Rupak Shivakoti, PhD, MSPH

Role: 
Faculty
Assistant Professor, Columbia University Mailman School of Public Health
Rupak Shivakoti, PhD, MSPH, is an Assistant Professor of Epidemiology at Columbia University Mailman School of Public Health, and an affiliated member of the faculty at CIDI. His formal training is in immunology, infectious diseases, and epidemiology.
 
Dr. Shivakoti’s primary research interest focuses on the central role of inflammation in HIV and TB outcomes, both in adult and maternal-infant populations. In addition, he is interested in the relationship of nutrition and gut microbiome with inflammation and health outcomes. He is the PI of NIH-funded projects related to these topics and conducted in diverse international settings, with a strong focus in India. More about Dr. Shivakoti's work can be found in the tabs below.
 
After completing his undergraduate degree in biology from DePauw University, Dr. Shivakoti received a MSPH in international health and a PhD in molecular microbiology and immunology from the Johns Hopkins Bloomberg School of Public Health. His PhD thesis, under the direction of Dr. Diane Griffin, focused on the innate and adaptive immune responses to the measles virus and measles vaccine. He completed his post-doctoral fellowship at JHU CCGHE with Dr. Amita Gupta serving as his mentor.

Vaginal Microbiota in HIV Infected and Uninfected Pregnant Women (Stand Alone)

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2018-10-16
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Amita Gupta, MD, MHS, and Shilpa Naik, MD, are PIs for this study; Rupak Shivakoti, PhD, MSPH, is Co-Investigator The makeup of vaginal microbiota is dynamic and may play a role in the birth outcomes of pregnant women. While HIV and pregnancy both uniquely impact vaginal microbiota, the impact of...

Gut Microbiota of HIV Infected Pregnant Women

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2018-06-14
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Birth Outcomes in HIV Both antiretroviral-therapy (ART)-naïve and ART-experienced HIV-infected pregnant women have higher incidences of pre-term birth (PTB) compared to HIV-uninfected women. For example, the global prevalence of PTB is around 8%, while the rates in in HIV-infected...

Lipid Mediators of Inflammation in TB and TB-Diabetes

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2017-10-02
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This study was terminated August 1, 2019. It was funded and conducted under the U.S. National Institutes of Health and is nested within Impact of Diabetes on TB Treatment Outcomes. Dr. Jonathan Golub was the PI. Studies have shown that individuals with...

Validation of Transcriptional Signature to Predict Active TB Disease among Advanced HIV Patients

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2017-08-15
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This study was terminated June 20, 2021. There have been tremendous advances in the diagnosis of patients with tuberculosis (TB) based on nucleic acid amplification of bacteria in the sputum. The GenXpert MTB/RIF provides results in 2 hours. However, in HIV-infected sputum...

Association of Lipid Mediators of Inflammation with TB Treatment Outcomes

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2017-08-03
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This study was terminated July 22, 2019. This study used stored samples from the Cohort for Tuberculosis Research by the Indo-US Medical Partnership (C-TRIUMPH), under the Regional Prospective Observational Research for Tuberculosis (RePORT) Network, an international TB...

TB and Pregnancy Impact of Immune Changes of HIV and Stages of Pregnancy on Tuberculosis: Nested Study on Temporal Dynamics of Gut Microbiota in HIV Infected Pregnant Women

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2016-07-05
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This is a nested prospective longitudinal cohort study of 35 HIV-infected and 35 HIV-noninfected pregnant women who are part of the parent study “Impact of Immune Changes of HIV and Stages of Pregnancy on Tuberculosis." The objectives are to: Determine the association...

Inflammation in HIV-infected Pregnant Women: Relationship with Diet, Gut Microbiome and Preterm Birth

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2014-10-28
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This study was terminated May 7, 2018. P regnancy is a state of relative immunosuppression in order to protect the fetus from being rejected. It has also been shown that the Th-1 helper cell response, which is normally necessary for overcoming TB infection...

Impact of Immune Changes of HIV and Stages of Pregnancy on Tuberculosis

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2014-09-01
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This is the Parent Study for CCGHE’s PRACHITI (PRegnancy And CHanges In TuberculosIs) effort. It's supported by the Eunice Kennedy Shriver National Institute of Child Health and Human Development at the U.S. National Institutes of Health. Purpose: TB is a...

ART Study 1: Database: Epidemiology of HIV/AIDS and Associated Comorbidities in a Public Antiretroviral Treatment (ART) Clinic at BJGMC in Pune

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2014-06-14
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Since 2004, the National AIDS Control Program of India has been rolling out free antiretroviral therapy. Byramjee Jeejeebhoy Government Medical College (BJGMC), located in Pune, India, is now the largest HIV clinic in India, with over 26,000 adult and pediatric patients registered since 2005...

Cohort for Tuberculosis Research by the Indo-US Medical Partnership (C-TRIUMPH)

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2013-09-28
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Collaboratively funded by the US NIH, India’s Department of Biotechnology [DBT], and Indian Council of Medical Research, the Cohort for TB Research by the Indo-US Medical Partnership (C-TRIUMPH) is an Indo-US research consortium that is part of RePORT India, a countrywide consortium for TB...

Impact of Malnutrition on HIV Treatment Failure in Resource-limited Settings

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2009-04-02
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This study, NWCS 319, was terminated August 20, 2019. Highly active antiretroviral therapy (HAART) has reduced morbidity and mortality among HIV-infected persons worldwide. However, early treatment failure (i.e. WHO stage 3 or 4 illnesses or death...

Pro-inflammatory and pro-resolving lipid mediators of inflammation in HIV: effect of aspirin intervention

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2023-03-01
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eBioMedicine
Background: Persons with HIV (PWH) have an increased risk of cardiovascular disease (CVD) compared to HIV-seronegative individuals (SN). Inflammation contributes to this risk but the role of lipid mediators, with central roles in inflammation, in HIV infection remain to be established; further...

TB-related Knowledge and Stigma Among Pregnant Women in Low Resource Settings of Pune, India

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2022-02-01
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The International Journal of Tuberculosis and Lung Disease,
TB is an important cause of maternal morbidity.1 Studies among adults with TB in several countries have consistently demonstrated that a lack of TB-related knowledge and increased stigma can be a barrier to early diagnosis, seeking treatment and treatment adherence.2–6 India has the highest number...

Host lipidome and tuberculosis treatment failure

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2022-01-06
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European Respiratory Journal
Introduction: Host lipids play important roles in tuberculosis (TB) pathogenesis. Whether host lipids at TB treatment initiation (baseline) affect subsequent treatment outcomes has not been well characterised. We used unbiased lipidomics to study the prospective association of host lipids with TB...

Impact of HIV status on systemic inflammation during pregnancy

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2021-11-15
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AIDS London
Objective: There are limited studies on the association of HIV infection with systemic inflammation during pregnancy. Design: A cohort study (N = 220) of pregnant women with HIV (N = 70) (all on antiretroviral therapy) and without HIV (N = 150) were enrolled from an...

Validation of New Interactive Nutrition Assistant - Diet in India Study of Health (NINA-DISH) FFQ with multiple 24-h dietary recalls among pregnant women in Pune, India

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2021-11-02
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The British Journal of Nutrition
Adequate dietary intake is critical to prevent adverse pregnancy outcomes. India has a high burden of maternal and child morbidity and mortality, but there is a lack of adequate tools to assess dietary intake. We validate an FFQ, New Interactive Nutrition Assistant - Diet in India Study of Health (NINA-DISH), among pregnant women living with and without HIV in Pune, India.

Systemic Inflammation in Pregnant Women With Latent Tuberculosis Infection

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2021-01-27
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Frontiers in Immunology
Background: Recent studies in adults have characterized differences in systemic inflammation between adults with and without latent tuberculosis infection (LTBI+ vs. LTBI-). Potential differences in systemic inflammation by LTBI status has not been assess in pregnant women. Methods: We conducted a...

Association of Maternal Inflammation During Pregnancy: Relationship with Birth Outcomes & Infant Growth Among Women with and without HIV in India

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2021-01-12
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JAMA Network Open
Abstract Importance The association of elevated levels of specific inflammatory markers during pregnancy with adverse birth outcomes and infant growth could indicate pathways for potential interventions. Objective To evaluate whether higher levels of certain inflammatory markers during pregnancy...

Validation of NINA-DISH food frequency questionnaire with multiple 24-hour dietary recalls among pregnant women in Pune, India

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2021-01-06
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The British Journal of Nutrition
Adequate dietary intake is critical to prevent adverse pregnancy outcomes. India has a high burden of maternal and child morbidity and mortality, but there is a lack of adequate tools to assess dietary intake. We validate a food frequency questionnaire (FFQ), New-Interactive Nutrition Assistant-...

Association of Vegetable and Animal Flesh Intake with Inflammation in Pregnant Women from India

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2020-12-08
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MDPI
In pregnant women, studies are lacking on the relationship of vegetable and animal flesh (poultry, red meat and seafood) intake with inflammation...

Lipid mediators of inflammation and resolution in individuals with tuberculosis and tuberculosis-diabetes

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2019-11-11
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Prostaglandins and Other Lipid Mediators
Individuals with concurrent tuberculosis (TB) and Type 2 diabetes (DM) have a higher risk of adverse outcomes. To better understand potential immunological differences, we utilized a comprehensive panel to characterize pro-inflammatory and pro-resolving (i.e., mediators involved in the resolution...

Inflammation and micronutrient biomarkers predict clinical HIV treatment failure and incident active TB in HIV-infected adults: a case-control study

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2018-09-24
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BMC Medicine
Factors identified through exploratory factor analysis were associated with adverse outcomes in HIV-infected individuals.

Trends in HbA1c levels and implications for diabetes screening in tuberculosis cases undergoing treatment in India

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2018-07-01
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International Journal of Tuberculosis and Lung Disease
SETTING: The optimal timing of screening for diabetes mellitus (DM) among tuberculosis (TB) cases is unclear due to the possibility of stress hyperglycemia. DESIGN: We evaluated adult (18 years) pulmonary TB cases at treatment initiation as well as at 3 months,...

Effect of baseline micronutrient and inflammation status on CD4 recovery post-cART initiation in the multinational PEARLS trial

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2018-05-29
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Clinical Nutrition
Nutritional deficiency and inflammation may impact CD4+ T cell recovery during combination antiretroviral therapy (cART), particularly in resource-limited settings where malnutrition is prevalent. The aim of this study was to investigate the relationship of micronutrient and inflammation biomarkers to CD4 recovery after cART initiation.

Intestinal barrier dysfunction and microbial translocation in HIV-infected pregnant women is associated with preterm birth

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2018-03-24
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Clinical Infectious Diseases
Our results show select immune markers can identify women at higher risk for PTB in HIV-1-infected populations and suggest modulating gut barrier integrity and microbial translocation may affect PTB.

Prevalence of dysglycemia and clinical presentation of pulmonary tuberculosis in Western India

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2017-12-01
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International Journal of Tuberculosis and Lung Disease
Objectives: To estimate the prevalence and risk factors of pre-diabetes mellitus (DM) and DM, and its associations with the clinical presentation of tuberculosis (TB). Design: Screening for DM was conducted among adults (age  18 years) with confirmed TB between December 2013 and...

Vitamin A and D deficiencies associated with incident tuberculosis in HIV-infected patients initiating antiretroviral therapy in multinational case-cohort study

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2017-07-01
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Journal of Acquired Immune Deficiency Syndromes
Introduction: Numerous micronutrients have immunomodulatory roles that may influence risk of tuberculosis (TB), but the association between baseline micronutrient deficiencies and incident TB after antiretroviral therapy (ART) initiation in HIV-infected individuals is not well characterized...

Continued elevation of interleukin-18 and interferon-γ after initiation of antiretroviral therapy and clinical failure in a diverse multicountry human immunodeficiency virus cohort

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2016-07-27
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Open Forum Infectious Diseases
Background: We assessed immune activation after antiretroviral therapy (ART) initiation to understand clinical failure in diverse settings. Methods: We performed a case-control study in ACTG Prospective Evaluation of Antiretrovirals in Resource-Limited Settings (...

Persistently elevated C-reactive protein level in the first year of antiretroviral therapy, despite virologic suppression, is associated with HIV disease progression in resource-constrained settings

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2016-04-01
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The Journal of Infectious Diseases
A case-cohort analysis of human immunodeficiency virus (HIV)-infected individuals receiving antiretroviral therapy (ART) was performed within a multicountry randomized trial (PEARLS) to assess the prevalence of persistently elevated C-reactive protein (CRP) levels, based on serial...

Prevalence and risk factors of micronutrient deficiencies pre- and post-antiretroviral therapy (ART) among a diverse multicountry cohort of HIV-infected adults

Post Date: 
2016-02-10
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Clinical Nutrition
Background & Aims: HIV-infected adults have increased risk of several individual micronutrient deficiencies. However, the prevalence and risk factors of concurrent and multiple micronutrient deficiencies and whether micronutrient concentrations change after antiretroviral therapy (ART)...

Soluble CD14: An independent biomarker for risk of HIV mother-to-child transmission in setting of pre- and post-exposure antiretroviral prophylaxis

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2015-10-06
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The Journal of Infectious Diseases
Elevated soluble CD14 (sCD14) concentrations, a marker of monocyte activation, predicts adverse outcomes in human immunodeficiency virus (HIV)-infected adults. To examine the association of sCD14 concentrations with the risk of mother-to-child transmission (MTCT) of HIV, we nested a case-...

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Shivani Mehta

Baltimore, Maryland
Shivani Mehta is a BS/BA candidate (2018) in public health at the Johns Hopkins Krieger School of Arts and Sciences, who is working with Drs. Rupak Shivakoti and Mallika Alexander on Maternal Inflammation, Diet and Gut Microbiome in HIV: Impact on Infant Outcomes. Ms. Mehta spent June and July 2016 at BJGMC in Pune, India, working under Dr. Alexander. Awards 2016 Global Health Established Field Placement Grant 2016 Johns Hopkins Provost Undergradulate Research Award for 2016-17 From Ms. Mehta's Field Report:...

Prarthana Vasudevan

Baltimore, Maryland
Prar Vasudevan is an international health graduate student at the Johns Hopkins School of Public Health. In Autumn 2015, she conducted a field placement in Pune, India, at BJGMC under Dr. Vidya Mave, where she worked on the study titled Maternal Inflammation, Diet and Gut Microbiome in HIV: Impact on Infant Outcomes. She is a 2015 recipient of the Global Health Established Field Placement Grant. From Prar Vasudevan's Field Report: At BJMC, I had the opportunity to make rounds in the hospital’s ART Clinic, Labor & Delivery wards, and children’s wards. I was immediately struck by the fact...

Up Close: Rupak Shivakoti

Post Date: 
2016-04-01
Improving Health of HIV-infected Mothers and their Infants in India Rupak Shivakoti’s work takes guts—no joke. “Our team is looking at whether inflammation, diet, and the gut microbiome of pregnant women are predictors of preterm delivery, low birth weight, and small-for-...

Advancing Global TB Research through RePORT

Post Date: 
2016-02-29
Regional Prospective Observational Research for Tuberculosis (RePORT) International is a large, international tuberculosis research effort being undertaken by 4 regional consortia: RePORT Brazil, RePORT South Africa, RePORT Indonesia, and RePORT India. While each region collects and maintains...