Estimation of Additive Cure Model with Applications

Survival analysis plays a crucial role in medical research for understanding the time until an event of interest occurs, such as disease recurrence or death. An important branch of survival analysis models is cure models, assuming that a proportion of subjects will never experience the event of interest. The value of the proportion is called the cured rate and is usually associated with many covariates with complex effect relationships. Studying cure models under such non-linear covariate effects remains an active research area. This thesis aims to investigate advancements in additive cure models, focusing on their ability to capture additive complex relationships between covariates and survival outcomes with a curedfraction through non-linear modeling techniques, such as basic splines. Additive cure models offer a robust framework for analyzing survival data when a subset of individuals is cured and does not experience the event. The thesis will involve simulation studies to assess the accuracy of parameter estimation and model fit in various scenarios, and the application of additive cure models to real-world datasets from medical research studies. The findings will enhance the understanding and application of additive cure models in analyzing survivaldata with non-linear covariate effects, with implications for clinical decision-making and prognostic modeling. The insights gained from this research have implications for various fields, including epidemiology, clinical research, and public health, providing valuable tools for analyzing survival data and enhancing decision-making processes

Identification of Subsets of Enteroaggregative Escherichia coli Associated with Diarrheal Disease among Under 5 Years of Age Children from Rural Gambia.

Enteroaggregative Escherichia coli (EAEC) cause acute and persistent diarrhea, mostly in children worldwide. Outbreaks of diarrhea caused by EAEC have been described, including a large outbreak caused by a Shiga toxin expressing strain. This study investigated the association of EAEC virulence factors with diarrhea in children less than 5 years. We characterized 428 EAEC strains isolated from stool samples obtained from moderate-to-severe diarrhea cases (157) and healthy controls (217) children aged 0-59 months recruited over 3 years as part of the Global Enteric Multicenter Study (GEMS) in The Gambia. Four sets of multiplex polymerase chain reaction were applied to detect 21 EAEC-virulence genes from confirmed EAEC strains that target pCVD432 (aatA) and AAIC (aaiC). In addition, Kirby-Bauer disc diffusion antimicrobial susceptibility testing was performed on 88 EAEC strains following Clinical Laboratory Standard Institute guidelines. We observed that the plasmid-encoded enterotoxin [odds ratio (OR): 6.9, 95% confidence interval (CI): 2.06-29.20, P 12 months). Our data suggest that some EAEC-virulent factors have age-specific associations with moderate-to-severe diarrhea in infants. Furthermore, our study showed that 85% and 72% of EAEC strains tested were resistant to sulphamethoxazole-trimethoprim and ampicillin, respectively. Sulphamethoxazole-trimethoprim and ampicillin are among the first-line antibiotics used for the treatment of diarrhea in The Gambia

A randomized trial to investigate the effects of pre-natal and infant nutritional supplementation on infant immune development in rural Gambia: the ENID trial: Early Nutrition and Immune Development.

BACKGROUND: Recent observational research indicates that immune development may be programmed by nutritional exposures early in life. Such findings require replication from trials specifically designed to assess the impact of nutritional intervention during pregnancy on infant immune development. The current trial seeks to establish: (a) which combination of protein-energy (PE) and multiple-micronutrient (MMN) supplements would be most effective; and (b) the most critical periods for intervention in pregnancy and infancy, for optimal immune development in infancy. METHODS/DESIGN: The ENID Trial is a 2 x 2 x 2 factorial randomized, partially blind trial to assess whether nutritional supplementation to pregnant women (from < 20 weeks gestation to term) and their infants (from 6 to 12 months of age) can enhance infant immune development. Eligible pregnant women from the West Kiang region of The Gambia (pregnancy dated by ultrasound examination) are randomized on entry to 4 intervention groups (Iron-folate (FeFol = standard care), multiple micronutrients (MMN), protein-energy (PE), PE + MMN). Women are visited at home weekly for supplement administration and morbidity assessment and seen at MRC Keneba at 20 and 30 weeks gestation for a detailed antenatal examination, including ultrasound. At delivery, cord blood and placental samples are collected, with detailed infant anthropometry collected within 72 hours. Infants are visited weekly thereafter for a morbidity questionnaire. From 6 to 12 months of age, infants are further randomized to a lipid-based nutritional supplement, with or without additional MMN. The primary outcome measures of this study are thymic development during infancy, and antibody response to vaccination. Measures of cellular markers of immunity will be made in a selected sub-cohort. Subsidiary studies to the main trial will additionally assess the impact of supplementation on infant growth and development to 24 months of age. DISCUSSION: The proposed trial is designed to test whether nutritional repletion can enhance early immune development and, if so, to help determine the most efficacious form of nutritional support. Where there is evidence of benefit from a specific intervention/combination of interventions, future research should focus on refining the supplements to achieve the optimal, most cost-effective balance of interventions for improved health outcomes

Status of insecticide resistance in Anopheles gambiae (s.l.) of The Gambia.

BACKGROUND: Vector control activities, namely long-lasting insecticidal nets (LLIN) and indoor residual spraying (IRS), have contributed significantly to the decreasing malaria burden observed in The Gambia since 2008. Nevertheless, insecticide resistance may threaten such success; it is important to regularly assess the susceptibility of local malaria vectors to available insecticides. METHODS: In the transmission seasons of 2016 and 2017, Anopheles gambiae (s.l.) larvae were sampled in or around the nine vector surveillance sentinel sites of the Gambia National Malaria Control Programme (GNMCP) and in a few additional sampling points. Using WHO susceptibility bioassays, female adult mosquitoes were exposed to insecticide-impregnated papers. Molecular identification of sibling species and insecticide resistance molecular markers was done on a subset of 2000 female mosquitoes. RESULTS: A total of 4666 wild-caught female adult mosquitoes were exposed to either permethrin (n = 665), deltamethrin (n = 744), DDT (n = 1021), bendiocarb (n = 990) or pirimiphos-methyl (n = 630) insecticide-impregnated papers and control papers (n = 616). Among the 2000 anophelines, 1511 (80.7%) were Anopheles arabiensis, 204 (10.9%) Anopheles coluzzii, 75 (4%) Anopheles gambiae (s.s.), and 83 (4.4%) An. gambiae (s.s.) and An. coluzzii hybrids. There was a significant variation in the composition and species distribution by regions and year, P = 0.009. Deltamethrin, permethrin and DDT resistance was found in An. arabiensis, especially in the coastal region, and was mediated by Vgsc-1014F/S mutations (odds ratio = 34, P = 0.014). There was suspected resistance to pirimiphos-methyl (actellic 300CS) in the North Bank Region although only one survivor had the Ace-1-119S mutation. CONCLUSIONS: As no confirmed resistance to bendiocarb and actellic 300CS was detected, the national malaria control programme can continue using these insecticides for IRS. Nevertheless, the detection of Ace-1 119S mutation warrants extensive monitoring. The source of insecticide pressure driving insecticide resistance to pyrethroids and DDT detected at the coastal region should be further investigated in order to properly manage the spread of resistance in The Gambia

Ochrobactrum anthropi sepsis in a 15-month-old child: A case report.

KEY CLINICAL MESSAGE: Ochrobactrum anthropi (O. anthropi), a rare opportunistic pathogen, caused sepsis in a malnourished 15-month-old African child. Early detection and appropriate antibiotics led to full recovery, highlighting the importance of robust surveillance for emerging pathogens in vulnerable populations. ABSTRACT: While rarely causing infections, O. anthropi, a non-fermenting, obligately aerobic, flagellated gram-negative bacillus, demonstrates oxidase positivity and indole negativity. Traditionally, Ochrobactrum spp is considered a low threat due to its environmental abundance and mild virulence. It is, however, a multidrug-resistant bacteria known for causing opportunistic infections in humans. O. anthropi is typically associated with catheter-related bloodstream infections. The first documented case was in 1998; most cases have been reported in developed countries. We present a case of O. anthropi sepsis in a malnourished child in sub-Saharan Africa. We report a case involving a 15-month-old African female who presented with symptoms and signs of protein-energy malnutrition and sepsis. The blood culture revealed O.anthropi. We treated the child with the empirical first-line antibiotics per the national guidelines, intravenous ampicillin and gentamicin for a week, and the child fully recovered. This report describes a rare case of O. anthropi sepsis with malnutrition in an African female child. O. anthropi is an emerging pathogen causing opportunistic infections in both immunocompetent and immunocompromised patients. We report that early bacterial detection, appropriate antibiotic susceptibility and antimicrobial management based on local antibiogram data may be essential for excellent patient outcomes. Additionally, we recommend more robust surveillance to detect such rare emerging pathogens

Impact of SARS-CoV-2 infection and mitigation strategy during pregnancy on prenatal outcome, growth and development in early childhood in India: a UKRI GCRF Action Against Stunting Hub protocol paper

INTRODUCTION: The COVID-19 pandemic has offset some of the gains achieved in global health, particularly in relation to maternal, child health and nutrition. As pregnancy is a period of plasticity where insults acting on maternal environment have far-reaching consequences, the pandemic has had a significant impact on prenatal outcomes, intrauterine and postnatal development of infants. This research will investigate both the direct and indirect impacts of the COVID-19 pandemic during pregnancy on prenatal outcomes, growth and development in early childhood. METHODS AND ANALYSIS: Community and hospital data in Hyderabad and Gujarat, India will be used to recruit women who were pregnant during the COVID-19 pandemic and contracted SARS-CoV-2 infection. In comparison with women who were pregnant around the same time and did not contract the virus, the study will investigate the impact of the pandemic on access to healthcare, diet, nutrition, mental health and prenatal outcomes in 712 women (356 per study arm). Children born to the women will be followed prospectively for an 18-month period to investigate the impact of the pandemic on nutrition, health, growth and neurocognition in early childhood. ETHICS AND DISSEMINATION: Ethics approval was granted from the institutional ethics committees of the Indian Institute of Public Health Gandhinagar (SHSRC/2021/2185), Indian Council of Medical Research-National Institute of Nutrition (EC/NEW/INST/2021/1206), and London School of Hygiene and Tropical Medicine (72848). The findings of the study will be disseminated to policy and research communities through engagements, scientific conferences, seminars, and open-access, peer-reviewed publication

Infectivity of patent Plasmodium falciparum gametocyte carriers to mosquitoes: establishing capacity to investigate the infectious reservoir of malaria in a low-transmission setting in The Gambia.

BACKGROUND: Understanding the human malaria infectious reservoir is important for elimination initiatives. Here, we implemented mosquito membrane feeding experiments to prepare for larger studies to quantify the transmission potential and relative contribution of the human infectious reservoir. METHODS: Patients with clinical malaria attending four health facilities with at least 16 Plasmodium falciparum gametocytes per μL were recruited during the 2018 transmission season. Infectiousness to mosquitoes was assessed by direct membrane feeding assay (DMFA). We compared our results with a Bayesian predictive model to investigate the relationship between infectiousness and gametocyte density and explore the impact of fever on gametocyte infectivity. RESULTS: A total of 3177 suspected malaria cases were screened; 43.3% (1376) had microscopically patent P. falciparum parasites and 3.6% (114) of them had gametocytes. Out of 68 DMFAs, 38 (55.9%) resulted in at least one infected mosquito, with a total of 15.4% (1178/7667) of mosquitoes infected with 1-475 oocysts per gut. The relationship between mosquito infection prevalence and gametocytaemia was similar to other African settings and negatively associated with fever (OR: 0.188, 95% CI 0.0603 to 0.585, p=0.0039). CONCLUSIONS: Among symptomatic malaria patients, fever is strongly associated with transmission failure. Future studies can use DMFA to better understand the human malaria reservoir in settings of low endemicity in The Gambia and inform malaria elimination initiatives

Eggs for Improving Nutrition, cognitive development and reducing linear growth retardation among Infants and young Children (ENRICH) : Protocol of an egg supplementation trial among children aged 9-18 months in Hyderabad, India

SKB, SRC and BK: conceptualised, designed the study and wrote first draft. LFA, TD, DPP, MC, KS and PA: developed detailed protocols, planned data collection, critical input to manuscript. RM, HD-K, CH, SFR, RPullakhandam, RPalika, RRK, RNK, MLJ and PH: concept, design, critical inputs to manuscript.Peer reviewe

Hypertension in Sub-Saharan Africa: Burden, Barriers and Priorities for Improving Treatment Outcomes

The burden of hypertension is rising rapidly in sub-Saharan Africa (SSA), posing significant health challenges and economic costs that hinder national development. Despite being well-studied in clinical medicine, the detection, treatment, and control of hypertension in SSA remain inadequate. This is due to barriers across the care continuum, including individual-, provider-, and system-level obstacles within the health system. A critical issue is the lack of contextualized mechanistic research to understand the mechanisms, phenotypes, and treatment responses in native SSA populations. Current treatment approaches are often based on data from diaspora Africans, particularly African Americans. Consequently, most guidelines do not recommend angiotensin system drugs as first-line agents for Black patients, a stance that should be reconsidered given some evidence of their effectiveness in native SSA populations. Addressing these barriers requires a comprehensive, multisectoral strategy that includes both preventative and clinical measures at the population and individual levels. Preventative approaches should encompass health and nutrition education, improving food supply quality, and implementing comprehensive transportation and environmental policies. In addition, strategies should be developed to increase the detection of undiagnosed cases through enhanced screening and treatment access to those not receiving care, and revisit current treatment approaches to ensure that they are more tailored to the specific populations and settings. In conclusion, innovative strategies are needed to identify and overcome barriers to hypertension diagnosis and management. A coordinated, multisectoral approach that includes a contextualized mechanistic research agenda, as well as task shifting and task sharing, will help prevent and reduce hypertension in SSA

Blood culture time to positivity in pediatric patients with bloodstream infection in rural Gambia.

OBJECTIVES: There is a lack of data on the time to blood culture positivity (TTP) in pediatric populations in low-income countries. We aimed to assess the host and pathogen factors associated with TTP in children aged under 5 years in rural Gambia. METHODS: Between September 2019 and December 2023, we collected blood cultures from children under 5 years with suspected bloodstream infections. We determined the TTP from the time of culture incubation to when bacterial growth was first detected. RESULTS: Overall, 547 invasive bacteria pathogens were evaluated. The median TTP was 19.2 hours and 70%, 76%, 89%, and 96% of cases had TTP at 24, 36, 48, and 72 hours, respectively. Streptococcus pneumoniae had the shortest median TTP (17.4 hours), whereas Neisseria species had the longest (45 hours). TTP was dependent on the pathogen and independent of age, sex, temperature, clinical outcome, nutritional status, and length of hospital stay. Gram-positive bacteria had shorter TTP than gram-negative bacteria (18.6 vs 19.6 hours, P < 0.01). CONCLUSIONS: In rural Gambia, most blood cultures from pediatric patients would turn positive within 48 hours of incubation. A maximum of 48 hours of observation after the commencement of antibiotic therapy in hospitalized children may be sufficient for clinicians to receive feedback on blood culture results