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Molecular surveillance of antimalarial partner drug resistance in sub-Saharan Africa: a spatial-temporal evidence mapping study.

ABSTRACT: Background:Molecular markers for antimalarial drug resistance can be used to rapidly monitor the emergence and spatial distribution of resistance to artemisinin-based combination therapies (ACTs). Little has been done to analyse molecular surveillance efforts or to assess surveillance coverage. This study aimed to develop an evidence map to characterise the spatial-temporal distribution and sampling methodologies of drug resistance surveillance in sub-Saharan Africa, specifically focusing on markers associated with ACT partner drugs. Methods:By use of a systematic search, we identified studies that reported data on the following mutations associated with ACT partner drug resistance: pfmdr1 Asn86Tyr, Tyr184Phe, Asp1246Tyr, and copy number variation and pfcrt Lys76Thr, with sample collection occurring in sub-Saharan Africa between Jan 1, 2004, and Dec 31, 2018, corresponding to the uptake of ACTs. For each identified study, we extracted information on its sampling and laboratory methods, author and publication affiliations, years of sampling and of publication, geographic coordinates of the study sites, and prevalence of the partner drug resistance-associated markers. We used linear models to test whether urbanicity, population density, and endemicity were predictors of drug resistance survey sites and linear regressions to identify associations between the number of resistance surveys within a given country and the at-risk malaria population in 2010, the per-capita GDP in 2010, and the mean amount of funding directed to malaria and to determine trends in marker prevalence over time. For country case studies with three or more datapoints, we assessed global spatial autocorrelation using Moran's I. Findings:Our search yielded 254 studies encompassing 492 year-specific and location-specific surveys from 35 malaria-endemic countries, the most complete set of molecular partner drug surveillance data to date. We observed a median time lag of 3·1 years (95% CI 1·0-7·7) from final sample acquisition to publication. 22 (49%) of the 44 countries in the study region conducted, on average, one or fewer studies every 3 years. The locations of surveillance sites were positively associated with urbanicity (p<0·0001), and the abundance of country-level data was associated with reported donor funding in 2004-18 (p=0·0011) and local government funding in 2004-09 (p=0·014). Nearly all molecular markers displayed significant regional trends over time and global spatial autocorrelation in space. For selected countries with more widespread coverage of surveillance data, some markers also displayed spatial heterogeneity. Interpretation:In most sub-Saharan countries, molecular data on antimalarial resistance might not be representative of the temporal and geographic heterogeneity of partner drug resistance, and likely do not represent the true spatially dependent distribution of partner drug resistance. Our results highlight several inefficiencies that can be improved upon to develop more accurate data landscapes, including the expansion of sentinel surveillance systems, syndemic usage of research samples, and increased participation in reporting published and unpublished data to centralised platforms.

SUBMITTER: Ehrlich HY

PROVIDER: S-EPMC7575134 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Molecular surveillance of antimalarial partner drug resistance in sub-Saharan Africa: a spatial-temporal evidence mapping study.

Ehrlich Hanna Y HY Jones Justin J Parikh Sunil S

The Lancet. Microbe 20200907 5

<h4>Background</h4>Molecular markers for antimalarial drug resistance can be used to rapidly monitor the emergence and spatial distribution of resistance to artemisinin-based combination therapies (ACTs). Little has been done to analyse molecular surveillance efforts or to assess surveillance coverage. This study aimed to develop an evidence map to characterise the spatial-temporal distribution and sampling methodologies of drug resistance surveillance in sub-Saharan Africa, specifically focusin ...[more]

PMID: 33089222

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Project description:Cervical cancer (CC) is the most common viral infection of the reproductive tract and in Sub-Saharan Africa (SSA), its morbidity and mortality rates are high. The aim of this review was to map evidence on CC management in SSA. The scoping review was conducted in accordance with Arksey and O'Malley's scoping review framework. The review included studies on different aspects of CC management. The review was also done following the steps and guidelines outlined in the PRISMA-Extension for Scoping Reviews (PRISMA-ScR) checklist. The following databases were searched: PubMed, EBSCOhost, Scopus and Cochrane Database of Systematic Review. A total of 1121 studies were retrieved and 49 which were eligible for data extraction were included in the review. The studies were classifiable in 5 groups: 14 (28.57%) were on barriers to CC screening, 10 (20.41%) on factors associated with late-stage presentation at diagnosis, 11 (22.45%) on status of radiotherapy, 4 (8.20%) on status of chemotherapy and 10 (20.41%) on factors associated with high HPV coverage. High HPV vaccine coverage can be achieved using the class school-based strategy with opt-out consent form process. Barriers to CC screening uptake included lack of knowledge and awareness and unavailability of screening services. The reasons for late-stage presentation at diagnosis were unavailability of screening services, delaying whilst using complementary and alternative medicines and poor referral systems. The challenges in chemotherapy included unavailability and affordability, low survival rates, treatment interruption due to stock-outs as well as late presentation. Major challenges on radiotherapy were unavailability of radiotherapy, treatment interruption due to financial constraints, and machine breakdown and low quality of life. A gap in understanding the status of CC management in SSA has been revealed by the study implying that, without full knowledge of the extent of CC management, the challenges and opportunities, it will be difficult to reduce infection, improve treatment and palliative care. Research projects assessing knowledge, attitude and practice of those in immediate care of girls at vaccination age, situational analysis with health professionals and views of patients themselves is important to guide CC management practice.

Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient.

Project description:In 2013, 78% of malaria deaths occurred in children aged 5 years and below, in sub-Saharan Africa. Treatment of severe malaria requires a health facility with inpatient care. However, in most sub-Sahara African countries, access to health facilities is a major problem. Pre-referral antimalarial treatments aim to delay the progress of severe malaria as patients seek to access health facilities. Rectal artesunate can be administered in the community as a pre-referral treatment in rural hard-to-reach areas. In Kenya, though pre-referral rectal artesunate has been included in the National Guidelines for pre-referral treatment, it is yet to be implemented in the public healthcare system. It is important, therefore, to establish its cost-utility compared to current parenteral treatments. This study evaluated the cost-utility of provision of pre-referral treatments by community health workers compared to similar services at a primary health facility.This was a decision model-based cost-utility analysis, comparing pre-referral antimalarial treatments provided by: community health workers (CHWs), primary health facility, direct access to a tertiary health facility and no access to treatment. A theoretical cohort, of 1000 children, who were below 5 years old; residing in rural hard-to-reach areas, was taken as the reference population. Data was collected through key informant interviews, to assess the costs, while key measures of effectiveness, were obtained from existing studies. The key measure of outcomes was Disability Adjusted Life Years (DALYS) averted. Probabilistic sensitivity analysis was carried out to assess the robustness of the model.Provision of rectal pre-referral treatment by community health workers was estimated to avert 13,276 DALYs, at a cost of $68,428 for a cohort of 1000 children. Provision of rectal pre-referral treatment at a primary health facility was estimated to avert 9993 DALYs, at a cost of $73,826 for a cohort of 1000 children, while going directly to a tertiary health facility was estimated to avert 15,801 DALYs, at a cost of $114,903 for a cohort of 1000 children. The incremental cost effectiveness ratios for provision of pre-referral treatment by community health care and primary health workers were $5.11 and $7.30 per DALYs averted respectively.Use of CHWs was more cost effective than provision of pre-referral treatments at a primary health facility especially, with high referral compliance. Rectal artesunate can easily be administered by community health workers, unlike parenteral pre-referral interventions.

Project description:ObjectiveThis study carried out a scoping review of research on intimate partner violence to determine the extent to which studies on sociocultural factors influencing intimate partner violence among young women (15-24 years) have been conducted, and how different geographical areas are represented. It also considered whether the methodologies used were sufficient to describe the risk factors, prevalence and health outcomes associated with intimate partner violence among young women.Study designScoping review.MethodsOnline databases were used to identify studies published between 2008 and 2019. The Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines by Arksey and O'Malley were used to select studies, and primary studies were assessed using the Mixed Method Appraisal Tool, V.2011. Thematic content analysis was used to summarise the findings of the scoping review.ResultsThe majority of publications eight (61.5%) reported cross-sectional studies, while four (31.5%) were qualitative studies. One of the studies (7%) collected measured data. Overall, 13 (100%) of the publications examined factors influencing intimate partner violence.Using a customised quality assessment instrument, 12 (92.3%) of studies achieved a 'high'-quality ranking with a score of 100%, and 7.7% of studies achieved an 'average' quality ranking with a score of 75%.ConclusionsWhile the quality of the studies is generally high, researches on sociocultural factors influencing intimate partner violence among young women would benefit from a careful selection of methods and reference standards, including direct measures of the violence affecting young women. Prospective cohort studies are required linking early exposure with individual, sociocultural and community factors, and detailing the abuse experienced from childhood, adolescence and youth.Prospero registration numberCRD42018116463. SCOPING PROTOCOL PUBLICATION: https://doi.org/10.1186/s13643-019-1234-y.

Project description:IntroductionThe dynamics of intimate partner violence (IPV)-one of the world's leading public health problems-in urban Africa remain poorly understood. Yet, urban areas are key to the future of women's health in Africa.Study objectivesWe explored survivor-, partner-, and household-level correlates of prevalence rates for types of IPV in urban SSA women.MethodThe study uses DHS data from 42,143 urban women aged 15-49 in 27 SSA countries. Associations at the bivariate level were examined using the Pearson Chi-square test. The modified Poisson regression test estimated the relative prevalence of IPV subtypes in the study population at the multivariate level.ResultsApproximately 36% of women in urban SSA experienced at least one form of IPV; 12.8% experienced two types; and 4.6% experienced all three types. SSA urban women who had only primary-level education, had 3 or more living children, were informally employed, were in polygynous unions, or who approved of wife-beating similarly displayed higher adjusted prevalence rates for all three forms of IPV compared respectively to their counterparts without formal education, without a living child, were unemployed, in monogamous unions, or who do not approve of wife-beating. On the other hand, the region's urban women who began cohabiting between ages 25 and 35 years or who lived in higher wealth households showed consistently lower adjusted prevalence rates for all three forms of IPV relative to their counterparts who began cohabiting before 18 years or who lived in lower wealth households. Compared to their counterparts without formal education, without a living child, or whose partners did not have formal education, women with secondary and higher education, with 1-2 living children, or whose partners had only primary level schooling displayed higher adjusted prevalence rates for both IPEV and IPPV, but not for IPSV. However, relative to their counterparts whose partners were aged 25 years or below, living with a partner aged 40 years and above was associated with statistically significant reduced prevalence rates for IPPV and IPSV, but not for IPEV. Only for IPPV did women with partners educated at secondary and above levels display statistically significant higher adjusted prevalence rates relative to their counterparts with uneducated partners. Also, solely for IPPV did women who began cohabiting between ages 18 and 24 years or whose partners were employed (whether formally or informally) show decreased adjusted prevalence rates relative to their counterparts who started cohabiting before 18 years or whose partners were unemployed. In addition, only for IPSV did women aged 40 years and above or living in middle wealth households show statistically significant reduced adjusted prevalence rates relative to their counterparts aged less than 25 years or living in lower wealth households.Discussion and conclusionBy 2030, the majority of SSA women will be urban dwellers. Complexities surround IPV in urban SSA, highlighting the unique dynamics of the problem in this setting. While affirming the link between IPV and marital power inequities and dynamics, findings suggest that the specific correlates of prevalence rates for different IPV sub-types in urban SSA women can, at once, be both similar and unique. The contextual drivers of the differences and similarities in the correlates of the prevalence rates of IPV sub-types among the region's urban women need further interrogation.

Dataset Information

Molecular surveillance of antimalarial partner drug resistance in sub-Saharan Africa: a spatial-temporal evidence mapping study.

Publications

Molecular surveillance of antimalarial partner drug resistance in sub-Saharan Africa: a spatial-temporal evidence mapping study.

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