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Next-Generation Sequencing Reveals a High Frequency of HIV-1 Minority Variants and an Expanded Drug Resistance Profile among Individuals on First-Line ART.
Get PDFWe assessed the performance and clinical relevance of Illumina MiSeq next-generation sequencing (NGS) for HIV-1 genotyping compared with Sanger sequencing (SS). We analyzed 167 participants, 45 with virologic failure (VL ≥ 1000 copies/mL), i.e., cases, and 122 time-matched participants with virologic suppression (VL < 1000 copies/mL), i.e., controls, 12 months post-ART initiation. Major surveillance drug resistance mutations (SDRMs) detected by SS were all detectable by NGS. Among cases at 12 months, SS identified SDRMs in 32/45 (71.1%) while NGS identified SDRMs among 35/45 (77.8%), increasing the number of cases with SDRMs by 3/45 (6.7%). Participants identified with, and proportions of major SDRMs increased when NGS was used. NGS vs. SS at endpoint revealed for NNRTIs: 36/45 vs. 33/45; Y181C: 26/45 vs. 24/45; K103N: 9/45 vs. 6/45 participants with SDRMs, respectively. At baseline, NGS revealed major SDRMs in 9/45 (20%) cases without SDRMs by SS. Participant MBL/043, among the nine, the following major SDRMs existed: L90M to PIs, K65R and M184V to NRTIs, and Y181C and K103N to NNRTIs. The SDRMs among the nine increased SDRMs to NRTIs, NNRTIs, and PIs. Only 43/122 (25.7%) of participants had pre-treatment minority SDRMs. Also, 24.4% of the cases vs. 26.2 of controls had minority SDRMs (p = 0.802); minority SDRMs were not associated with virologic failure. NGS agreed with SS in HIV-1 genotyping but detected additional major SDRMs and identified more participants harboring major SDRMs, expanding the HIV DRM profile of this cohort. NGS could improve HIV genotyping to guide treatment decisions for enhancing ART efficacy, a cardinal pre-requisite in the pursuit of the UNAIDS 95-95-95 targets
Molecular Epidemiology and AMR Perspective of Diarrhoeagenic Escherichia coli in Africa: A Systematic Review and Meta-analysis.
Get PDFINTRODUCTION: Diarrhoeagenic Escherichia coli (DEC) persistently challenges public health in Africa, contributing substantially to the diarrhoeal disease burden. This systematic review and meta-analysis illuminate the distribution and antimicrobial resistance (AMR) patterns of DEC pathotypes across the continent. METHODS: The review selectively focused on pathotype-specific studies reporting prevalence and/or AMR of human-derived DEC pathotypes from African nations, excluding data from extra-intestinal, animal, and environmental sources and studies focused on drug and mechanism experiments. Pertinent studies were retrieved from SCOPUS, PubMed, and EBSCOhost, processed with Covidence, and screened in alignment with PRISMA guidelines. RESULTS: The reviewed studies were predominantly hospital-based (80%) and paediatric-focused (91%), with a meagre 4.4% documenting DEC outbreaks. Seven DEC pathotypes were discerned, with Enteroaggregative E. coli (EAEC) being notably prevalent (43%, 95% CI 30-55%) and Enteroinvasive E. coli (EIEC) least prevalent (24%, 95% CI 17-32%). Identified non-susceptibilities were noted against essential antibiotics including ciprofloxacin, ceftriaxone, and ampicillin, while instances of carbapenem and Extended-Spectrum ß-Lactamase (ESBL) resistance were scarce. CONCLUSION: Despite sporadic data on DEC prevalence and AMR in Africa, particularly in community settings, a palpable gap remains in real-time outbreak surveillance and comprehensive data documentation. Augmenting surveillance and embracing advancements in molecular/genomic characterisation techniques are crucial to precisely discerning DEC's actual impact and resistance continuum in Africa
Association of COVID-19 with acute and post-acute risk of multiple different complications and mortality in patients infected with omicron variant stratified by initial disease severity: a cohort study in Hong Kong.
Get PDFBACKGROUND: Few studies have attempted to use clinical and laboratory parameters to stratify COVID-19 patients with severe versus non-severe initial disease and evaluate age-specific differences in developing multiple different COVID-19-associated disease outcomes. METHODS: A retrospective cohort included patients from the electronic health database of Hong Kong Hospital Authority between 1 January 2022 and 15 August 2022 until 15 November 2022. The cohort was divided into three cohorts by age (≤ 40, 41-64, and ≥ 65 years old). Each age cohort was stratified into four groups: (1) COVID-19 critically exposed group (ICU admission, mechanical ventilation support, CRP > 80 mg/L, or D-dimer > 2 g/mL), (2) severely exposed group (CRP 30-80 mg/L, D-dimer 0.5-2 g/mL, or CT value 40) for the disease outcomes in the acute phase of infection (e.g., mortality risk HR (aged ≤ 40): 1.0 (95%CI: 0.5,2.0), HR (aged 41-64): 2.1 (95%CI: 1.8, 2.6), HR (aged > 65): 4.8 (95%CI: 4.6, 5.1)); while in the post-acute phase, these risks were largely insignificant in those aged 65): 1.5 (95%CI: 1.5,1.6)). Fully vaccinated patients were associated with lower risks of disease outcomes than those receiving less than two doses of vaccination. CONCLUSIONS: The risk of multiple different disease outcomes in both acute and post-acute phases increased significantly with the increasing severity of acute COVID-19 illness, specifically among the elderly. Moreover, future studies could improve by risk-stratifying patients based on universally accepted thresholds for clinical parameters, particularly biomarkers, using biological evidence from immunological studies
Post-transcriptional reprogramming by thousands of mRNA untranslated regions in trypanosomes.
Get PDFAlthough genome-wide polycistronic transcription places major emphasis on post-transcriptional controls in trypanosomatids, messenger RNA cis-regulatory untranslated regions (UTRs) have remained largely uncharacterised. Here, we describe a genome-scale massive parallel reporter assay coupled with 3'-UTR-seq profiling in the African trypanosome and identify thousands of regulatory UTRs. Increased translation efficiency was associated with dosage of adenine-rich poly-purine tracts (pPuTs). An independent assessment of native UTRs using machine learning based predictions confirmed the robust correspondence between pPuTs and positive control, as did an assessment of synthetic UTRs. Those 3'-UTRs associated with upregulated expression in bloodstream-stage cells were also enriched in uracil-rich poly-pyrimidine tracts, suggesting a mechanism for developmental activation through pPuT 'unmasking'. Thus, we describe a cis-regulatory UTR sequence 'code' that underpins gene expression control in the context of a constitutively transcribed genome. We conclude that thousands of UTRs post-transcriptionally reprogram gene expression profiles in trypanosomes
Neurological Symptoms and Cause of Death Among Young Children in Low- and Middle-Income Countries.
Get PDFIMPORTANCE: The emergence of acute neurological symptoms in children necessitates immediate intervention. Although low- and middle-income countries (LMICs) bear the highest burden of neurological diseases, there is a scarcity of diagnostic and therapeutic resources. Therefore, current understanding of the etiology of neurological emergencies in LMICs relies mainly on clinical diagnoses and verbal autopsies. OBJECTIVE: To characterize the association of premortem neurological symptoms and their management with postmortem-confirmed cause of death among children aged younger than 5 years in LMICs and to identify current gaps and improve strategies to enhance child survival. DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study was conducted between December 3, 2016, and July 22, 2022, at the 7 participating sites in the Child Health and Mortality Prevention Surveillance (CHAMPS) network (Bangladesh, Ethiopia, Kenya, Mali, Mozambique, Sierra Leone, and South Africa). Minimally invasive tissue sampling was performed at the CHAMPS sites with specimens from deceased children aged younger than 5 years. This study included deceased children who underwent a premortem neurological evaluation and had a postmortem-confirmed cause of death. Data analysis was performed between July 22, 2022, and January 15, 2023. MAIN OUTCOMES AND MEASURES: Descriptive analysis was performed using neurological evaluations from premortem clinical records and from postmortem determination of cause of death (based on histopathology, microbiological testing, clinical records, and verbal autopsies). RESULTS: Of the 2127 deaths of children codified during the study period, 1330 (62.5%) had neurological evaluations recorded and were included in this analysis. The 1330 children had a median age of 11 (IQR, 2-324) days; 745 (56.0%) were male and 727 (54.7%) presented with neurological symptoms during illness before death. The most common postmortem-confirmed neurological diagnoses related to death were hypoxic events (308 [23.2%]), meningoencephalitis (135 [10.2%]), and cerebral malaria (68 [5.1%]). There were 12 neonates with overlapping hypoxic events and meningoencephalitis, but there were no patients with overlapping meningoencephalitis and cerebral malaria. Neurological symptoms were similar among diagnoses, and no combination of symptoms was accurate in differentiating them without complementary tools. However, only 25 children (18.5%) with meningitis had a lumbar puncture performed before death. Nearly 90% of deaths (442 of 511 [86.5%]) with neurological diagnoses in the chain of events leading to death were considered preventable. CONCLUSIONS AND RELEVANCE: In this cross-sectional study of children aged younger than 5 years, neurological symptoms were frequent before death. However, clinical phenotypes were insufficient to differentiate the most common underlying neurological diagnoses. The low rate of lumbar punctures performed was especially worrying, suggesting a challenge in quality of care of children presenting with neurological symptoms. Improved diagnostic management of neurological emergencies is necessary to ultimately reduce mortality in this vulnerable population
Impacts of climate change on diarrhoeal disease hospitalisations: How does the global warming targets of 1.5-2°C affect Dhaka, Bangladesh?
Get PDFDhaka is one of the world's densely populated cities and faces significant public health challenges including high burden of diarrhoeal diseases. Climate change is intensifying existing environmental problems including urban heat island effect and poor water quality. While numerous epidemiological studies have linked meteorological factors to diarrhoeal diseases in Bangladesh, assessment of the impacts of future climate change on diarrhoeal diseases is scarce. We provide the assessment of climate change impacts on diarrhoeal disease in Dhaka and project future health risks under climate change scenarios. About 3 million acute diarrhoea cases presenting to the Dhaka Hospital of the International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b) during 1981-2010 were linked to daily temperature, rainfall and humidity and association investigated using time series adapted negative binomial regression models employing constrained distributed lag linear models. The findings were applied to climate projections to estimate future risks of diarrhoea under various global warming scenarios. There was a significantly raised risk of diarrhoea hospitalisation in all ages with daily mean temperature (RR: 3.4, 95% CI: 3.0-3.7) after controlling for the confounding effects of heavy rainfall, humidity, autocorrelations, day of the week effect, long-term time, and seasonal trends. Using the incidence rate ratio (IRR) of 1.034, temperature increases based on the global warming targets of 1.5-2°C could result in an increase of diarrhoea hospitalisations by 4.5-7.4% in all age groups by the 2100s. These effects were more pronounced among <5 children where the predicted temperature increases could raise diarrhoea hospitalisation by 5.7% - 9.4%. Diarrhoea hospitalisation will increase significantly in Dhaka even if the global warming targets adopted by the Paris Agreement is reached. This underscores the importance of preparing the city for management and prevention of diarrhoeal diseases
Forgotten and ignored: making digital health work for migrant population in Africa.
Get PDFThe African continent has experienced an alarming increase in forcibly displaced individuals, driven by socio-political conflict, economic instability and climate-induced calamities. The urgent need for contextualized and adaptable health solutions in the face of ongoing conflicts and crises underscores the importance of harnessing digital health innovations while ensuring inclusivity and equity for all. This commentary explores the potential of digital health to address healthcare disparities among migrant populations, examining the barriers to adoption and providing recommendations for policymakers and stakeholders to promote inclusivity and improve healthcare access. While digital health emerged as a promising avenue for improving healthcare access, there is also a greater necessity for tailoring these innovations to the specific needs and vulnerabilities of the target populations
School Meals Case Study: Senegal [Étude de cas sur l’alimentation scolaire : Sénégal]
Get PDFCette étude de cas sur les repas scolaires fait partie d'une collection dirigée par la Communauté de Pratique « Bonnes Pratiques » du Consortium de Recherche pour la Santé et la Nutrition Scolaires. Développée par Sidy Tounkara et Seyni Kébé, l'Étude de Cas sur l’alimentation scolaire au Sénégal a pour objectif de documenter l'organisation, le financement et le suivi du programme national de repas scolaires à travers le pays. Les objectifs de cette étude de cas incluent la présentation d'une introduction au profil du pays, l'exposition de la conception et de la mise en œuvre des programmes de repas scolaires, la description de leurs processus de suivi et d'évaluation, ainsi que la mise en lumière des leçons apprises, des meilleures pratiques et des défis rencontrés. Cette étude de cas est rédigée sous forme de document de travail et peut être mise à jour pour refléter l'évolution des circonstances. La Communauté de Pratique « Bonnes Pratiques » soutient la production de preuves du Consortium de Recherche pour la Santé et la Nutrition Scolaires, la branche dédiée à la recherche de la Coalition pour l’alimentation scolaire. L'objectif du Consortium de Recherche est de mener des recherches indépendantes dans divers secteurs et de générer des preuves solides, convaincantes et exploitables concernant les avantages des programmes de repas scolaires afin d'informer la prise de décision basée sur des preuves en matière de politiques et de pratiques de santé et de nutrition scolaires.
This school meals case study forms part of a collection led by the Research Consortium for School Health and Nutrition’s "Good Examples" Community of Practice. Developed by Sidy Toukara and Seyni Kébé, the School Meals Case Study of Senegal serves to document how the national school meals programme is organized, funded, and monitored throughout the country. The objectives of this case study include presenting an introduction to the country profile, outlining the design and implementation of school feeding programmes, describing their monitoring and evaluation processes, and highlighting lessons learned, best practices, and challenges. This case study is written as a working paper, and can be updated to reflect evolving circumstances. The ‘Good Examples’ Community of Practice supports the evidence generation of the Research Consortium for School Health and Nutrition, the evidence-generating arm of the School Meals Coalition. The Research Consortium’s objective is to carry out independent research across diverse sectors and generate solid, compelling, and actionable evidence regarding the benefits of school food programs to inform evidence-based decision-making on school health and nutrition policies and practices
Migrant-sensitive healthcare in Europe: advancing health equity through accessibility, acceptability, quality, and trust.
Get PDFThe advancement of migrant-sensitive health care in Europe has been a topic of many initiatives and academics debates for over 20 years in Europe, yet with rather limited progress in terms of comprehensive and sustainable implementation. We argue that a human rights-based approach with clearly defined duties and responsibilities of governments, relevant public and private institutions as well as professionals is needed, in line with a sound understanding and thoughtful implementation and further development of concepts and standards for providing migrant sensitive care as an essential component of Universal Health Coverage. We suggest drawing particular attention to the interrelated features of accessibility, acceptability, quality, and trust to inform policies and practice. Innovative approaches with substantial involvement of social and cultural sciences are needed for adapting clinical care and health services to the growing social and cultural diversity of European societies
Shigella Detection and Molecular Serotyping With a Customized TaqMan Array Card in the Enterics for Global Health (EFGH): Shigella Surveillance Study.
Get PDFBACKGROUND: Quantitative polymerase chain reaction (qPCR) targeting ipaH has been proven to be highly efficient in detecting Shigella in clinical samples compared to culture-based methods, which underestimate Shigella burden by 2- to 3-fold. qPCR assays have also been developed for Shigella speciation and serotyping, which is critical for both vaccine development and evaluation. METHODS: The Enterics for Global Health (EFGH) Shigella surveillance study will utilize a customized real-time PCR-based TaqMan Array Card (TAC) interrogating 82 targets, for the detection and differentiation of Shigella spp, Shigella sonnei, Shigella flexneri serotypes, other diarrhea-associated enteropathogens, and antimicrobial resistance (AMR) genes. Total nucleic acid will be extracted from rectal swabs or stool samples, and assayed on TAC. Quantitative analysis will be performed to determine the likely attribution of Shigella and other particular etiologies of diarrhea using the quantification cycle cutoffs derived from previous studies. The qPCR results will be compared to conventional culture, serotyping, and phenotypic susceptibility approaches in EFGH. CONCLUSIONS: TAC enables simultaneous detection of diarrheal etiologies, the principal pathogen subtypes, and AMR genes. The high sensitivity of the assay enables more accurate estimation of Shigella-attributed disease burden, which is critical to informing policy and in the design of future clinical trials