) has been classified in two distinct variants, HHV6A and HHV6B. Although distinct epidemiology, disease association, biological and immunological properties, their genomes are 90% homologous. Less is known about HHV6A which is typically asymptomatic but can cause severe infection in patients with neurological disorders or HIV. HHV6B infection occurs during childhood, but can reactivate after solid organ and stem cell transplantation. Antibody assays may indicate previous, recent or current infection. Quantitative PCR cannot differentiate active from latent infections and some available qualitative PCR assays are unable to differentiate the two variants. A single open-ended test through plasma-based microbial cell-free DNA (mcfDNA) metagenomic next-generation sequencing (NGS) may overcome these limitations. Methods Karius TestTM (KT) developed and validated in Karius’s CLIA certified/CAP accredited lab, detects mcfDNA from plasma. mcfDNA is extracted, NGS performed, human sequences removed and remaining sequences aligned to a curated pathogen database of > 1500 organisms. Organisms present above a statistical threshold are reported and quantified. For > 85% of tests the time to result reporting is the next day from sample receipt. KT results were reviewed from November-2018 to May-2021 for detections of HHV6A and HHV6B. The comparative incidence of HHV6A and HHVB detections, their age distributions and their quantitative viral concentration in molecules/µL (MPM) were assessed. Results KT detected 322 cases of HHV6; 10% (n=32) were HHV6A and 90% (n=290) HHV6B (Table 1). HHV6B had a higher relative abundance in children (with a distribution into adolescence) compared to adults (Figure 1). The average HHV6A MPM was 860 (range 27 - 10,472); the average HHV6B MPM was 3,361 (range 21 - 131,518). Table 1. Summary of HHV-6 Detections Figure 1. Distribution of HHV6A and HHV6B by Age Group Conclusion The distribution of the HHV6 variants detected through KT shows an overwhelming 9:1 predominance of HHV6B to HHV6A. The application of mcfDNA metagenomic sequencing for open-ended detection, variant determination and quantification of HHV6 provides more specific resolution than serological and PCR methods. KT may lend important insights into the association of specific HHV6 variants with clinical syndromes affecting vulnerable populations. Disclosures Jose Alexander, MD, D(ABMM), FCCM, CIC, SM, MB(ASCP), BCMAS, Karius (Employee) Sivan Bercovici, PhD, Karius (Employee) Nicholas R. Degner, MD, MPH, MS, Karius Inc. (Employee, Shareholder) Ricardo Castillo-Galvan, MD MPH, Karius Inc. (Consultant) Aparna Arun, MD, Karius (Employee) Ann Macintyre, DO, Karius, Inc. (Employee) Bradley Perkins, MD, Karius, Inc. (Employee) Asim A. Ahmed, MD, Karius, Inc. (Employee) Matthew Smollin, PharmD, Karius, Inc. (Employee)
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- 2021
37. Circulating microbial cell-free DNA is associated with inflammatory host-responses in severe pneumonia
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Sudeb C. Dalai, Carine Ho, Ghady Haidar, Haopu Yang, Haris Zia, Alison Morris, Nameer Al-Yousif, Lily Blair, Asim A. Ahmed, Daniel Kotok, Bryan J. McVerry, Georgios D Kitsios, and Sivan Bercovici
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0301 basic medicine ,Pulmonary and Respiratory Medicine ,Inflammation ,Systemic circulation ,Procalcitonin ,Article ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Humans ,Host (biology) ,business.industry ,Plasma levels ,Pneumonia ,medicine.disease ,Inflammatory biomarkers ,030104 developmental biology ,030228 respiratory system ,Cell-free fetal DNA ,Immunology ,medicine.symptom ,business ,Cell-Free Nucleic Acids ,Biomarkers - Abstract
Host inflammatory responses predict worse outcome in severe pneumonia, yet little is known about what drives dysregulated inflammation. We performed metagenomic sequencing of microbial cell-free DNA (mcfDNA) in 83 mechanically ventilated patients (26 culture-positive, 41 culture-negative pneumonia, 16 uninfected controls). Culture-positive patients had higher levels of mcfDNA than those with culture-negative pneumonia and uninfected controls (p
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- 2021
38. Characteristics of Rickettsia typhi Infections Detected with Next-Generation Sequencing of Microbial Cell-Free Deoxyribonucleic Acid in a Tertiary Care Hospital
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Fernando H Centeno, Mayar Al Mohajer, Todd M. Lasco, and Asim A. Ahmed
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0301 basic medicine ,biology ,business.industry ,medicine.drug_class ,030231 tropical medicine ,Antibiotics ,Tertiary care hospital ,bacterial infections and mycoses ,Murine typhus ,medicine.disease ,biology.organism_classification ,DNA sequencing ,Microbiology ,Serology ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Infectious Diseases ,Oncology ,Cell-free fetal DNA ,Rickettsia typhi ,medicine ,bacteria ,business - Abstract
We present 10 patients with Rickettsia typhi infection in whom next-generation sequencing of microbial cell-free deoxyribonucleic acid (mcfDNA) was used as a diagnostic tool. Rickettsia typhi mcfDNA was detected in all cases and was more rapid and specific than rickettsial serology. Rickettsia typhi mcfDNA impacted antibiotic management in 50% of patients.
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- 2021
39. Microbial Cell-Free DNA Identifies Etiology of Bloodstream Infections, Persists Longer Than Conventional Blood Cultures, and Its Duration of Detection Is Associated With Metastatic Infection in Patients With Staphylococcus aureus and Gram-Negative Bacteremia
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Asim A. Ahmed, Felicia Ruffin, Erick R Scott, Batu K. Sharma-Kuinkel, Desiree H Hollemon, Hon Seng, Nicholas R. Degner, Lily Blair, Lisa Wanda, Lawrence P. Park, Carine Ho, Emily M. Eichenberger, Pratik Shah, Vance G. Fowler, David S. Hong, Timothy A. Blauwkamp, and Christiaan R de Vries
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Microbiology (medical) ,medicine.medical_specialty ,Staphylococcus aureus ,Bacteremia ,medicine.disease_cause ,Gastroenterology ,Internal medicine ,Sepsis ,medicine ,Humans ,Blood culture ,Pathogen ,medicine.diagnostic_test ,business.industry ,Odds ratio ,Staphylococcal Infections ,medicine.disease ,Confidence interval ,Major Articles and Commentaries ,Infectious Diseases ,Cell-free fetal DNA ,Blood Culture ,Etiology ,business ,Cell-Free Nucleic Acids - Abstract
Background Microbial cell-free DNA (mcfDNA) sequencing of plasma can identify the presence of a pathogen in a host. In this study, we evaluated the duration of pathogen detection by mcfDNA sequencing vs conventional blood culture in patients with bacteremia. Methods Blood samples from patients with culture-confirmed bloodstream infection were collected within 24 hours of the index positive blood culture and 48 to 72 hours thereafter. mcfDNA was extracted from plasma, and next-generation sequencing was applied. Reads were aligned against a curated pathogen database. Statistical significance was defined with Bonferroni adjustment for multiple comparisons (P Results A total of 175 patients with Staphylococcus aureus bacteremia (n = 66), gram-negative bacteremia (n = 74), or noninfected controls (n = 35) were enrolled. The overall sensitivity of mcfDNA sequencing compared with index blood culture was 89.3% (125 of 140), and the specificity was 74.3%. Among patients with bacteremia, pathogen-specific mcfDNA remained detectable for significantly longer than conventional blood cultures (median 15 days vs 2 days; P Conclusions Pathogen mcfDNA identified the bacterial etiology of bloodstream infection for a significantly longer interval than conventional cultures, and its duration of detection was associated with increased risk for metastatic infection. mcfDNA could play a role in the diagnosis of partially treated endovascular infections.
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- 2021
40. Characteristics of
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Fernando H, Centeno, Todd, Lasco, Asim A, Ahmed, and Mayar, Al Mohajer
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animal structures ,AcademicSubjects/MED00290 ,Brief Report ,bacteria ,murine typhus ,next-generation sequencing ,Rickettsia typhi ,bacterial infections and mycoses ,complex mixtures ,clinical characteristics - Abstract
We present 10 patients with Rickettsia typhi infection in whom next-generation sequencing of microbial cell-free deoxyribonucleic acid (mcfDNA) was used as a diagnostic tool. Rickettsia typhi mcfDNA was detected in all cases and was more rapid and specific than rickettsial serology. Rickettsia typhi mcfDNA impacted antibiotic management in 50% of patients.
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- 2021
41. Plasma microbial cell-free DNA load is associated with mortality in patients with COVID-19
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Bryan J. McVerry, Alison Morris, Asim A. Ahmed, Georgios D Kitsios, Nameer Al-Yousif, William Bain, and Radha Duttagupta
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DNA, Bacterial ,Male ,Coronavirus disease 2019 (COVID-19) ,Bacterial genetics ,Microbiology ,chemistry.chemical_compound ,Predictive Value of Tests ,Pneumonia, Bacterial ,Humans ,Medicine ,In patient ,Prospective Studies ,Letter to the Editor ,lcsh:RC705-779 ,Coinfection ,SARS-CoV-2 ,business.industry ,COVID-19 ,lcsh:Diseases of the respiratory system ,Sequence Analysis, DNA ,Middle Aged ,Viral Load ,Prognosis ,medicine.disease ,Bacterial Load ,Cell-Free Nucleic Acids ,chemistry ,Cell-free fetal DNA ,COVID-19 Nucleic Acid Testing ,DNA, Viral ,Female ,Metagenomics ,business ,Viral load ,DNA - Published
- 2021
42. 390. Non-invasive Detection of Co-infections in Hospitalized Patients with COVID-19 using the Karius Test, A Plasma-based Next-Generation Sequencing Test for Microbial Cell-free DNA
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A. Macintyre, W. V. La Via, Asim A. Ahmed, C. R. De Vries, and S. Dalai
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medicine.medical_specialty ,business.industry ,medicine.disease ,Antimicrobial ,medicine.disease_cause ,DNA sequencing ,Herpesviridae ,AcademicSubjects/MED00290 ,Infectious Diseases ,Cell-free fetal DNA ,Oncology ,Internal medicine ,Superinfection ,Poster Abstracts ,Coinfection ,medicine ,Medical diagnosis ,business ,Pathogen - Abstract
Background Patients hospitalized with SARS-CoV2 infections (Covid-19) are frequently febrile and can become critically ill quickly often leading to intervention with antimicrobial therapy. An etiologic diagnosis of superinfections can be difficult to obtain through the usual invasive procedures because of patient instability and the desire to avoid them because they may not be tolerated by the patient. Providers may also be hesitant to embark on such interventions in order to avoid healthcare personnel (HCP) exposure to aerosols. Methods Karius Test (KT) results are presented from 30 patients who presented with Covid-19. The KT is a CLIA certified/CAP-accredited next-generation sequencing (NGS) plasma test that detects pathogen cell free DNA (cfDNA). After cfDNA is extracted and NGS performed, human reads are removed and remaining sequences are aligned to a curated database of > 1400 organisms. Organisms present above a statistical threshold are reported. Results The KT detected pathogens in the majority of patients (n=20) with COVID-19. The most common infections were herpesviruses in 60% of patients. The most common bacterial pathogen was E. coli seen in 25% of patients. 15 out of 20 patients had more than one pathogen detected. 15% of patients had fungal pathogens, including one detection of Lichtheimia ramosa, in an immunocompromised patient. The results are summarized in the table. Co-infections detected by the Karius Test in patients hospitalized with COVID-19 Conclusion Open-ended, plasma-based NGS for mcfDNA provides a non-invasive method to assess for co-infections in critically ill patients with COVID-19. This report highlights the potential to increase diagnostic yield as well as to decrease the need for invasive procedures – and their attendant risks to patients and HCP – to obtain etiologic diagnoses to better inform antimicrobial therapy for superinfection. It also serves to highlight the variety of pathogens affecting these patients during the COVID-19 pandemic. Disclosures William V. La Via, MD, Karius (Employee) Sudeb Dalai, MD, Karius (Employee) Christiaan R. de Vries, MD, PhD, Karius (Consultant, Independent Contractor)Stanford University (Employee) Ann Macintyre, DO, Karius (Employee) Asim A. Ahmed, MD, Karius (Employee)
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- 2020
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43. Enhanced virus detection and metagenomic sequencing in patients with meningitis and encephalitis
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Asim A. Ahmed, Sanjat Kanjilal, Tracey A. Cho, Bridget Ostrem, Gordon Adams, Daniel J. Park, Shibani S. Mukerji, Marcia B. Goldberg, Jacob E. Lemieux, Robert B. Goldstein, Lisa Freimark, Michael J. Leone, Vijay S. Ganesh, Isaac H. Solomon, Jesse M. Thon, Pardis C. Sabeti, Cormac M. Kinsella, Eric S. Rosenberg, Anne Piantadosi, Simon Ye, Kaelyn C. Cummins, and Matthew P. Frosch
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biology ,business.industry ,Disease ,biology.organism_classification ,medicine.disease ,medicine.disease_cause ,Virology ,Serology ,medicine ,Enterovirus ,Powassan virus ,Borrelia burgdorferi ,business ,Pathogen ,Meningitis ,Encephalitis - Abstract
Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific diagnostic tests, sometimes over days to weeks. Metagenomic next-generation sequencing (mNGS) is a high-throughput platform that profiles all nucleic acid in a sample. We prospectively enrolled 68 patients from New England with known or suspected CNS infection and performed mNGS from both RNA and DNA to identify potential pathogens. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects. This included some pathogens traditionally diagnosed by serology or not typically identified in CSF, including three transmitted by Ixodes scapularis ticks (Powassan virus, Borrelia burgdorferi, Anaplasma phagocytophilum). Among 24 subjects with no clinical diagnosis, we detected enterovirus in two subjects and Epstein Barr virus in one subject. We also evaluated two methods to enhance detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed detection of varicella zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with similar efficacy to pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis.ImportanceMeningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40-60% of people with meningitis or encephalitis have no clear cause of their CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 patients with suspected CNS infection, and define enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become a mainstay in the diagnostic toolkit for CNS infections.
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- 2020
44. TIM-family proteins promote infection of multiple enveloped viruses through virion-associated phosphatidylserine.
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Stephanie Jemielity, Jinyize J Wang, Ying Kai Chan, Asim A Ahmed, Wenhui Li, Sheena Monahan, Xia Bu, Michael Farzan, Gordon J Freeman, Dale T Umetsu, Rosemarie H Dekruyff, and Hyeryun Choe
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Immunologic diseases. Allergy ,RC581-607 ,Biology (General) ,QH301-705.5 - Abstract
Human T-cell Immunoglobulin and Mucin-domain containing proteins (TIM1, 3, and 4) specifically bind phosphatidylserine (PS). TIM1 has been proposed to serve as a cellular receptor for hepatitis A virus and Ebola virus and as an entry factor for dengue virus. Here we show that TIM1 promotes infection of retroviruses and virus-like particles (VLPs) pseudotyped with a range of viral entry proteins, in particular those from the filovirus, flavivirus, New World arenavirus and alphavirus families. TIM1 also robustly enhanced the infection of replication-competent viruses from the same families, including dengue, Tacaribe, Sindbis and Ross River viruses. All interactions between TIM1 and pseudoviruses or VLPs were PS-mediated, as demonstrated with liposome blocking and TIM1 mutagenesis experiments. In addition, other PS-binding proteins, such as Axl and TIM4, promoted infection similarly to TIM1. Finally, the blocking of PS receptors on macrophages inhibited the entry of Ebola VLPs, suggesting that PS receptors can contribute to infection in physiologically relevant cells. Notably, infection mediated by the entry proteins of Lassa fever virus, influenza A virus and SARS coronavirus was largely unaffected by TIM1 expression. Taken together our data show that TIM1 and related PS-binding proteins promote infection of diverse families of enveloped viruses, and may therefore be useful targets for broad-spectrum antiviral therapies.
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- 2013
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45. #35: Rapid, Non-invasive Detection and Serial Monitoring of Invasive Fungal Infections in Immunocompromised Children Using the Karius Test (a Plasma-based Microbial Cell-free DNA Sequencing Test)
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Nick Degner, Asim A Ahmed, Aparna Arun, Christiaan DeVries, Ann MacIntyre, Matthew Smollin, and Ozlem Equils
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Aspergillus ,biology ,Systemic mycosis ,business.industry ,PNEUMOCYSTIS JIROVECI ,Non invasive ,General Medicine ,medicine.disease_cause ,biology.organism_classification ,Herpesviridae ,Pathogenic organism ,Microbiology ,Infectious Diseases ,Cell-free fetal DNA ,Pediatrics, Perinatology and Child Health ,medicine ,business - Abstract
Background A diverse spectrum of invasive molds and fungi cause serious opportunistic infections in immunocompromised (IC) children. Their overlap in clinical presentation can make it challenging to differentiate among etiologies and optimally tailor antifungal therapy. Current methods to identify these pathogens lack sensitivity, are limited by long turnaround times and require an array of individual tests on invasively obtained specimens. The delay or lack of a pathogen diagnosis in combination with the reliance on invasive procedures leads to a dependence on broad empiric therapy, the development of antimicrobial resistance and increases in morbidity and mortality. Rapid, non-invasive diagnosis of invasive fungal infections through next-generation sequencing (NGS) of plasma microbial cell-free DNA (mcfDNA) offers a means to overcome these limitations. Methods Karius® Test (KT) results were reviewed for detections of Aspergillus, non-Aspergillus molds and Pneumocystis jirovecii (PJP) in children. KT, developed and validated in Karius’ CLIA certified/CAP accredited lab, detects microbial cell-free DNA (mcfDNA) can assist with the diagnosis of invasive infections. McfDNA is extracted, NGS is performed, human sequences removed and remaining sequences aligned to a curated pathogen database of >1400 organisms. Organisms present above a statistical threshold are reported and quantified. For > 85% of tests the time to result reporting is 24 hours from sample receipt. Clinical information was included from data submitted with the requisition or obtained at the time of reporting from clinical consultations with the provider. Results KT detected 7 different species of Aspergillus in 61 patients (74% IC, 40% with a pulmonary focus). KT detected 15 different non-Aspergillus molds in 51 patients (80% IC, 36% with a pulmonary focus). KT detected PJP in 37 patients (73% IC, 76% with a pulmonary focus, 54% with a DNA virus co-detection and 32% with a herpesvirus co-detections). There were 31 subjects with serial monitoring (97% IC, 70% with a pulmonary focus) including 48% with Aspergillus, 39% with non-Aspergillus molds and 12% with PJP (Figure 1). 71% of subjects demonstrated a decline in the quantitative mcfDNA signal over time; the duration of a positive mcfDNA signal ranged from 3–92 days (median 16 days, SD 22.4). Conclusions Plasma mcfDNA NGS offers a rapid, non-invasive means of detecting a broad diversity of invasive pathogens that overlap in their clinical presentations and are difficult to identify in immunocompromised children. The rapid turnaround time, non-invasive sampling and 1-sample-1000+test-solution may lead to a faster time to pathogen diagnosis, faster time to targeted therapy and obviate the need for invasive diagnostic procedures. The ability with a single test to concomitantly diagnose co-pathogens including reactivating herpesviruses that modulate the progression of principal infecting fungal pathogens (i.e. cytomegalovirus modulation of PJP) can help optimize care. Additionally, this convenient non-invasive means of serial testing of invasive fungal infections may serve as an indicator of burden of infection, provide insight into treatment efficacy and ultimately help define the length and mode (medical/surgical) of therapy required to improve outcomes. Additional studies correlating the mcfDNA signal with individual patient clinical and radiographic parameters will be important to further define the utility of serial mcfDNA monitoring.
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- 2021
46. TO DETERMINE THE EFFICACY OF TOPICAL TREATMENT WITH 1% PROPRANOLOL FOR INFANTILE HEMANGIOMA
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Asim, Sadaf Ahmed, Humaira Maryum Agha, Furquana Niaz, Nisa, Qamar Un, and Meeraal Asim Kaikaus
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Infantile Hemangioma (IH) Topical Propranolol Birthmark Topical Treatment - Abstract
Objective: To determine the efficacy of topical treatment with 1% propranolol in the infants with hemangioma. Methodology:This was a prospective study conducted from August 2018 till December 2019 through non-probability convenient sampling technique. Study comprised of 27 infants from the Dermatology Department of Dow University Hospital, Karachi. Infants having hemangioma in any part of body except near orifical opening were included in the study. 1% topical propranolol was applied twice daily to the lesion and any change is size, colour , discharge before and after treatment was noted at each follow up till 3 months.Resolution was recorded at each follow up. Data was analysed in SPSS version 20.0. P-value ≤0.05 was taken as significant. Results:From the total of 27 infants enrolled in the study, 09 (33.3%) were male and 18 were female (66.7%). After treatment, 26 (96.3%)hemangiomas had shrunken. 14 (51.9%) of patients parents termed it as a very good response to treatment and 07 (25.9%) felt complete satisfaction to treatment. On first follow up, only 01 (3.7%) had complete resolution, 04 (14.8%) on second follow up and 06 (22.2%) on third follow up. Conclusion: The present study concluded that 1% topical propranolol was effective as well as safe and convenient to apply for treating infantile hemangiomas. 
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- 2020
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47. Detection of Borrelia burgdorferi Cell-free DNA in Human Plasma Samples for Improved Diagnosis of Early Lyme Borreliosis
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Timothy J. Lepore, Carine Ho, Nitin Damle, Nira R. Pollock, Desiree Hollemon, Lily Blair, John A. Branda, Sivan Bercovici, Jacob E. Lemieux, Timothy A. Blauwkamp, Klemen Strle, Asim A. Ahmed, and David K. Hong
- Subjects
0301 basic medicine ,Microbiology (medical) ,DNA, Bacterial ,medicine.medical_specialty ,030106 microbiology ,Gastroenterology ,Asymptomatic ,law.invention ,Serology ,03 medical and health sciences ,0302 clinical medicine ,law ,Internal medicine ,medicine ,Humans ,030212 general & internal medicine ,Seroconversion ,Borrelia burgdorferi ,Online Only Articles ,Polymerase chain reaction ,Lyme Disease ,biology ,medicine.diagnostic_test ,business.industry ,Borrelia ,biology.organism_classification ,LYME ,Infectious Diseases ,Cell-free fetal DNA ,Skin biopsy ,Erythema Chronicum Migrans ,Metagenomics ,medicine.symptom ,business ,Cell-Free Nucleic Acids - Abstract
Background Laboratory confirmation of early Lyme borreliosis (LB) is challenging. Serology is insensitive during the first days to weeks of infection, and blood polymerase chain reaction (PCR) offers similarly poor performance. Here, we demonstrate that detection of Borrelia burgdorferi (B.b.) cell-free DNA (cfDNA) in plasma can improve diagnosis of early LB. Methods B.b. detection in plasma samples using unbiased metagenomic cfDNA sequencing performed by a commercial laboratory (Karius Inc) was compared with serology and blood PCR in 40 patients with physician-diagnosed erythema migrans (EM), 28 of whom were confirmed to have LB by skin biopsy culture (n = 18), seroconversion (n = 2), or both (n = 8). B.b. sequence analysis was performed using investigational detection thresholds, different from Karius’ clinical test. Results B.b. cfDNA was detected in 18 of 28 patients (64%) with laboratory-confirmed EM. In comparison, sensitivity of acute-phase serology using modified 2-tiered testing (MTTT) was 50% (P = .45); sensitivity of blood PCR was 7% (P = .0002). Combining B.b. cfDNA detection and MTTT increased diagnostic sensitivity to 86%, significantly higher than either approach alone (P ≤ .04). B.b. cfDNA sequences matched precisely with strain-specific sequence generated from the same individual’s cultured B.b. isolate. B.b. cfDNA was not observed at any level in plasma from 684 asymptomatic ambulatory individuals. Among 3000 hospitalized patients tested as part of clinical care, B.b. cfDNA was detected in only 2 individuals, both of whom had clinical presentations consistent with LB. Conclusions This is the first report of B.b. cfDNA detection in early LB and a demonstration of potential diagnostic utility. The combination of B.b. cfDNA detection and acute-phase MTTT improves clinical sensitivity for diagnosis of early LB.
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- 2020
48. Rapid, Noninvasive Diagnosis of Balamuthia mandrillaris Encephalitis by a Plasma-Based Next-Generation Sequencing Test
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Jesse Kresak, David K. Hong, Asim A. Ahmed, Karim M Ali Ibne, Jennifer R. Cope, Shantanu Roy, Gautam Kalyatanda, Martin S. Lindner, Varalakshmi Ballur Narayna Reddy, Kenneth H. Rand, Mehmet S. Albayram, Jason Gregory, and Joy Gary
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0301 basic medicine ,Pathology ,medicine.medical_specialty ,030106 microbiology ,Autopsy ,DNA sequencing ,Balamuthia mandrillaris ,03 medical and health sciences ,0302 clinical medicine ,medicine ,030212 general & internal medicine ,Amoebic encephalitis ,Granulomatous amoebic encephalitis ,rapid diagnosis ,next generation sequencing ,biology ,medicine.diagnostic_test ,business.industry ,Brain biopsy ,Brief Report ,Subacute infection ,medicine.disease ,biology.organism_classification ,Infectious Diseases ,AcademicSubjects/MED00290 ,Oncology ,business ,Encephalitis ,granulomatous amoebic encephalitis - Abstract
Granulomatous amoebic encephalitis (GAE) caused by Balamuthia mandrillaris is a rare subacute infection with exceptionally high mortality. Diagnosis is typically made by brain biopsy or at autopsy. Detection of Balamuthia mandrillaris cell-free DNA by next-generation sequencing of plasma enabled rapid, noninvasive diagnosis in a case of amoebic encephalitis.
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- 2020
49. PREVALENCE OF HYPERTENSION AMONG OUTDOOR PATIENTS
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Quratulain Asma, Maheen Asim, Waqas Ahmed
- Abstract
Hypertension is an increasingly global issue and causes multiple complications if not controlled early. Objective: To see the prevalence of hypertension among the patients presenting in the outdoor department. Material and Methods: This cross-sectional study included 134 patients of either gender. Patient of age 18 years and above were included. Data was collected and analyzed using SPSS V. 23. Results: Mean age of the patients was 38.98±13.35 years. There were 69 female patients (51.49%) and 65 male patients (48.51%). Mean systolic blood pressure was 140.01±20.15 mmHg with a minimum value of 110 mmHg and a maximum value of 175 mmHg. Mean diastolic blood pressure was 88.21±5.45 mmHg with a minimum value of 80 mmHg and a maximum value of 99 mmHg. Nineteen (14.18%) patients were having normal systolic blood pressure, 23 (17.16%) patients were suffering from pre-hypertension, 50 (37.31%) were class I hypertensive and and 42 (31.34%) were class II hypertensive. Conclusion: This study concludes the higher frequency of hypertension in patients presenting in the outdoor department. Keywords: Hypertension, outdoor department, Pakistan.  
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- 2019
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50. 1026. Following the Hoof Prints: Detecting Coxiella and Brucella infections with A Plasma-based Microbial Cell-Free DNA Next-generation Sequencing Test
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Nicholas R Degner, Ricardo Castillo-Galvan, Jose Alexander, Aparna Arun, Christiaan R de Vries, Ann Macintyre, Bradley Perkins, Asim A Ahmed, and Matthew Smollin
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Infectious Diseases ,AcademicSubjects/MED00290 ,Oncology ,Poster Abstracts - Abstract
Background Coxiella burnetii and Brucella spp. are zoonotic bacterial pathogens responsible for Q fever and Brucellosis, respectively. Both pathogens have a global distribution and Brucellosis is the most common zoonosis in the world. However, the CDC reports only 80-120 cases of human brucellosis and ~150 cases of acute Q fever annually. The diagnosis of these infections can be limited by: (1) their difficulty to culture; (2) the insensitivity and nonspecificity of serology; (3) the clinical overlap with other infections; and (4) the unreliability of epidemiological exposure history for these zoonoses. Unbiased microbial cell free DNA (mcfDNA) next-generation sequencing (NGS) offers a potential solution to overcome these limitations. Methods The Karius TestTM (KT) developed and validated in Karius’s CLIA certified/CAP accredited lab in Redwood City, CA detects mcfDNA in plasma. After mcfDNA is extracted and NGS performed, human reads are removed, and remaining sequences are aligned to a curated database of > 1500 organisms. McfDNA from organisms present above a statistical threshold are reported and quantified in molecules/µL (MPM). KT detections of Coxiella and Brucella were reviewed from August 2017 - present; clinical information was obtained with test requisition or consultation upon result reporting. Results KT detected 8 cases of Coxiella burnetii (1735 MPM +/- 3000) and 5 cases of Brucella melitensis (avg 296 MPM +/- 223) (Table 1), representing approximately 1-2% of all detections in the US during this period. All of the Coxiella detections were in adults (100% male) with 5 cases of fever of unknown origin, 2 cases of culture-negative endocarditis and one case of endovascular graft infection. Brucella detections occurred in 3 adults and 2 children (60% male), 3 with exposure to unpasteurized dairy and included 3 cases of spine infection (2 vertebral osteomyelitis, 1 epidural abscess). Conclusion Open-ended, plasma-based mcfDNA NGS provides a rapid, non-invasive test to diagnose diverse clinical manifestations of zoonotic infections such as Q fever and Brucellosis against competing broad differential diagnoses. Furthermore, these cases highlight the potential of the KT to diagnose infections caused by fastidious/unculturable pathogens with cryptic clinical presentations. Disclosures Nicholas R. Degner, MD, MPH, MS, Karius Inc. (Employee, Shareholder) Ricardo Castillo-Galvan, MD MPH, Karius Inc. (Consultant) Jose Alexander, MD, D(ABMM), FCCM, CIC, SM, MB(ASCP), BCMAS, Karius (Employee) Aparna Arun, MD, Karius (Employee) Ann Macintyre, DO, Karius, Inc. (Employee) Bradley Perkins, MD, Karius, Inc. (Employee) Asim A. Ahmed, MD, Karius, Inc. (Employee) Matthew Smollin, PharmD, Karius, Inc. (Employee)
- Published
- 2021
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