Publications by authors named "Shannan N Rich"

9 Publications

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Challenges in replicating secondary analysis of electronic health records data with multiple computable phenotypes: A case study on methicillin-resistant Staphylococcus aureus bacteremia infections.

Int J Med Inform 2021 09 16;153:104531. Epub 2021 Jul 16.

Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA. Electronic address:

Background: Replication of prediction modeling using electronic health records (EHR) is challenging because of the necessity to compute phenotypes including study cohort, outcomes, and covariates. However, some phenotypes may not be easily replicated across EHR data sources due to a variety of reasons such as the lack of gold standard definitions and documentation variations across systems, which may lead to measurement error and potential bias. Methicillin-resistant Staphylococcus aureus (MRSA) infections are responsible for high mortality worldwide. With limited treatment options for the infection, the ability to predict MRSA outcome is of interest. However, replicating these MRSA outcome prediction models using EHR data is problematic due to the lack of well-defined computable phenotypes for many of the predictors as well as study inclusion and outcome criteria.

Objective: In this study, we aimed to evaluate a prediction model for 30-day mortality after MRSA bacteremia infection diagnosis with reduced vancomycin susceptibility (MRSA-RVS) considering multiple computable phenotypes using EHR data.

Methods: We used EHR data from a large academic health center in the United States to replicate the original study conducted in Taiwan. We derived multiple computable phenotypes of risk factors and predictors used in the original study, reported stratified descriptive statistics, and assessed the performance of the prediction model.

Results: In our replication study, it was possible to (re)compute most of the original variables. Nevertheless, for certain variables, their computable phenotypes can only be approximated by proxy with structured EHR data items, especially the composite clinical indices such as the Pitt bacteremia score. Even computable phenotype for the outcome variable was subject to variation on the basis of the admission/discharge windows. The replicated prediction model exhibited only a mild discriminatory ability.

Conclusion: Despite the rich information in EHR data, replication of prediction models involving complex predictors is still challenging, often due to the limited availability of validated computable phenotypes. On the other hand, it is often possible to derive proxy computable phenotypes that can be further validated and calibrated.
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http://dx.doi.org/10.1016/j.ijmedinf.2021.104531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8451470PMC
September 2021

Gut microbiome, body weight, and mammographic breast density in healthy postmenopausal women.

Cancer Causes Control 2021 Jul 27;32(7):681-692. Epub 2021 Mar 27.

H. Lee Moffitt Cancer Center, Tampa, FL, USA.

Purpose: We examined gut microbiome (GM) profiles in relation to mammographic breast density (BD) and body mass index (BMI) in healthy postmenopausal women.

Methods: Eligible women were postmenopausal, had a BMI ≤ 35 kg/m, and had not recently taken oral/IV antibiotics. All women provided a fecal sample and information on breast cancer risk factors. Mammographic BD was classified with the American College of Radiology's BI-RADS BD classification system. Bacterial DNA was isolated from fecal samples and the V1-V2 hypervariable regions of 16S rRNA were sequenced on the Illumina MiSeq platform. We examined associations of GM with indices of within-sample (alpha) diversity and the ratio of the two main phyla (Firmicutes and Bacteroidetes; F/B ratio) with BD and BMI.

Results: Among 69 women with BD data, 39 had low BD (BI-RADS I/II) and 30 had high BD (BI-RADS III/IV). BMI was inversely associated with BD (mean BMI = 23.8 and 28.0 in women with high and low BD, respectively, p = 1.07 × 10). Similar levels of GM diversity were found across weight groups according to Shannon (p = 0.83); Inverse Simpson (p = 0.97); and Chao1 (p = 0.31) indices. F/B ratio and microbiota diversity were suggestively greater in women with high vs. low BD (p = 0.35, 0.14, 0.15, and 0.17 for F/B ratio, Shannon, Inverse Simpson and Chao1, respectively).

Conclusion: Suggestive differences observed in women with high and low BD with respect to GM alpha diversity and prevalence of specific GM taxa need to be confirmed in larger studies.
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http://dx.doi.org/10.1007/s10552-021-01420-6DOI Listing
July 2021

Factors Contributing to Missing COVID-19 Cases During Contact Tracing.

JAMA Intern Med 2021 07;181(7):1014-1015

Department of Epidemiology, University of Florida College of Public Health and Health Professions and College of Medicine, Gainesville, Florida.

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http://dx.doi.org/10.1001/jamainternmed.2021.0077DOI Listing
July 2021

Brain tissue transcriptomic analysis of SIV-infected macaques identifies several altered metabolic pathways linked to neuropathogenesis and poly (ADP-ribose) polymerases (PARPs) as potential therapeutic targets.

J Neurovirol 2021 02 6;27(1):101-115. Epub 2021 Jan 6.

Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA.

Despite improvements in antiretroviral therapy, human immunodeficiency virus type 1 (HIV-1)-associated neurocognitive disorders (HAND) remain prevalent in subjects undergoing therapy. HAND significantly affects individuals' quality of life, as well as adherence to therapy, and, despite the increasing understanding of neuropathogenesis, no definitive diagnostic or prognostic marker has been identified. We investigated transcriptomic profiles in frontal cortex tissues of Simian immunodeficiency virus (SIV)-infected Rhesus macaques sacrificed at different stages of infection. Gene expression was compared among SIV-infected animals (n = 11), with or without CD8+ lymphocyte depletion, based on detectable (n = 6) or non-detectable (n = 5) presence of the virus in frontal cortex tissues. Significant enrichment in activation of monocyte and macrophage cellular pathways was found in animals with detectable brain infection, independently from CD8+ lymphocyte depletion. In addition, transcripts of four poly (ADP-ribose) polymerases (PARPs) were up-regulated in the frontal cortex, which was confirmed by real-time polymerase chain reaction. Our results shed light on involvement of PARPs in SIV infection of the brain and their role in SIV-associated neurodegenerative processes. Inhibition of PARPs may provide an effective novel therapeutic target for HIV-related neuropathology.
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http://dx.doi.org/10.1007/s13365-020-00927-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7786889PMC
February 2021

Risk factors for delayed viral suppression on first-line antiretroviral therapy among persons living with HIV in Haiti, 2013-2017.

PLoS One 2020 29;15(10):e0240817. Epub 2020 Oct 29.

College of Pharmacy, Institute for Pharmaceutical Outcomes and Policy, University of Kentucky, Lexington, KY, United States of America.

Studies of viral suppression on first-line antiretroviral therapy (ART) in persons living with human immunodeficiency virus (PLHIV) in Haiti are limited, particularly among PLHIV outside of the Ouest department, where the capital Port-au-Prince is located. This study described the prevalence and risk factors for delayed viral suppression among PLHIV in all geographic departments of Haiti between 2013 and 2017. Individuals who received viral load testing 3 to 12 months after ART initiation were included. Data on demographics and clinical care were obtained from the Haitian Active Longitudinal Tracking of HIV database. Multivariable logistic regression was performed to predict delayed viral suppression, defined as a viral load ≥1000 HIV-1 RNA copies/mL after at least 3 months on ART. Viral load test results were available for 3,368 PLHIV newly-initiated on ART. Prevalence of delayed viral suppression was 40%, which is slightly higher than previous estimates in Haiti. In the multivariable analysis, delayed viral suppression was significantly associated with younger age, receiving of care in the Ouest department, treatment with lamivudine (3TC), zidovudine (AZT), and nevirapine (NVP) combined ART regimen, and CD4 counts below 200 cells/mm3. In conclusion, this study was the first to describe and compare differences in delayed viral suppression among PLHIV by geographic department in Haiti. We identified populations to whom public health interventions, such as more frequent viral load testing, drug resistance testing, and ART adherence counseling should be targeted.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0240817PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7595392PMC
December 2020

Employing Molecular Phylodynamic Methods to Identify and Forecast HIV Transmission Clusters in Public Health Settings: A Qualitative Study.

Viruses 2020 08 22;12(9). Epub 2020 Aug 22.

Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, Gainesville, FL 32610, USA.

Molecular HIV surveillance is a promising public health strategy for curbing the HIV epidemic. Clustering technologies used by health departments to date are limited in their ability to infer/forecast cluster growth trajectories. Resolution of the spatiotemporal dynamics of clusters, through phylodynamic and phylogeographic modelling, is one potential strategy to develop a forecasting tool; however, the projected utility of this approach needs assessment. Prior to incorporating novel phylodynamic-based molecular surveillance tools, we sought to identify possible issues related to their feasibility, acceptability, interpretation, and utility. Qualitative data were collected via focus groups among field experts ( = 17, 52.9% female) using semi-structured, open-ended questions. Data were coded using an iterative process, first through the development of provisional themes and subthemes, followed by independent line-by-line coding by two coders. Most participants routinely used molecular methods for HIV surveillance. All agreed that linking molecular sequences to epidemiological data is important for improving HIV surveillance. We found that, in addition to methodological challenges, a variety of implementation barriers are expected in relation to the uptake of phylodynamic methods for HIV surveillance. The participants identified several opportunities to enhance current methods, as well as increase the usability and utility of promising works-in-progress.
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http://dx.doi.org/10.3390/v12090921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551766PMC
August 2020

Sociodemographic, Ecological, and Spatiotemporal Factors Associated with Human Immunodeficiency Virus Drug Resistance in Florida: A Retrospective Analysis.

J Infect Dis 2021 Mar;223(5):866-875

Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, USA.

Background: Persons living with human immunodeficiency virus (HIV) with resistance to antiretroviral therapy are vulnerable to adverse HIV-related health outcomes and can contribute to transmission of HIV drug resistance (HIVDR) when nonvirally suppressed. The degree to which HIVDR contributes to disease burden in Florida-the US state with the highest HIV incidence- is unknown.

Methods: We explored sociodemographic, ecological, and spatiotemporal associations of HIVDR. HIV-1 sequences (n = 34 447) collected during 2012-2017 were obtained from the Florida Department of Health. HIVDR was categorized by resistance class, including resistance to nucleoside reverse-transcriptase , nonnucleoside reverse-transcriptase , protease , and integrase inhibitors. Multidrug resistance and transmitted drug resistance were also evaluated. Multivariable fixed-effects logistic regression models were fitted to associate individual- and county-level sociodemographic and ecological health indicators with HIVDR.

Results: The HIVDR prevalence was 19.2% (nucleoside reverse-transcriptase inhibitor resistance), 29.7% (nonnucleoside reverse-transcriptase inhibitor resistance), 6.6% (protease inhibitor resistance), 23.5% (transmitted drug resistance), 13.2% (multidrug resistance), and 8.2% (integrase strand transfer inhibitor resistance), with significant variation by Florida county. Individuals who were older, black, or acquired HIV through mother-to-child transmission had significantly higher odds of HIVDR. HIVDR was linked to counties with lower socioeconomic status, higher rates of unemployment, and poor mental health.

Conclusions: Our findings indicate that HIVDR prevalence is higher in Florida than aggregate North American estimates with significant geographic and socioecological heterogeneity.
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http://dx.doi.org/10.1093/infdis/jiaa413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7938178PMC
March 2021

Impact of the 12 January 2010 earthquake on HIV case reporting in Haiti.

AIDS 2020 04;34(5):777-782

National Alliance of State and Territorial AIDS Directors (NASTAD).

Objective: To evaluate the impact of the 12 January 2010 earthquake on HIV cases from Haiti's national HIV surveillance system and assess the characteristics of people living with HIV 1-year before and after the earthquake.

Design: An interrupted time-series design and cross-sectional analysis.

Methods: We used autoregressive integrated moving average structures to model abrupt changes to the monthly, incident HIV case counts from HIV care clinics as reported to the Haitian Active Longitudinal Tracking of HIV System (French acronym SALVH) by clinical networks (n = 3) and earthquake instrumental intensity zones (n = 4). Preearthquake and postearthquake differences in patient-level characteristics including clinical values were examined using the χ test, t tests, Wilcoxon rank-sum test.

Results: In the month immediately following the earthquake, all three clinical networks experienced statistically significant declines in cases reported: iSanté (-31.4%), Groupe Haïtien d'Etude du Sarcome de Kaposi et des Infections Opportunistes (-29.9%) and Zamni Lasante (-32.2%). Zone 8 (the most severe) was the only area with a statistically significant decline (-45.5%). Of the three clinical networks, only iSanté returned to preearthquake reporting levels by the end of our study period. Patient-level characteristics did not change dramatically after the earthquake.

Conclusion: Despite case reporting declines, especially in clinics near the earthquake epicenter, SALVH remained intact with less impact than expected. This national system is a critical component of Haiti's strategic health information system initiative and plays a central role to HIV monitoring and evaluation efforts.
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http://dx.doi.org/10.1097/QAD.0000000000002466DOI Listing
April 2020
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