Cryo-EM analysis of Pseudomonas phage Pa193 structural components.

The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various clinical settings, commonly called phage therapy, to address this growing public health crisis. Here, we describe a high-resolution structural atlas of a therapeutic, contractile-tailed Pseudomonas phage, Pa193. We used bioinformatics, proteomics, and cryogenic electron microscopy single particle analysis to identify, annotate, and build atomic models for 21 distinct structural polypeptide chains forming the icosahedral capsid, neck, contractile tail, and baseplate. We identified a putative scaffolding protein stabilizing the interior of the capsid 5-fold vertex. We also visualized a large portion of Pa193 ~ 500 Å long tail fibers and resolved the interface between the baseplate and tail fibers. The work presented here provides a framework to support a better understanding of phages as biomedicines for phage therapy and inform engineering opportunities.

The effects of a novel, continuous disinfectant technology on methicillin-resistant Staphylococcus aureus (MRSA), fungi, and aerobic bacteria in 2 separate intensive care units in 2 different states: An experimental design with observed impact on health care associated infections (HAIs).

BACKGROUND: Hospitals are exposed to abundant contamination sources with limited remediation strategies. Without new countermeasures or treatments, the risk of health care-associated infections will remain high. This study explored the impact of advanced photohydrolysis continuous disinfection technology on hospital environmental bioburden. METHODS: Two acute care intensive care units in different locations (ie, Kentucky, Louisiana) during different time periods were sampled every 4 weeks for 4 months for colony-forming units (CFUs) of methicillin-resistant Staphylococcus aureus (MRSA) and fungi on surfaces and floors and fungi and aerobic bacteria in the air. RESULTS: At both sites, surface testing showed greater than 98% reduction in mean fungi and MRSA CFUs. Floor results had reductions by more than 96% for fungi and MRSA at both sites. Aerobic bacterial air and fungal CFUs had reductions up to 72% and 89%, respectively. HAIs declined 70% when postactivation data were compared to preactivation data. DISCUSSION: The continuous nature of advanced photohydrolysis decontamination, its ability to be used in occupied rooms, and its independence of human resources provide an innovative intervention for complex health care environments. CONCLUSIONS: This study is on the pioneering edge of demonstrating that continuous decontamination can reduce surface, floor, and air contamination and thereby reduce the acquisition of HAIs.

The evolution of DREAMS: using data for continuous program improvement.

The DREAMS (Determined, Resilient, Empowered, AIDS-Free, Mentored, and Safe) Partnership, a public-private partnership launched by the United States President's Emergency Plan for AIDS Relief (PEPFAR), represents the largest investment in comprehensive HIV prevention for adolescent girls and young women (AGYW) ever made in a single global initiative. This paper describes the evolution of programming over time using the triangulation of multiple data sources to develop and refine an impactful program, as well as to improve efficacy and resource investment. Methods of analysis used to evolve this programming include reviews of literature on behavioral, biomedical and structural interventions, and HIV vulnerability; PEPFAR program data; external implementation science and impact studies;observations from site visits; in-depth reviews of program materials; and inputs from AGYW and other stakeholders. Key program improvements made in response to this real-time data use are described, including the rationale for programmatic changes and the evidence base for continual program refinements. This review emphasizes the importance and process of implementing the most effective combination of structural and biomedical HIV prevention programming, based on the best available science, while also adapting to local context in a way that does not compromise effectiveness or violate core implementation principles. Data from research and evaluation are critical to move the HIV prevention field toward more impactful and efficient programming responsive to the lived realities of AGYW. A central tenant to using these data sources effectively is the inclusion of AGYW in decision-making throughout the planning and implementation of programming.

Modeling DREAMS impact: trends in new HIV diagnoses among women attending antenatal care clinics in DREAMS countries.

OBJECTIVES: To understand the impact of United States President's Emergency Plan for AIDS Relief (PEPFAR's) DREAMS (Determined, Resilient, Empowered, AIDS-Free, Mentored, and Safe) Partnership on new HIV diagnoses among women in antenatal care (ANC) settings in 10 African countries from 2015 to 2020. DESIGN: We modeled spatiotemporal changes in new HIV diagnoses among women in ANC settings using PEPFAR data. Statistical tests were performed in R to compare differences in new diagnoses rates between DREAMS and non-DREAMS subnational units (SNUs) and to explore predictors of new diagnoses declines within DREAMS SNUs. METHODS: We used a predictive geospatial model to forecast the rate of new diagnoses for each time period in a 5 km grid cell (n = 861 SNUs). Linear model analyses were conducted using predictor variables: urbanicity, DREAMS geographic footprint, 'layering' proxy, and community-level male viral load suppression. RESULTS: New HIV diagnoses in ANC from 2015 to 2020 declined in nearly all SNUs. 'Always' DREAMS SNUs reported declines of 45% while 'Never' DREAMS SNUs reported a decline of only 37% (F = 8.1, 1 and 829 DF, P < 0.01). Within Always DREAMS SNUs, greater declines were seen in areas with a higher number of minimum services in their DREAMS primary package (t = 2.77, P < 0.01). CONCLUSION: New HIV diagnoses among women are declining in both DREAMS and non-DREAMS SNUs; mirroring HIV incidence decreases and reflecting increasing community viral load suppression and voluntary male medical circumcision rates. DREAMS programming may have contributed to accelerated declines of new HIV diagnoses in DREAMS SNUs compared with non-DREAMS SNUs. Increased progress is needed to further reduce the disparities between adolescent girls and young women (AGYW) and young men to achieve epidemic control.

Association of the US President's Emergency Plan for AIDS Relief's Funding With Prevention of Mother-to-Child Transmission of HIV in Kenya.

Importance: From 2004 to 2014, the US President's Emergency Plan for AIDS Relief (PEPFAR) invested more than $248 000 000 in the prevention of mother-to-child transmission (PMTCT) of HIV in Kenya. Concurrently, child mortality in Kenya decreased by half. Objective: To identify the extent to which the decrease in child mortality in Kenya is associated with PEPFAR funding for PMTCT of HIV. Design, Setting, and Participants: This population-based survey study conducted in Kenya estimated the association between annual per capita PEPFAR funding for PMTCT (annual PCF) and cumulative per capita PEPFAR funding for PMTCT (cumulative PCF), extracted using 2004-2014 country operational reports as well as individual-level health outcomes, extracted from the 2003, 2008-2009, and 2014 Kenya Demographic and Health Surveys and the 2007 and 2012 Kenya AIDS Indicator Surveys. The study included children of female respondents to the 2003, 2008-2009, and 2014 Kenya Demographic and Health Surveys who were born 1 to 60 months (for neonatal mortality) or 12 to 60 months (for infant mortality) before the survey, as well as female respondents who had recently given birth and reported on HIV testing during antenatal care (ANC) during the 2007-2014 surveys. Results were adjusted for year, province, and survey respondent characteristics. Statistical analysis was performed from July 8, 2016, to December 10, 2018. Main Outcomes and Measures: Neonatal mortality was defined as death within the first month of life and infant mortality was defined as death within the first year of life. HIV testing during ANC was defined as receiving counseling on PMTCT, undergoing an HIV test, and receiving test results during ANC. Results: The analysis included 33 181 neonates (16 870 boys), 26 876 infants (13 679 boys), and 20 775 mothers (mean [SD] age, 28.0 [6.7] years). PEPFAR funding was not associated with neonatal mortality. A $0.33 increase in annual PCF, corresponding to the difference between the 75th and 25th (interquartile range) percentiles of funding, was significantly associated with a 16% (95% CI, 4%-27%) reduction in infant mortality after a 1-year lag. A 14% to 16% reduction persisted after 2- and 3-year lags, and comparable reductions were observed for unlagged and 1-year lagged cumulative PCF. An increase of 1 interquartile range in cumulative PCF was associated with a 7% (95% CI, 3%-11%) increase in HIV testing during ANC, which intensified with subsequent lags. Between 2004 and 2014, sustained funding levels of $0.33 annual PCF could have averted 118 039 to 273 924 infant deaths. Conclusions and Relevance: Evidence from publicly available data suggests that PEPFAR's PMTCT funding was associated with a reduction in infant mortality and an increase in HIV testing during ANC in Kenya. The full outcome of funding may not be realized until several years after allocation.

Laboratory medicine in Africa since 2008: then, now, and the future.

The Maputo Declaration of 2008 advocated for commitment from global stakeholders and national governments to prioritise support and harmonisation of laboratory systems through development of comprehensive national laboratory strategies and policies in sub-Saharan Africa. As a result, HIV laboratory medicine in Africa has undergone a transformation, and substantial improvements have been made in diagnostic services, networks, and institutions, including the development of a competent workforce, introduction of point-of-care diagnostics, and innovative quality improvement programmes that saw more than 1100 laboratories enrolled and 44 accredited to international standards. These improved HIV laboratories can now be used to combat emerging continental and global health threats in the decades to come. For instance, the unprecedented Ebola virus disease outbreak in west Africa exposed the severe weaknesses in the overall national health systems in affected countries. It is now possible to build robust health-care systems in Africa and to combat emerging continental and global health threats in the future. In this Personal View, we aim to describe the remarkable transformation that has occurred in laboratory medicine to combat HIV/AIDS and improve global health in sub-Saharan Africa since 2008.

Expansion of Viral Load Testing and the Potential Impact on HIV Drug Resistance.

The US President's Emergency Plan for AIDS Relief (PEPFAR) supports aggressive scale-up of antiretroviral therapy (ART) in high-burden countries and across all genders and populations at risk toward global human immunodeficiency virus (HIV) epidemic control. PEPFAR recognizes the risk of HIV drug resistance (HIVDR) as a consequence of aggressive ART scale-up and is actively promoting 3 key steps to mitigate the impact of HIVDR: (1) routine access to routine viral load monitoring in all settings; (2) optimization of ART regimens; and (3) routine collection and analysis of HIVDR data to monitor the success of mitigation strategies. The transition to dolutegravir-based regimens in PEPFAR-supported countries and the continuous evolution of HIVDR surveillance strategies are essential elements of PEPFAR implementation.

Prevention of HIV in Adolescent Girls and Young Women: Key to an AIDS-Free Generation.

The Global Plan towards the elimination of new HIV infections among children by 2015 and keeping their mothers alive (Global Plan) has ensured that more infants in high-HIV burden countries survive childhood HIV-free. Although equal numbers of boy and girl children have survived to age 10, a gender divergence starts to emerge as they enter adolescence. Up to 3 times as many young women aged 15-24 years in eastern and southern Africa are living with HIV compared with their male peers. Further, more adolescent girls and young women are sick and/or dying from AIDS-related or HIV-related complications during pregnancy and in the postpartum period, underscoring the importance of strengthening HIV treatment and prevention services for this group. Failure to prevent HIV in adolescent girls and young women and keep them alive will reverse the infant HIV prevention and survival gains made under the Global Plan. The promising global declines in HIV infection in young women need to be strengthened to realize the goals of an AIDS-free generation. The DREAMS initiative of the United States President's Emergency Plan for AIDS Relief (PEPFAR), which specifically addresses adolescent girls and young women at highest risk of HIV acquisition, brings new hope for meeting the prevention and care needs of this important and vulnerable population through political commitment, leadership, financial and human resource investments, advocacy efforts, and a focus on the highest priority settings. Importantly, to achieve the goal of keeping mothers alive, we have to place more emphasis on access to sexual and reproductive health services that (1) include HIV prevention and treatment services for adolescent girls and young women; (2) increase male/paternal responsibility in mother and infant health; and (3) ensure a supportive social environment that enables young women to grow up into young adults who are free to graduate from high school and plan their pregnancies, ultimately entering adulthood safe, healthy, and free from HIV.

HIV-1 Genetic Diversity Among Incident Infections in Mbeya, Tanzania.

In preparation for vaccine trials, HIV-1 genetic diversity was surveyed between 2002 and 2006 through the Cohort Development study in the form of a retrospective and prospective observational study in and around the town of Mbeya in Tanzania's Southwest Highlands. This study describes the molecular epidemiology of HIV-1 strains obtained from 97 out of 106 incident HIV-1 infections identified in three subpopulations of participants (one rural, two urban) from the Mbeya area. Near full-genome or half-genome sequencing showed a subtype distribution of 40% C, 17% A1, 1% D, and 42% inter-subtype recombinants. Compared to viral subtyping results previously obtained from the retrospective phase of this study, the overall proportion of incident viral strains did not change greatly during the study course, suggesting maturity of the epidemic. A comparison to a current Phase I-II vaccine being tested in Africa shows ∼17% amino acid sequence difference between the gp120 of the vaccine and subtype C incident strains. Phylogenetic and recombinant breakpoint analysis of the incident strains revealed the emergence of CRF41_CD and many unique recombinants, as well as the presence of six local transmission networks most of which were confined to the rural subpopulation. In the context of vaccine cohort selection, these results suggest distinct infection transmission dynamics within these three geographically close subpopulations. The diversity and genetic sequences of the HIV-1 strains obtained during this study will greatly contribute to the planning, immunogen selection, and analysis of vaccine-induced immune responses observed during HIV-1 vaccine trials in Tanzania and neighboring countries.

Sequential Dysfunction and Progressive Depletion of Candida albicans-Specific CD4 T Cell Response in HIV-1 Infection.

Loss of immune control over opportunistic infections can occur at different stages of HIV-1 (HIV) disease, among which mucosal candidiasis caused by the fungal pathogen Candida albicans (C. albicans) is one of the early and common manifestations in HIV-infected human subjects. The underlying immunological basis is not well defined. We have previously shown that compared to cytomegalovirus (CMV)-specific CD4 cells, C. albicans-specific CD4 T cells are highly permissive to HIV in vitro. Here, based on an antiretroviral treatment (ART) naïve HIV infection cohort (RV21), we investigated longitudinally the impact of HIV on C. albicans- and CMV-specific CD4 T-cell immunity in vivo. We found a sequential dysfunction and preferential depletion for C. albicans-specific CD4 T cell response during progressive HIV infection. Compared to Th1 (IFN-γ, MIP-1ß) functional subsets, the Th17 functional subsets (IL-17, IL-22) of C. albicans-specific CD4 T cells were more permissive to HIV in vitro and impaired earlier in HIV-infected subjects. Infection history analysis showed that C. albicans-specific CD4 T cells were more susceptible to HIV in vivo, harboring modestly but significantly higher levels of HIV DNA, than CMV-specific CD4 T cells. Longitudinal analysis of HIV-infected individuals with ongoing CD4 depletion demonstrated that C. albicans-specific CD4 T-cell response was preferentially and progressively depleted. Taken together, these data suggest a potential mechanism for earlier loss of immune control over mucosal candidiasis in HIV-infected patients and provide new insights into pathogen-specific immune failure in AIDS pathogenesis.

Safety and Immunogenicity of a Randomized Phase 1 Prime-Boost Trial With ALVAC-HIV (vCP205) and Oligomeric Glycoprotein 160 From HIV-1 Strains MN and LAI-2 Adjuvanted in Alum or Polyphosphazene.

BACKGROUND: Prime-boost regimens comprising ALVAC-HIV (prime) and human immunodeficiency virus type 1 (HIV) Env (boost) induce HIV-specific neutralizing antibody and cell-mediated immune responses, but the impact of boost schedule and adjuvant requires further definition. METHODS: A phase 1 trial was conducted. In part A (open label), 19 volunteers received oligomeric glycoprotein 160 from HIV strains MN and LAI-2 (ogp160 MN/LAI-2) with dose escalation (25, 50, 100 µg) and either polyphosphazene (pP) or alum adjuvant. In part B, 72 volunteers received either placebo (n=12) or recombinant canarypox virus expressing HIV antigens (ALVAC-HIV [vCP205]) with different doses and schedules of ogp160 MN/LAI-2 in pP or alum (n = 60). RESULTS: The vaccines were safe and well tolerated, with no vaccine-related serious adverse events. Anti-gp70 V1V2 antibody responses were detected in 17 of 19 part A volunteers (89%) and 10%-100% of part B volunteers. Use of a peripheral blood mononuclear cell-based assay revealed that US-1 primary isolate neutralization was induced in 2 of 19 recipients of ogp160 protein alone (10.5%) and 5 of 49 prime-boost volunteers (10.2%). Among ogp160 recipients, those who received pP were more likely than those who received alum to have serum that neutralized tier 2 viruses (12% vs 0%; P = .015). CONCLUSIONS: Administration of ogp160 with pP induces primary isolate tier 2 neutralizing antibody responses in a small percentage of volunteers, demonstrating proof of concept and underscoring the importance of further optimization of prime-boost strategies for HIV infection prevention. CLINICAL TRIALS REGISTRATION: NCT00004579.

The Number and Complexity of Pure and Recombinant HIV-1 Strains Observed within Incident Infections during the HIV and Malaria Cohort Study Conducted in Kericho, Kenya, from 2003 to 2006.

Characterization of HIV-1 subtype diversity in regions where vaccine trials are conducted is critical for vaccine development and testing. This study describes the molecular epidemiology of HIV-1 within a tea-plantation community cohort in Kericho, Kenya. Sixty-three incident infections were ascertained in the HIV and Malaria Cohort Study conducted in Kericho from 2003 to 2006. HIV-1 strains from 58 of those individuals were full genome characterized and compared to two previous Kenyan studies describing 41 prevalent infections from a blood bank survey (1999-2000) and 21 infections from a higher-risk cohort containing a mix of incident and prevalent infections (2006). Among the 58 strains from the community cohort, 43.1% were pure subtypes (36.2% A1, 5.2% C, and 1.7% G) and 56.9% were inter-subtype recombinants (29.3% A1D, 8.6% A1CD, 6.9% A1A2D, 5.2% A1C, 3.4% A1A2CD, and 3.4% A2D). This diversity and the resulting genetic distance between the observed strains will need to be addressed when vaccine immunogens are chosen. In consideration of current vaccine development efforts, the strains from these three studies were compared to five candidate vaccines (each of which are viral vectored, carrying inserts corresponding to parts of gag, pol, and envelope), which have been developed for possible use in sub-Saharan Africa. The sequence comparison between the observed strains and the candidate vaccines indicates that in the presence of diverse recombinants, a bivalent vaccine is more likely to provide T-cell epitope coverage than monovalent vaccines even when the inserts of the bivalent vaccine are not subtype-matched to the local epidemic.