Improvements in the South African HIV care cascade: findings on 90-90-90 targets from successive population-representative surveys in North West Province.

IntroductionTo achieve epidemic control of HIV by 2030, countries aim to meet 90-90-90 targets to increase knowledge of HIV-positive status, initiation of antiretroviral therapy (ART) and viral suppression by 2020. We assessed the progress towards these targets from 2014 to 2016 in South Africa as expanded treatment policies were introduced using population-representative surveys.MethodsData were collected in January to March 2014 and August to November 2016 in Dr. Ruth Segomotsi Mompati District, North West Province. Each multi-stage cluster sample included 46 enumeration areas (EA), a target of 36 dwelling units (DU) per EA, and a single resident aged 18 to 49 per DU. Data collection included behavioural surveys, rapid HIV antibody testing and dried blood spot collection. We used weighted general linear regression to evaluate differences in the HIV care continuum over time.ResultsOverall, 1044 and 971 participants enrolled in 2014 and 2016 respectively with approximately 77% undergoing HIV testing. Despite increases in reported testing, known status among people living with HIV (PLHIV) remained similar at 68.7% (95% Confidence Interval (CI) = 60.9-75.6) in 2014 and 72.8% (95% CI = 63.6-80.4) in 2016. Men were consistently less likely than women to know their status. Among those with known status, PLHIV on ART increased significantly from 80.9% (95% CI = 71.9-87.4) to 91.5% (95% CI = 84.4-95.5). Viral suppression (<5000 copies/mL using DBS) among those on ART increased significantly from 55.0% (95% CI = 39.6-70.4) in 2014 to 81.4% (95% CI = 72.0-90.8) in 2016. Among all PLHIV an estimated 72.0% (95% CI = 63.8-80.1) of women and 45.8% (95% CI = 27.0-64.7) of men achieved viral suppression by 2016.ConclusionsOver a period during which fixed-dose combination was introduced, ART eligibility expanded, and efforts to streamline treatment were implemented, major improvements in the second and third 90-90-90 targets were achieved. Achieving the first 90 target will require targeted and improved testing models for men

Risk factors associated with the prevalence of Shiga-toxin-producing Escherichia coli in manured soils on certified organic farms in four regions of the USA

IntroductionBiological soil amendments of animal origin (BSAAO), including untreated amendments are often used to improve soil fertility and are particularly important in organic agriculture. However, application of untreated manure on cropland can potentially introduce foodborne pathogens into the soil and onto produce. Certified organic farms follow the USDA National Organic Program (NOP) standards that stipulate a 90- or 120-day interval between application of untreated manure and crop harvest, depending on whether the edible portion of the crop directly contacts the soil. This time-interval metric is based on environmental factors and does not consider a multitude of factors that might affect the survival of the main pathogens of concern. The objective of this study was to assess predictors for the prevalence of Shiga-toxin-producing Escherichia coli (non-O157 STEC) in soils amended with untreated manure on USDA-NOP certified farms.MethodsA longitudinal, multi-regional study was conducted on 19 farms in four USA regions for two growing seasons (2017–2018). Untreated manure (cattle, horse, and poultry), soil, and irrigation water samples were collected and enrichment cultured for non-O157 STEC. Mixed effects logistic regression models were used to analyze the predictors of non-O157 STEC in the soil up to 180 days post-manure application.Results and discussionResults show that farm management practices (previous use with livestock, presence of animal feces on the field, season of manure application) and soil characteristics (presence of generic E. coli in the soil, soil moisture, sodium) increased the odds of STEC-positive soil samples. Manure application method and snowfall decreased the odds of detecting STEC in the soil. Time-variant predictors (year and sampling day) affected the presence of STEC. This study shows that a single metric, such as the time interval between application of untreated manure and crop harvest, may not be sufficient to reduce the food safety risks from untreated manure, and additional environmental and farm-management practices should also be considered. These findings are of particular importance because they provide multi-regional baseline data relating to current NOP wait-time standards. They can therefore contribute to the development of strategies to reduce pathogen persistence that may contribute to contamination of fresh produce typically eaten raw from NOP-certified farms using untreated manure

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

Outcomes and costs of publicly funded patient navigation interventions to enhance HIV care continuum outcomes in the United States: A before-and-after study.

BackgroundIn the United States, patients with HIV face significant barriers to linkage to and retention in care which impede the necessary steps toward achieving the desired clinical outcome of viral suppression. Individual-level interventions, such as patient navigation, are evidence based, effective strategies for improving care engagement. In addition, use of surveillance and clinical data to identify patients who are not fully engaged in care may improve the effectiveness and cost-effectiveness of these programs.Methods and findingsWe employed a pre-post design to estimate the outcomes and costs, from the program perspective, of 5 state-level demonstration programs funded under the Health Resources and Services Administration's Special Projects of National Significance Program (HRSA/SPNS) Systems Linkages Initiative that employed existing surveillance and/or clinical data to identify individuals who had never entered HIV care, had fallen out of care, or were at risk of falling out of care and navigation strategies to engage patients in HIV care. Outcomes and costs were measured relative to standard of care during the first year of implementation of the interventions (2013 to 2014). We followed patients to estimate the number and proportion of additional patients linked, reengaged, retained, and virally suppressed by 12 months after enrollment in the interventions. We employed inverse probability weighting to adjust for differences in patient characteristics across programs, missing data, and loss to follow-up. We estimated the additional costs expended during the first year of each intervention and the cost per outcome of each intervention as the additional cost per HIV additional care continuum target achieved (cost per patient linked, reengaged, retained, and virally suppressed) 12 months after enrollment in each intervention. In this study, 3,443 patients were enrolled in Louisiana (LA), Massachusetts (MA), North Carolina (NC), Virginia (VA), and Wisconsin (WI) (147, 151, 2,491, 321, and 333, respectively). Patients were a mean of 40 years old, 75% male, and African American (69%) or Caucasian (22%). At baseline, 24% were newly diagnosed, 2% had never been in HIV care, 45% had fallen out of care, and 29% were at risk of falling out of care. All 5 interventions were associated with increases in the number and proportion of patients with viral suppression [percent increase: LA = 90.9%, 95% confidence interval (CI) = 88.4 to 93.4; MA = 78.1%, 95% CI = 72.4 to 83.8; NC = 47.5%, 95% CI = 45.2 to 49.8; VA = 54.6, 95% CI = 49.4 to 59.9; WI = 58.4, 95% CI = 53.4 to 63.4]. Overall, interventions cost an additional $4,415 (range =$3,746 to $5,619),$2,009 (range = $1,516 to$2,274), $920 (range =$627 to $941),$2,212 (range = $1,789 to$2,683), and $3,700 ($2,734 to $4,101), respectively per additional patient virally suppressed. The results of this study are limited in that we did not have contemporaneous controls for each intervention; thus, we are only able to assess patients against themselves at baseline and not against standard of care during the same time period.ConclusionsPatient navigation programs were associated with improvements in engagement of patients in HIV care and viral suppression. Cost per outcome was minimized in states that utilized surveillance data to identify individuals who were out of care and/or those that were able to identify a larger number of patients in need of improvement at baseline. These results have the potential to inform the targeting and design of future navigation-type interventions

Outcomes and costs of publicly funded patient navigation interventions to enhance HIV care continuum outcomes in the United States: A before-and-after study.

BackgroundIn the United States, patients with HIV face significant barriers to linkage to and retention in care which impede the necessary steps toward achieving the desired clinical outcome of viral suppression. Individual-level interventions, such as patient navigation, are evidence based, effective strategies for improving care engagement. In addition, use of surveillance and clinical data to identify patients who are not fully engaged in care may improve the effectiveness and cost-effectiveness of these programs.Methods and findingsWe employed a pre-post design to estimate the outcomes and costs, from the program perspective, of 5 state-level demonstration programs funded under the Health Resources and Services Administration's Special Projects of National Significance Program (HRSA/SPNS) Systems Linkages Initiative that employed existing surveillance and/or clinical data to identify individuals who had never entered HIV care, had fallen out of care, or were at risk of falling out of care and navigation strategies to engage patients in HIV care. Outcomes and costs were measured relative to standard of care during the first year of implementation of the interventions (2013 to 2014). We followed patients to estimate the number and proportion of additional patients linked, reengaged, retained, and virally suppressed by 12 months after enrollment in the interventions. We employed inverse probability weighting to adjust for differences in patient characteristics across programs, missing data, and loss to follow-up. We estimated the additional costs expended during the first year of each intervention and the cost per outcome of each intervention as the additional cost per HIV additional care continuum target achieved (cost per patient linked, reengaged, retained, and virally suppressed) 12 months after enrollment in each intervention. In this study, 3,443 patients were enrolled in Louisiana (LA), Massachusetts (MA), North Carolina (NC), Virginia (VA), and Wisconsin (WI) (147, 151, 2,491, 321, and 333, respectively). Patients were a mean of 40 years old, 75% male, and African American (69%) or Caucasian (22%). At baseline, 24% were newly diagnosed, 2% had never been in HIV care, 45% had fallen out of care, and 29% were at risk of falling out of care. All 5 interventions were associated with increases in the number and proportion of patients with viral suppression [percent increase: LA = 90.9%, 95% confidence interval (CI) = 88.4 to 93.4; MA = 78.1%, 95% CI = 72.4 to 83.8; NC = 47.5%, 95% CI = 45.2 to 49.8; VA = 54.6, 95% CI = 49.4 to 59.9; WI = 58.4, 95% CI = 53.4 to 63.4]. Overall, interventions cost an additional $4,415 (range =$3,746 to $5,619),$2,009 (range = $1,516 to$2,274), $920 (range =$627 to $941),$2,212 (range = $1,789 to$2,683), and $3,700 ($2,734 to $4,101), respectively per additional patient virally suppressed. The results of this study are limited in that we did not have contemporaneous controls for each intervention; thus, we are only able to assess patients against themselves at baseline and not against standard of care during the same time period.ConclusionsPatient navigation programs were associated with improvements in engagement of patients in HIV care and viral suppression. Cost per outcome was minimized in states that utilized surveillance data to identify individuals who were out of care and/or those that were able to identify a larger number of patients in need of improvement at baseline. These results have the potential to inform the targeting and design of future navigation-type interventions

Outcomes and costs of publicly funded patient navigation interventions to enhance HIV care continuum outcomes in the United States: A before-and-after study.

BackgroundIn the United States, patients with HIV face significant barriers to linkage to and retention in care which impede the necessary steps toward achieving the desired clinical outcome of viral suppression. Individual-level interventions, such as patient navigation, are evidence based, effective strategies for improving care engagement. In addition, use of surveillance and clinical data to identify patients who are not fully engaged in care may improve the effectiveness and cost-effectiveness of these programs.Methods and findingsWe employed a pre-post design to estimate the outcomes and costs, from the program perspective, of 5 state-level demonstration programs funded under the Health Resources and Services Administration's Special Projects of National Significance Program (HRSA/SPNS) Systems Linkages Initiative that employed existing surveillance and/or clinical data to identify individuals who had never entered HIV care, had fallen out of care, or were at risk of falling out of care and navigation strategies to engage patients in HIV care. Outcomes and costs were measured relative to standard of care during the first year of implementation of the interventions (2013 to 2014). We followed patients to estimate the number and proportion of additional patients linked, reengaged, retained, and virally suppressed by 12 months after enrollment in the interventions. We employed inverse probability weighting to adjust for differences in patient characteristics across programs, missing data, and loss to follow-up. We estimated the additional costs expended during the first year of each intervention and the cost per outcome of each intervention as the additional cost per HIV additional care continuum target achieved (cost per patient linked, reengaged, retained, and virally suppressed) 12 months after enrollment in each intervention. In this study, 3,443 patients were enrolled in Louisiana (LA), Massachusetts (MA), North Carolina (NC), Virginia (VA), and Wisconsin (WI) (147, 151, 2,491, 321, and 333, respectively). Patients were a mean of 40 years old, 75% male, and African American (69%) or Caucasian (22%). At baseline, 24% were newly diagnosed, 2% had never been in HIV care, 45% had fallen out of care, and 29% were at risk of falling out of care. All 5 interventions were associated with increases in the number and proportion of patients with viral suppression [percent increase: LA = 90.9%, 95% confidence interval (CI) = 88.4 to 93.4; MA = 78.1%, 95% CI = 72.4 to 83.8; NC = 47.5%, 95% CI = 45.2 to 49.8; VA = 54.6, 95% CI = 49.4 to 59.9; WI = 58.4, 95% CI = 53.4 to 63.4]. Overall, interventions cost an additional $4,415 (range =$3,746 to $5,619),$2,009 (range = $1,516 to$2,274), $920 (range =$627 to $941),$2,212 (range = $1,789 to$2,683), and $3,700 ($2,734 to $4,101), respectively per additional patient virally suppressed. The results of this study are limited in that we did not have contemporaneous controls for each intervention; thus, we are only able to assess patients against themselves at baseline and not against standard of care during the same time period.ConclusionsPatient navigation programs were associated with improvements in engagement of patients in HIV care and viral suppression. Cost per outcome was minimized in states that utilized surveillance data to identify individuals who were out of care and/or those that were able to identify a larger number of patients in need of improvement at baseline. These results have the potential to inform the targeting and design of future navigation-type interventions

Attrition and Opportunities Along the HIV Care Continuum

BackgroundAttrition along the HIV care continuum slows gains in mitigating the South African HIV epidemic. Understanding population-level gaps in HIV identification, linkage, retention in care, and viral suppression is critical to target programming.MethodsWe conducted a population-based household survey, HIV rapid testing, point-of-care CD4 testing, and viral load measurement from dried blood spots using multistage cluster sampling in 2 subdistricts of North West Province from January to March, 2014. We used weighting and multiple imputation of missing data to estimate HIV prevalence, undiagnosed infection, linkage and retention in care, medication adherence, and viral suppression.ResultsWe sampled 1044 respondents aged 18-49. HIV prevalence was 20.0% (95% confidence interval: 13.7 to 26.2) for men and 26.7% (95% confidence interval: 22.1 to 31.4) for women. Among those HIV positive, 48.4% of men and 75.7% of women were aware of their serostatus; 44.0% of men and 74.8% of women reported ever linking to HIV care; 33.1% of men and 58.4% of women were retained in care; and 21.6% of men and 50.0% of women had dried blood spots viral loads <5000 copies per milliliter. Among those already linked to care, 81.7% on antiretroviral treatment (ART) and 56.0% of those not on ART were retained in care, and 51.8% currently retained in care on ART had viral loads <5000 copies per milliliter.ConclusionsDespite expanded treatment in South Africa, attrition along the continuum of HIV care is slowing prevention progress. Improved detection is critically needed, particularly among men. Reported linkage and retention is reasonable for those on ART; however, failure to achieve viral suppression is worrisome

Impact of SMS and peer navigation on retention in HIV care among adults in South Africa: results of a three-arm cluster randomized controlled trial.

IntroductionFew interventions have demonstrated improved retention in care for people living with HIV (PLHIV) in sub-Saharan Africa. We tested the efficacy of two personal support interventions - one using text messaging (SMS-only) and the second pairing SMS with peer navigation (SMS+PN) - to improve HIV care retention over one year.MethodsIn a cluster randomized control trial (NCT# 02417233) in North West Province, South Africa, we randomized 17 government clinics to three conditions: SMS-only (6), SMS+PN (7) or standard of care (SOC; 4). Participants at SMS-only clinics received appointment reminders, biweekly healthy living messages and twice monthly SMS check-ins. Participants at SMS+PN clinics received SMS appointment reminders and healthy living messages and spoke at least twice monthly with peer navigators (PLHIV receiving care) to address barriers to care. Outcomes were collected through biweekly clinical record extraction and surveys at baseline, six and 12 months. Retention in HIV care over one year was defined as clinic visits every three months for participants on antiretroviral therapy (ART) and CD4 screening every six months for pre-ART participants. We used generalized estimating equations, adjusting for clustering by clinic, to test for differences across conditions.ResultsBetween October 2014 and April 2015, we enrolled 752 adult clients recently diagnosed with HIV (SOC: 167; SMS-only: 289; SMS+PN: 296). Individuals in the SMS+PN arm had approximately two more clinic visits over a year than those in other arms (p < 0.01) and were more likely to be retained in care over one year than those in SOC clinics (54% vs. 38%; OR: 1.77, CI: 1.02, 3.10). Differences between SMS+PN and SOC conditions remained significant when restricting analyses to the 628 participants on ART (61% vs. 45% retained; OR: 1.78, CI: 1.08, 2.93). The SMS-only intervention did not improve retention relative to SOC (40% vs. 38%, OR: 1.12, CI: 0.63, 1.98).ConclusionsA combination of SMS appointment reminders with personalized, peer-delivered support proved effective at enhancing retention in HIV care over one year. While some clients may only require appointment reminders, the SMS+PN approach offers increased flexibility and tailored, one-on-one support for patients struggling with more substantive challenges