I am an infectious diseases-trained physician-investigator dedicated to translating novel diagnostics and diagnostic strategies that advance the management of infections in transplantation. My research focuses on the use of next-generation sequencing (NGS) to better understand and improve the care of viral infections in transplant recipients. I evaluate novel virus-disease associations, the virome in transplantation, and host-virus responses in solid organ and hematopoietic cell transplant recipients. I perform clinical validation and utility studies of NGS-based broad pathogen assays and targeted assays based on NGS-derived findings. I have particular interests in polyomaviruses and donor-derived infections in solid organ transplantation.
Honors & Awards
Spectrum TL-1 Clinical Research Training Program Award, Stanford University (2016)
Helena Anna Henzl-Gabor Young Women in Science Fund, Stanford University (2015)
Translational Research and Applied Medicine (TRAM) Fellow Pilot Award, Stanford University (2015)
Boards, Advisory Committees, Professional Organizations
Trainee Representative, American Society of Transplantation, Infectious Disease Community of Practice, Executive Committee (2016 - Present)
Member, American Society of Transplantation (2015 - Present)
Member, American Society for Microbiology (2015 - Present)
Member, Infectious Diseases Society of America (2013 - Present)
Board Certification, American Board of Internal Medicine, Infectious Diseases (2015)
Board Certification, American Board of Internal Medicine, Internal Medicine (2012)
Chief Fellow, Stanford University, Infectious Diseases (2016)
Fellowship, Stanford University, Infectious Diseases (2016)
Chief Resident, California Pacific Medical Center, Internal Medicine (2013)
Residency, California Pacific Medical Center, Internal Medicine (2012)
Doctor of Medicine, Northwestern University (2009)
Bachelor of Arts, Stanford University, HUMBI-BAH (2005)
Benjamin Pinsky, Postdoctoral Research Mentor
Molecular and Culture-Based Bronchoalveolar Lavage Fluid Testing for the Diagnosis of Cytomegalovirus Pneumonitis.
Open forum infectious diseases
2016; 3 (1): ofv212-?
Background. Cytomegalovirus (CMV) is a major cause of morbidity and mortality in immunocompromised patients, with CMV pneumonitis among the most severe manifestations of infection. Although bronchoalveolar lavage (BAL) samples are frequently tested for CMV, the clinical utility of such testing remains uncertain. Methods. Retrospective analysis of adult patients undergoing BAL testing via CMV polymerase chain reaction (PCR), shell vial culture, and conventional viral culture between August 2008 and May 2011 was performed. Cytomegalovirus diagnostic methods were compared with a comprehensive definition of CMV pneumonitis that takes into account signs and symptoms, underlying host immunodeficiency, radiographic findings, and laboratory results. Results. Seven hundred five patients underwent 1077 bronchoscopy episodes with 1090 BAL specimens sent for CMV testing. Cytomegalovirus-positive patients were more likely to be hematopoietic cell transplant recipients (26% vs 8%, P < .0001) and less likely to have an underlying condition not typically associated with lung disease (3% vs 20%, P < .0001). Histopathology was performed in only 17.3% of CMV-positive bronchoscopy episodes. When CMV diagnostic methods were evaluated against the comprehensive definition, the sensitivity and specificity of PCR, shell vial culture, and conventional culture were 91.3% and 94.6%, 54.4% and 97.4%, and 28.3% and 96.5%, respectively. Compared with culture, PCR provided significantly higher sensitivity and negative predictive value (P ≤ .001), without significantly lower positive predictive value. Cytomegalovirus quantitation did not improve test performance, resulting in a receiver operating characteristic curve with an area under the curve of 0.53. Conclusions. Cytomegalovirus PCR combined with a comprehensive clinical definition provides a pragmatic approach for the diagnosis of CMV pneumonitis.
View details for DOI 10.1093/ofid/ofv212
View details for PubMedID 26885542
Limited Variation in BK Virus T-Cell Epitopes Revealed by Next-Generation Sequencing
JOURNAL OF CLINICAL MICROBIOLOGY
2015; 53 (10): 3226-3233
BK virus (BKV) infection and end-organ disease remains a formidable challenge to the hematopoietic cell transplant (HCT) and kidney transplant fields. As BKV-specific treatments are limited, immunologic-based therapies may be a promising and novel therapeutic option for transplant recipients with persistent BKV infection. Here, we describe a whole-genome, deep sequencing methodology and bioinformatics pipeline that identifies BKV variants across the genome and at BKV-specific HLA-A2, HLA-B0702, and HLA-B08 restricted CD8 T-cell epitopes. BKV whole genomes were amplified using long-range PCR with four inverse primer sets and fragmentation libraries were sequenced on the Ion Torrent PGM. An error model and variant calling algorithm were developed to accurately identify rare variants. 65 samples from 18 pediatric HCT and kidney recipients with quantifiable BKV DNAemia underwent whole-genome sequencing. Limited genetic variation was observed. The median number of amino acid variants identified per sample was 8 (range 2-37, interquartile range 10), with the majority of variants (77%) detected at a frequency of less than 5%. When normalized for length, there was no statistical difference in the median number of variants across all genes. Similarly, the predominant virus population within samples harbored T-cell epitopes similar to the reference BKV strain that was matched for BKV genotype. Despite the conservation of epitopes, low-level variants in T-cell epitopes were detected in 77.7% (14/18) of patients. Understanding epitope variation across the whole genome provides insight into the virus-immune interface and may help guide the development of protocols for novel immunologic-based therapies.
View details for DOI 10.1128/JCM.01385-15
View details for Web of Science ID 000365625300017
Cytomegalovirus load at treatment initiation is predictive of time to resolution of viremia and duration of therapy in hematopoietic cell transplant recipients
JOURNAL OF CLINICAL VIROLOGY
2015; 69: 179-183
Preemptive antiviral therapy relies on viral load measurements and is the mainstay of cytomegalovirus (CMV) prevention in hematopoietic cell transplant (HCT) recipients. However, optimal CMV levels for the initiation of preemptive therapy have not been defined.The objectives of our work were to evaluate the relationship between plasma CMV DNA levels at initiation of preemptive therapy with time to resolution of viremia and duration of treatment.Retrospective analysis of HCT recipients undergoing serial CMV PCR testing between June 2011 and June 2014 was performed.221 HCT recipients underwent preemptive therapy for 305 episodes of CMV viremia. Median time to resolution was shorter when treatment was initiated at lower CMV levels (15 days at 135-440 international units (IU)/mL, 18 days at 441-1000IU/mL, and 21 days at >1000IU/mL, P<.001). Prolonged viremia lasting >30 days occurred less frequently when treatment was initiated at 135-440IU/mL compared to 441-1000IU/mL and >1000IU/mL (1%, 15%, 24%, P<.001). Median treatment duration was also shorter in the lower viral load groups (28, 34, 37 days, P<.001).Initiation of preemptive therapy at low CMV levels was associated with shorter episodes of viremia and courses of antiviral therapy. These data support the utility of initiating preemptive CMV therapy at viral loads as low as 135IU/mL in HCT recipients.
View details for DOI 10.1016/j.jcv.2015.06.006
View details for Web of Science ID 000358318400037
- Fatal acanthamoeba encephalitis in a patient with a total artificial heart (syncardia) device. Open forum infectious diseases 2014; 1 (2): ofu057-?
- Hematocrit Effect in Bilateral Subdural Hematomas JOURNAL OF GENERAL INTERNAL MEDICINE 2013; 28 (2): 321-321
- A Common Fungus, an Unusual (and Deadly) Infection AMERICAN JOURNAL OF MEDICINE 2011; 124 (11): 1023-1024
Greater osteoporosis educational outreach is desirable among Chinese immigrants in Chinatown, Chicago
2009; 20 (9): 1517-1522
Osteoporosis beliefs were assessed in immigrant Chinese women in Chinatown, Chicago. Results from a survey utilizing the Osteoporosis Health Belief Scale showed that women expressed concern about osteoporosis but lacked both knowledge of preventive care and health motivation.The objective of this study was to assess osteoporosis beliefs in immigrant Chinese women in Chinatown, Chicago.In a community-based health fair, osteoporosis knowledge and self-efficacy among postmenopausal Chinese immigrants were assessed using the translated Osteoporosis Health Belief Scale. Bone mineral density (BMD) was assessed with calcaneal ultrasound.The study population included 94 women with mean age of 51 +/- 9 years, mean length of residence in the United States of 9 +/- 7 years, and 73% (n = 76) of whom were recent immigrants. Women expressed concern about the seriousness of osteoporosis and their relative susceptibility to osteoporosis. In particular, women with a prior fracture reported higher seriousness to osteoporosis. Nonetheless, women exhibited low health motivation and low awareness of the benefits of calcium and exercise. Bone densitometry results corresponded to a T score of -1.2 +/- 1.5. Multiple regression analysis revealed that a younger age and longer length of residence in the USA were associated with higher BMD.Chinese immigrant women in Chicago exhibit concern regarding osteoporosis, but are unaware of the benefits of calcium and exercise, and exhibit low health motivation. Chinese women in Chinatown lack necessary knowledge about osteoporosis to develop adequate self-efficacy. Public health initiatives should be undertaken among recent immigrant Chinese women.
View details for DOI 10.1007/s00198-008-0828-3
View details for Web of Science ID 000269080100007
View details for PubMedID 19148565
Acute Myocardial Infarction After Treatment of Thrombocytopenia in a Young Woman With Systemic Lupus Erythematosus
JCR-JOURNAL OF CLINICAL RHEUMATOLOGY
2008; 14 (6): 350-352
We describe a case of an acute myocardial infarction (MI) coincident with correction of severe thrombocytopenia in a 23-year old African American woman with systemic lupus erythematosus (SLE) in the absence of coronary artery disease on angiography. Despite a history of anticardiolipin and beta(2)-glycoprotein I antibodies, she had no prior thromboembolic events. The occurrence of an acute MI after rapid normalization in the platelet count suggests the need for close monitoring of possible cardiovascular events during and after treatment of severe thrombocytopenia in the presence of antiphospholipid antibodies.
View details for DOI 10.1097/RHU.0b013e31817de0fb
View details for Web of Science ID 000261654400008
View details for PubMedID 19086148
Disparities in mammographic screening for Asian women in California: a cross-sectional analysis to identify meaningful groups for targeted intervention
Breast cancer is the most commonly diagnosed cancer among the rapidly growing population of Asian Americans; it is also the most common cause of cancer mortality among Filipinas. Asian women continue to have lower rates of mammographic screening than women of most other racial/ethnic groups. While prior studies have described the effects of sociodemographic and other characteristics of women on non-adherence to screening guidelines, they have not identified the distinct segments of the population who remain at highest risk of not being screened.To better describe characteristics of Asian women associated with not having a mammogram in the last two years, we applied recursive partitioning to population-based data (N = 1521) from the 2001 California Health Interview Survey (CHIS), for seven racial/ethnic groups of interest: Chinese, Japanese, Filipino, Korean, South Asian, Vietnamese, and all Asians combined.We identified two major subgroups of Asian women who reported not having a mammogram in the past two years and therefore, did not follow mammography screening recommendations: 1) women who have never had a pap exam to screen for cervical cancer (68% had no mammogram), and 2) women who have had a pap exam, but have no women's health issues (osteoporosis, using menopausal hormone therapies, and/or hysterectomy) nor a usual source of care (62% had no mammogram). Only 19% of Asian women who have had pap screening and have women's health issues did not have a mammogram in the past two years. In virtually all ethnic subgroups, having had pap or colorectal screening were the strongest delineators of mammography usage. Other characteristics of women least likely to have had a mammogram included: Chinese non-U.S. citizens or citizens without usual source of health care, Filipinas with no health insurance, Koreans without women's health issues and public or no health insurance, South Asians less than age 50 who were unemployed or non-citizens, and Vietnamese women who were never married.We identified distinct subgroups of Asian women at highest risk of not adhering to mammography screening guidelines; these data can inform outreach efforts aimed at reducing the disparity in mammography screening among Asian women.
View details for DOI 10.1186/1471-2407-7-201
View details for Web of Science ID 000252447400001
View details for PubMedID 17961259