Determinants and rates of retention in HIV care among adolescents receiving antiretroviral therapy in Windhoek, Namibia: A baseline cohort analysis

Long-term engagement in HIV care is essential to achieving and maintaining viral suppression. Adolescents living with HIV (ALHIV) experience many barriers to remaining engaged in care and treatment programs. Higher attrition among adolescents compared to adults remains a huge concern due to unique psychosocial and health systems challenges adolescents face, and recently the COVID-19 pandemic effects. We report on determinants and rates of retention in care in adolescents aged 10–19 years enrolled on antiretroviral therapy (ART) in Windhoek, Namibia. A retrospective cohort analysis of routine clinical data of 695 adolescents aged 10–19 years enrolled for ART at 13 Windhoek district public healthcare facilities, between January 2019 and December 2021 was conducted. Anonymized patient data were extracted from an electronic database and registers. Bivariate and Cox proportional hazards analysis were performed to determine factors associated with retention in care among ALHIV at 6, 12, 18, 24 and 36 months. Retention in care trends were also described using the Kaplan-Meier survival analysis

Whole genome sequencing and identification of Bacillus endophyticus and B. anthracis isolated from anthrax outbreaks in South Africa

Abstract Background Bacillus endophyticus is a soil plant-endophytic bacterium, while B. anthracis is the causative agent of anthrax. The virulence factors of B. anthracis are the plasmid encoded tripartite toxins (pXO1) and poly-γ-glutamic acid (PGA) capsule (pXO2). B. endophyticus isolated alongside B. anthracis from animals that died of anthrax in Northern Cape Province (NCP), South Africa, harbored polyglutamate genes. The study compared the characteristics of B. anthracis and B. endophyticus with other Bacillus species with a focus on the presence of the PGA capsule or/and unbound PGA. The morphology and whole genome sequence analysis of B. endophyticus strains and B. anthracis were compared. Results In conventional microbiology, B. endophyticus showed gram-positive round-shaped rods in single/short chains, which were endospore-forming, non-motile, non-haemolytic with white and dry colonies, and γ-phage resistant. B. anthracis was differentiated from B. endophyticus based on the latter’s box-shaped rods in pairs/long chains, white-grey and slimy colonies, encapsulated and γ-phage susceptible. The study identified a PGA polyglutamate synthase operon that consisted of pgsBCA, γ-glutamyltranspeptidase (ggt) and pgsE in B. endophyticus genomes. Conclusions PGA regions of B. anthracis contain capBCADE genes located in the pXO2 required for capsulation formation, while B. endophyticus contain the pgsBCAE genes in the chromosome. Whole genome and microbiology analysis identified B. endophyticus, as a non-capsuled endospore-forming bacterium that consists of PGA required for biosynthesis. B. endophyticus strains do not synthesize surface associated PGA, therefore capsule visualization of B. anthracis is a key diagnostic characteristic. The study highlights the significance of using whole genome shotgun sequencing to identify virulence and other important genes that might be present amongst unknown samples from natural outbreaks. None of the B. anthracis related plasmids or virulence genes were found in the B. endophyticus genomes

Structural basis for activation of calcineurin by calmodulin

The highly conserved phosphatase calcineurin plays vital roles in numerous processes including T-cell activation, development and function of the central nervous system, and cardiac growth. It is activated by the calcium sensor calmodulin. Calmodulin binds to a regulatory domain within calcineurin, causing a conformational change that displaces an autoinhibitory domain from the active site, resulting in activation of the phosphatase. This is the same general mechanism by which calmodulin activates calmodulin-dependent protein kinases. Previously published data has hinted that the regulatory domain of calcineurin is intrinsically disordered. In this work we demonstrate that the regulatory domain is unstructured and that it folds upon binding calmodulin, ousting the autoinhibitory domain from the catalytic site. The regulatory domain is 95 residues long, with the autoinhibitory domain attached to its C-terminal end and the 24 residue calmodulin binding region towards the N-terminal end. This is unlike the calmodulin-dependent protein kinases which have calmodulin binding sites and autoinhibitory domains immediately adjacent in sequence. Our data demonstrate that not only does the calmodulin binding region fold, but that an ~25-30 residue region between it and the autoinhibitory domain also folds, resulting in over half of the regulatory domain adopting α-helical structure. This appears to be the first observation of calmodulin inducing folding of this scale outside of its binding site on a target protein

Structural Basis for Activation of Calcineurin by Calmodulin

The highly conserved phosphatase calcineurin (CaN) plays vital roles in numerous processes including T-cell activation, development and function of the central nervous system, and cardiac growth. It is activated by the calcium sensor calmodulin (CaM). CaM binds to a regulatory domain (RD) within CaN, causing a conformational change that displaces an autoinhibitory domain (AID) from the active site, resulting in activation of the phosphatase. This is the same general mechanism by which CaM activates CaM-dependent protein kinases. Previously published data have hinted that the RD of CaN is intrinsically disordered. In this work, we demonstrate that the RD is unstructured and that it folds upon binding CaM, ousting the AID from the catalytic site. The RD is 95 residues long, with the AID attached to its C-terminal end and the 24-residue CaM binding region toward the N-terminal end. This is unlike the CaM-dependent protein kinases that have CaM binding sites and AIDs immediately adjacent in sequence. Our data demonstrate that not only does the CaM binding region folds but also an ∼25- to 30-residue region between it and the AID folds, resulting in over half of the RD adopting α-helical structure. This appears to be the first observation of CaM inducing folding of this scale outside of its binding site on a target protein

Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites

Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutant

Microbial Cr(VI) reduction by indigenous activated sludge bacilli and pure culture of escherichia coli ATCC 33456

Cr(VI) reducing microbial species Bacillus thuringiensis, Bacillus cereus and Bacillus mycoides were isolated from dried sludge collected from sand drying beds at a local wastewater treatment plant in Brits (South Africa). The plant received high periodic loadings of Cr(VI) contaminated effluent from an abandoned chrome processing foundry within the chrome mining town of Brits. Other Cr(VI) producing organisms in the sludge sample were identified as Microbacterium foliorum and Lycinobacillus sphaerococcus. Among the five confirmed Cr(VI) reducers, B. thuringiensis was determined to have the highest performance in reducing Cr(VI) to Cr(III). The Cr(VI) reducing capability of organisms isolated at the site has not diminished over a 15 year period (2006- 2021). In the current study, the performance and pathway structures responsible for Cr(VI) reduction are analysed and compared with the activity of a metabolically versatile Escherichia coli ATCC 33456. The observations from this study showcase advanced enzymatic Cr(VI) reductase structures in B. thuringiensis never before observed in other microbial species. Blocking of electron carrier enzymes suggested the involvement of dissolved thioredoxin in the cytosol and bulk media as possible biocatalysis activators for Cr(VI) reduction in resting cells.The National Research Foundation (NRF), Sedibeng Water through a Research Chair in Water Utilisation Engineering and the Rand Water Chair in Water Utilisation.http://www.aidic.it/cetam2023Chemical Engineerin

Renal function of MDR-TB patients treated with kanamycin regimens or concomitantly with antiretroviral agents

SETTING: To compare renal insufficiency among mul-tidrug-resistant tuberculosis (MDR-TB) patients treated with kanamycin (KM) based regimens and those treated concomitantly with tenofovir disoproxil fumarate (TDF) or other antiretroviral therapy (ART) regimens in Namibia. DESIGN: Retrospective review of the treatment records and laboratory tests of patients initiated on MDR-TB treatment (January–December 2014). The glomerular filtration rates (eGFR) estimated pre- and post-treatment were compared using the analysis of variance test. Renal insufficiency was defined as an eGFR of,60 ml/ min/1.73 m2. Use of KM or TDF and association with renal insufficiency was assessed using Kaplan-Meier plots and Cox proportional hazards analysis. RESULTS: The baseline mean eGFR for the three groups was similar (P ¼ 0.24): 139.3 6 25.6 ml/min for the KM group (n ¼ 68), 131.1 6 25.7 ml/min for the KMþTDF group (n ¼ 44) and 134.2634.4 ml/min for the KMþOther group (n ¼ 23). After 8 months, the values had declined significantly to respectively 104.8 6 37.5 ml/min (P, 0.001), 101.5 6 38.3 ml/min (P, 0.001) and 111.5 6 41.7 ml/min (P ¼ 0.01). Co-treatment with KMþART was associated with an increased risk of renal insufficiency (hazard ratio [HR] 1.8, 95%CI 0.7–4.1, P ¼ 0.20 for KMþTDF, and HR 3.5, 95%CI 1.4–8.2, P ¼ 0.005 for KMþOther ART). CONCLUSION: Renal function declined at a similar rate in MDR-TB patients treated with KM-based regimens compared with patients treated concomitantly with TDF-based or other ART. The risk of renal insufficiency was greater for patients on ART

Meta-omics approaches to understand and improve wastewater treatment systems

Biological treatment of wastewaters depends on microbial processes, usually carried out by mixed microbial communities. Environmental and operational factors can affect microorganisms and/or impact microbial community function, and this has repercussion in bioreactor performance. Novel high-throughput molecular methods (metagenomics, metatranscriptomics, metaproteomics, metabolomics) are providing detailed knowledge on the microorganisms governing wastewater treatment systems and on their metabolic capabilities. The genomes of uncultured microbes with key roles in wastewater treatment plants (WWTP), such as the polyphosphate-accumulating microorganism Candidatus Accumulibacter phosphatis, the nitrite oxidizer Candidatus Nitrospira defluvii or the anammox bacterium Candidatus Kuenenia stuttgartiensis are now available through metagenomic studies. Metagenomics allows to genetically characterize full-scale WWTP and provides information on the lifestyles and physiology of key microorganisms for wastewater treatment. Integrating metagenomic data of microorganisms with metatranscriptomic, metaproteomic and metabolomic information provides a better understanding of the microbial responses to perturbations or environmental variations. Data integration may allow the creation of predictive behavior models of wastewater ecosystems, which could help in an improved exploitation of microbial processes. This review discusses the impact of meta-omic approaches on the understanding of wastewater treatment processes, and the implications of these methods for the optimization and design of wastewater treatment bioreactors.Research was supported by the Spanish Ministry of Education and Science (Contract Project CTQ2007-64324 and CONSOLIDER-CSD 2007-00055) and the Regional Government of Castilla y Leon (Ref. VA038A07). Research of AJMS is supported by the European Research Council (Grant 323009