scholarly journals The Effect of Antiretroviral Therapy Initiation on the Vaginal Microbiome in HIV-Infected Women

2019 ◽  
Vol 6 (9) ◽  
Author(s):  
Cindy M Liu ◽  
Zoe R Packman ◽  
Alison G Abraham ◽  
David M Serwadda ◽  
Fred Nalugoda ◽  
...  
Keyword(s):  
Antiretroviral Therapy ◽  
Immune Reconstitution ◽  
Bacterial Load ◽  
Sub Saharan Africa ◽  
Rrna Gene ◽  
Host Immune System ◽  
Vaginal Microbiome ◽  
Microbiome Composition ◽  
Art Initiation ◽  
The Impact

Abstract Background The impact of antiretroviral therapy (ART) initiation on the vaginal microbiome is unknown. This is of particular importance among women living in sub-Saharan Africa. Understanding this relationship could help elucidate if and how the host immune system interacts with the vaginal microbiome. Methods The vaginal microbiome of HIV-1/HSV-2-coinfected women (n = 92) in Uganda was evaluated from self-collected vaginal swabs 1 month pre-ART and at 4 and 6 months post–ART initiation. The vaginal microbiome was characterized by 16S rRNA gene-based sequencing and quantitative polymerase chain reaction. Vaginal community state types (CSTs) were identified using proportional abundance data. Changes in microbiome composition were assessed with permutational analyses of variance (PerMANOVA). Results Five vaginal CSTs were identified, which varied significantly by bacterial load (P < .01): CST-1 was characterized by Lactobacillus iners, CST-2 by Gardnerella, CST-3 by Gardnerella and Prevotella, CST-4 by Lactobacillus crispatus, and CST-5 was highly diverse. Vaginal microbiome composition also did not change significantly after ART initiation (P = .985). Immune reconstitution after ART initiation did not affect vaginal microbiome CST assignment (P = .722) or individual-level changes in bacterial load (log response ratio [interquartile range], –0.50 [–2.75 to 0.38] vs –0.29 [–2.03 to 1.42]; P = .40). Conclusions The vaginal microbiome of HIV-infected women was not affected by the initiation of ART or immune reconstitution in this observational study. Further research is needed to explore the long-term effects of ART treatment on the vaginal microbiome.

scholarly journals Vaginal Microbiome Topic Modelling of Laboring Ugandan Women With and Without Fever

2020 ◽  
Author(s):  
Mercedeh Movassagh ◽  
Lisa M. Bebell ◽  
Kathy Burgoine ◽  
Christine Hehnly ◽  
Lijun Zhang ◽  
...  
Keyword(s):  
Topic Model ◽  
Neonatal Infection ◽  
Sub Saharan Africa ◽  
Mining Machine ◽  
Vaginal Microbiome ◽  
Microbiome Composition ◽  
Clinical Variables ◽  
Microbiome Research ◽  
Sub Saharan ◽  
The Impact

AbstractThe composition of the maternal vaginal microbiome may influence the duration of pregnancy, onset of labor and even neonatal outcomes. Maternal microbiome research in sub Saharan-Africa has focused on non-pregnant and postpartum composition of the vaginal microbiome. We examined the vaginal microbiome composition of 99 laboring Ugandan women using routine microbiology and 16S ribosomal DNA sequencing from two hypervariable regions (V1-V2 and V3-V4), using standard hierarchical methods. We then introduce Grades of Membership (GoM) modeling for the vaginal microbiome, a method often used in the text mining machine learning literature. Leveraging GoM models, we create a basis composed of a small number of microbial ‘topic’s whose linear combination optimally represents each patient yielding more accurate associations. We identified relationships between defined communities and the presentation or absence of intrapartum fever. Using a random forest model we showed that by including novel microbial topic models we improved upon clinical variables to predict maternal fever. We also show by integrating clinical variables with a microbial topic model into this model found young maternal age, fever report earlier in the current pregnancy, and longer labors, as well as a more diverse, less Lactobacillus dominated microbiome were features of labor associated with intrapartum fever. These results better define relationships between presentation or absence of intrapartum fever, demographics, peripartum course, and vaginal microbial communities, and improve our understanding of the impact of the microbiome on maternal and neonatal infection risk.

scholarly journals Exploring protocol bias in airway microbiome studies: one versus two PCR steps and 16S rRNA gene region V3 V4 versus V4

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Christine Drengenes ◽  
Tomas M. L. Eagan ◽  
Ingvild Haaland ◽  
Harald G. Wiker ◽  
Rune Nielsen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Load ◽  
Marker Gene ◽  
Gene Region ◽  
Lower Airway ◽  
Rrna Gene ◽  
Wide Range ◽  
Airway Microbiome ◽  
The Impact

Abstract Background Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the impact of number of polymerase chain reaction (PCR) steps (1- or 2- steps) and choice of target marker gene region (V3 V4 and V4) on the presentation of the upper and lower airway microbiome. Our analyses included lllumina MiSeq sequencing following three setups: Setup 1 (2-step PCR; V3 V4 region), Setup 2 (2-step PCR; V4 region), Setup 3 (1-step PCR; V4 region). Samples included oral wash, protected specimen brushes and protected bronchoalveolar lavage (healthy and obstructive lung disease), and negative controls. Results The number of sequences and amplicon sequence variants (ASV) decreased in order setup1 > setup2 > setup3. This trend appeared to be associated with an increased taxonomic resolution when sequencing the V3 V4 region (setup 1) and an increased number of small ASVs in setups 1 and 2. The latter was considered a result of contamination in the two-step PCR protocols as well as sequencing across multiple runs (setup 1). Although genera Streptococcus, Prevotella, Veillonella and Rothia dominated, differences in relative abundance were observed across all setups. Analyses of beta-diversity revealed that while oral wash samples (high biomass) clustered together regardless of number of PCR steps, samples from the lungs (low biomass) separated. The removal of contaminants identified using the Decontam package in R, did not resolve differences in results between sequencing setups. Conclusions Differences in number of PCR steps will have an impact of final bacterial community descriptions, and more so for samples of low bacterial load. Our findings could not be explained by differences in contamination levels alone, and more research is needed to understand how variations in PCR-setups and reagents may be contributing to the observed protocol bias.

scholarly journals Cardiovascular Biomarker Profile on Antiretroviral Therapy Is Not Influenced by History of an IRIS Event in People With HIV and Suppressed Viremia

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Aurelie Gouel-Cheron ◽  
Martha Nason ◽  
Adam Rupert ◽  
Virginia Sheikh ◽  
Greg Robby ◽  
...  
Keyword(s):  
Cardiovascular Risk ◽  
Antiretroviral Therapy ◽  
Chronic Inflammation ◽  
Immune Reconstitution Inflammatory Syndrome ◽  
Immune Reconstitution ◽  
Art Initiation ◽  
History Of ◽  
Cardiovascular Biomarker ◽  
Inflammatory Syndrome

Abstract Immune reconstitution inflammatory syndrome (IRIS) is characterized by release of proinflammatory cytokines and tissue inflammation occurring early after antiretroviral therapy (ART) initiation. The role of previous IRIS events in persistent chronic inflammation in people with HIV is currently unclear. In this retrospective analysis of 143 participants who maintained suppression of HIV viremia, we compared biomarkers related to inflammation, coagulation, and cardiovascular risk after 3 years on ART in participants with and without a history of IRIS. There was no evidence of higher levels of persistent chronic inflammation in people with HIV who had a history of an IRIS event. ClinicalTrials.gov Identifier . NCT00286767.

scholarly journals Trends in one-year cumulative incidence of death between 2005 and 2013 among patients initiating antiretroviral therapy in Uganda

2016 ◽  
Vol 28 (8) ◽  
pp. 800-807 ◽  
Author(s):  
Lisa M Bebell ◽  
Mark J Siedner ◽  
Nicholas Musinguzi ◽  
Yap Boum ◽  
Bosco M Bwana ◽  
...  
Keyword(s):  
Antiretroviral Therapy ◽  
Cumulative Incidence ◽  
Quality Care ◽  
Sub Saharan Africa ◽  
Ecological Data ◽  
Cd4 Cell Count ◽  
Infected People ◽  
Risk Of Death ◽  
Art Initiation ◽  
One Year

Recent ecological data demonstrate improving outcomes for HIV-infected people in sub-Saharan Africa. Recently, Uganda has experienced a resurgence in HIV incidence and prevalence, but trends in HIV-related deaths have not been well described. Data were collected through the Uganda AIDS Rural Treatment Outcomes (UARTO) Study, an observational longitudinal cohort of Ugandan adults initiating antiretroviral therapy (ART) between 2005 and 2013. We calculated cumulative incidence of death within one year of ART initiation, and fit Poisson models with robust variance estimators to estimate the effect enrollment period on one-year risk of death and loss to follow-up. Of 760 persons in UARTO who started ART, 30 deaths occurred within one year of ART initiation (cumulative incidence 3.9%, 95% confidence interval [CI] 2.7–5.6%). Risk of death was highest for those starting ART in 2005 (13.0%, 95% CI 6.0–24.0%), decreased in 2006–2007 to 4% (95% CI 2.0–6.0%), and did not change thereafter ( P = 0.61). These results were robust to adjustment for age, sex, CD4 cell count, viral load, asset wealth, baseline depression, and body mass index. Here, we demonstrate that one-year cumulative incidence of death was high just after free ART rollout, decreased the following year, and remained low thereafter. Once established, ART programs in President’s Emergency Fund for AIDS Relief-supported countries can maintain high quality care.

scholarly journals Predictors of Delayed Antiretroviral Therapy Initiation, Mortality, and Loss to Followup in HIV Infected Patients Eligible for HIV Treatment: Data from an HIV Cohort Study in India

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Gerardo Alvarez-Uria ◽  
Raghavakalyan Pakam ◽  
Manoranjan Midde ◽  
Praveen Kumar Naik
Keyword(s):  
Cohort Study ◽  
Antiretroviral Therapy ◽  
Rural Areas ◽  
Hiv Treatment ◽  
Cd4 Count ◽  
Sub Saharan Africa ◽  
Hiv Patients ◽  
Disadvantaged Community ◽  
Timely Initiation ◽  
Art Initiation

Studies from Sub-Saharan Africa have shown that a substantial number of HIV patients eligible for antiretroviral therapy (ART) do not start treatment. However, data from other low- or middle-income countries are scarce. In this study, we describe the outcomes of 4105 HIV patients who became ART eligible from January 2007 to November 2011 in an HIV cohort study in India. After three years of ART eligibility, 78.4% started ART, 9.3% died before ART initiation, and 10.3% were lost to followup. Diagnosis of tuberculosis, being homeless, lower CD4 count, longer duration of pre-ART care, belonging to a disadvantaged community, being widowed, and not living near a town were associated with delayed ART initiation. Diagnosis of tuberculosis, being homeless, lower CD4 count, shorter duration of pre-ART care, belonging to a disadvantaged community, illiteracy, and age >45 years were associated with mortality. Being homeless, being single, not living near a town, having a CD4 count <150 cells/μL, and shorter duration of pre-ART care were associated with loss to followup. These results highlight the need to improve the timely initiation of ART in HIV programmes in India, especially in ART eligible patients with tuberculosis, low CD4 counts, living in rural areas, or having a low socioeconomic status.

scholarly journals THE THE IMPACT OF ANTIRETROVIRAL THERAPY ON HEMOGLOBIN LEVELS OF HIV/AIDS PATIENTS AT MERPATI CLINIC, WANGAYA HOSPITAL, DENPASAR, BALI, INDONESIA

2020 ◽  
pp. 13-16
Author(s):  
PUTU DEWINTA DARMADA ◽  
KETUT SURYANA
Keyword(s):  
Antiretroviral Therapy ◽  
Total Sample ◽  
Hemoglobin Level ◽  
P Value ◽  
Aids Patients ◽  
Chi Square ◽  
Art Initiation ◽  
Chi Square Analysis ◽  
The Impact ◽  
Hiv Aids

Objective: Anemia is responsible for poor outcomes in HIV/AIDS patients. It’s related to disease progression, morbidity, and mortality. Antiretroviral therapy (ART) agent, zidovudine (ZDV) is also known to trigger anemia in the early initiation. However, studies found improved hemoglobin (Hb) levels of HIV/AIDS patients several months after ART routinely taken. This study aims to find the impact and correlation of ART on the hemoglobin level of HIV/AIDS patients. Methods: A retrospective cohort study was done at Merpati Clinic, Wangaya Hospital, Denpasar-Bali, Indonesia. Data were collected from medical records and laboratory results. A total sample of 64 HIV/AIDS patients with at least 6 mo on ART was included in this study. Results: Anemia was found in 34 (53.1%) of patients before ART initiation. After taking ART for 6 mo, we observed a significant improvement in patients’ hemoglobin levels, 48 (75%) shows increased hemoglobin levels. The paired t-test revealed a correlation between ART and Hb level (p<0.001). Fourteen (43.8%) patient taking ZDV shows no improvement, even declining of Hb level. Chi-square analysis performed with p = 0.001 to ZDV and lower or no improvement of hemoglobin level. Both results considered statistically significant (p-value less than 0.05) with a confidence interval (CI) of 95%. Relative risk (RR) of no improvement or decline in Hb level is 7 folds higher in the ZDV group than the non-ZDV group. Conclusion: This study concludes that ART affects hemoglobin levels in HIV/AIDS patients. Zidovudine regimen is more prone to lower or no increase of Hb.

scholarly journals Vaginal microbiome topic modeling of laboring Ugandan women with and without fever

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Mercedeh Movassagh ◽  
Lisa M. Bebell ◽  
Kathy Burgoine ◽  
Christine Hehnly ◽  
Lijun Zhang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Sub Saharan Africa ◽  
Vaginal Microbiome ◽  
Clustering Methods ◽  
Clinical Variables ◽  
Hypervariable Regions ◽  
Microbiome Research ◽  
Hierarchical Clustering Methods ◽  
Sub Saharan ◽  
The Impact

AbstractThe composition of the maternal vaginal microbiome influences the duration of pregnancy, onset of labor, and even neonatal outcomes. Maternal microbiome research in sub-Saharan Africa has focused on non-pregnant and postpartum composition of the vaginal microbiome. Here we aimed to illustrate the relationship between the vaginal microbiome of 99 laboring Ugandan women and intrapartum fever using routine microbiology and 16S ribosomal RNA gene sequencing from two hypervariable regions (V1–V2 and V3–V4). To describe the vaginal microbes associated with vaginal microbial communities, we pursued two approaches: hierarchical clustering methods and a novel Grades of Membership (GoM) modeling approach for vaginal microbiome characterization. Leveraging GoM models, we created a basis composed of a preassigned number of microbial topics whose linear combination optimally represents each patient yielding more comprehensive associations and characterization between maternal clinical features and the microbial communities. Using a random forest model, we showed that by including microbial topic models we improved upon clinical variables to predict maternal fever. Overall, we found a higher prevalence of Granulicatella, Streptococcus, Fusobacterium, Anaerococcus, Sneathia, Clostridium, Gemella, Mobiluncus, and Veillonella genera in febrile mothers, and higher prevalence of Lactobacillus genera (in particular L. crispatus and L. jensenii), Acinobacter, Aerococcus, and Prevotella species in afebrile mothers. By including clinical variables with microbial topics in this model, we observed young maternal age, fever reported earlier in the pregnancy, longer labor duration, and microbial communities with reduced Lactobacillus diversity were associated with intrapartum fever. These results better defined relationships between the presence or absence of intrapartum fever, demographics, peripartum course, and vaginal microbial topics, and expanded our understanding of the impact of the microbiome on maternal and potentially neonatal outcome risk.

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