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Journal articleMangal T, Mohan S, Colbourn T, et al., 2024,
Assessing the impact of health system frailties on HIV and TB programmes: a modelling study in Malawi
, The Lancet Global Health, ISSN: 2214-109XBackgroundMalawi is progressing towards UNAIDS and WHO End TB targets to eliminate AIDS and TB. We assess the prospective impact of achieving these goals and the influence of consumables constraints.MethodsThe Thanzi la Onse model is an individual-based multi-disease simulation model which represents HIV and TB, alongside other diseases, and gates access to essential medicines according to empirical estimates of availability. The model integrates dynamic disease modelling with health system engagement behaviour, health system usage and capabilities (personnel and consumables). HIV and TB programme scale-up are projected until 2033. Findings With uninterrupted medical supplies, HIV and TB incidence could drop to 26 and 55 cases/100,000 person-years by 2033 (from 152 and 123 cases /100,000 person-years in 2023) with programme scale-up, averting 12.21 million DALYs. However, the impact is compromised by limited access to key medicines, resulting in 58,700 additional deaths (33,400 AIDS and 25,300 TB deaths) attributed to consumables stockouts. Eliminating HIV treatment stockouts could avert 12,100 deaths, and improved TB prevention access could prevent 5,600 deaths above those achieved through programme scale-up alone. Consumables stockouts strain the healthcare system, requiring 14.3 million extra patient-facing hours between 2023-2033, mostly from clinical staff. With enhanced screening, 80.9% of individuals could start TB treatment within two weeks of initial presentation if all required consumables were available, but only 57.0% with current levels of availability. InterpretationIgnoring frailties in the healthcare system, in particular the non-availability of consumables, in projections of HIV and TB scale-up may risk over-estimating potential health impacts and under-estimating required health system resources. Simultaneous health system strengthening alongside programme scale-up is crucial, which should yield greater benefits to population health while mitigat
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Journal articleOkiring J, Gonahasa S, Maiteki-Sebuguzi C, et al., 2024,
LLIN Evaluation in Uganda Project (LLINEUP): modelling the impact of COVID-19-related disruptions on delivery of long-lasting insecticidal nets on malaria indicators in Uganda
, Malaria Journal, Vol: 23, ISSN: 1475-2875BACKGROUND: Disruptions in malaria control due to COVID-19 mitigation measures were predicted to increase malaria morbidity and mortality in Africa substantially. In Uganda, long-lasting insecticidal nets (LLINs) are distributed nationwide every 3-4 years, but the 2020-2021 campaign was altered because of COVID-19 restrictions so that the timing of delivery of new nets was different from the original plans made by the National Malaria Control Programme. METHODS: A transmission dynamics modelling exercise was conducted to explore how the altered delivery of LLINs in 2020-2021 impacted malaria burden in Uganda. Data were available on the planned LLIN distribution schedule for 2020-2021, and the actual delivery. The transmission model was used to simulate 100 health sub-districts, and parameterized to match understanding of local mosquito bionomics, net use estimates, and seasonal patterns based on data collected in 2017-2019 during a cluster-randomized trial (LLINEUP). Two scenarios were compared; simulated LLIN distributions matching the actual delivery schedule, and a comparable scenario simulating LLIN distributions as originally planned. Model parameters were otherwise matched between simulations. RESULTS: Approximately 70% of the study population received LLINs later than scheduled in 2020-2021, although some areas received LLINs earlier than planned. The model indicates that malaria incidence in 2020 was substantially higher in areas that received LLINs late. In some areas, early distribution of LLINs appeared less effective than the original distribution schedule, possibly due to attrition of LLINs prior to transmission peaks, and waning LLIN efficacy after distribution. On average, the model simulations predicted broadly similar overall mean malaria incidence in 2021 and 2022. After accounting for differences in cluster population size and LLIN distribution dates, no substantial increase in malaria burden was detected. CONCLUSIONS: The model results sugge
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Journal articleMallawaarachchi S, Tonkin-Hill G, Pontinen AK, et al., 2024,
Detecting co-selection through excess linkage disequilibrium in bacterial genomes
, NAR GENOMICS AND BIOINFORMATICS, Vol: 6 -
Journal articleHall E, Davis K, Ohrnberger J, et al., 2024,
Associations between HIV stigma and health-related quality-of-life among people living with HIV: cross-sectional analysis of data from HPTN 071 (PopART)
, Scientific Reports, Vol: 14, ISSN: 2045-2322People living with HIV (PLHIV) report lower health-related quality-of-life (HRQoL) than HIV-negative people. HIV stigma may contribute to this. We explored the association between HIV stigma and HRQoL among PLHIV. We used cross-sectional data from 3,991 randomly selected PLHIV who were surveyed in 2017-2018 for HPTN 071 (PopART), a cluster randomised trial in Zambia and South Africa. Participants were 18-44 years, had laboratory-confirmed HIV infection, and knew their status. HRQoL was measured using the EuroQol-5-dimensions-5-levels (EQ-5D-5L) questionnaire. Stigma outcomes included: internalised stigma, stigma experienced in the community, and stigma experienced in healthcare settings. Associations were examined using logistic regression. Participants who had experienced community stigma (n=693/3991) had higher odds of reporting problems in at least one HRQoL domain, compared to those who had not (adjusted odds ratio, aOR: 1.51, 95% confidence interval, 95% Cl: 1.16-1.98, p=0.002). Having experienced internalised stigma was also associated with reporting problems in at least one HRQoL domain (n=552/3991, aOR: 1.98, 95% CI: 1.54-2.54, p<0.001). However, having experienced stigma in a healthcare setting was less common (n=158/3991) and not associated with HRQoL (aOR: 1.04, 95% CI: 0.68-1.58, p=0.850). A stronger focus on interventions for internalised stigma and stigma experienced in the community is required.
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Journal articleHui ST, Gifford H, Rhodes J, 2024,
Emerging Antifungal Resistance in Fungal Pathogens
, Current Clinical Microbiology Reports, Vol: 11, Pages: 43-50Purpose of Review: Over recent decades, the number of outbreaks caused by fungi has increased for humans, plants (including important crop species) and animals. Yet this problem is compounded by emerging antifungal drug resistance in pathogenic species. Resistance develops over time when fungi are exposed to drugs either in the patient or in the environment. Recent Findings: Novel resistant variants of fungal pathogens that were previously susceptible are evolving (such as Aspergillus fumigatus) as well as newly emerging fungal species that are displaying antifungal resistance profiles (e.g. Candida auris and Trichophyton indotineae). Summary: This review highlights the important topic of emerging antifungal resistance in fungal pathogens and how it evolved, as well as how this relates to a growing public health burden.
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Journal articleBecker M, Mishra S, Bhattacharjee P, et al., 2024,
Differential burden of HIV among adolescent girls and young women by places associated with sex work: an observational study in Mombasa, Kenya
, JAIDS: Journal of Acquired Immune Deficiency Syndromes, Vol: 96, Pages: 121-129, ISSN: 1525-4135BACKGROUND: The design of HIV prevention programs for adolescent girls and young women (AGYW) are informed by data on who is at highest risk and where they can be reached. Places (hotspots) associated with selling sex are an established outreach strategy for sex work (SW) programs but could be used to reach other AGYW at high risk. SETTING: This study took place in Mombasa, Kenya. METHODS: We conducted a cross-sectional, bio-behavioural survey among (N = 1193) sexually active AGYW aged 14-24 years recruited at hotspots. We compared HIV prevalence by subgroup (SW; transactional sex, TS; and non-transactional sex), stratified by hotspot type (venues and nonvenues). We examined whether associations between HIV prevalence and hotspot/subgroup remained after adjustment for individual-level risk factors, and estimated HIV prevalence ratio with and without adjustment for these individual-level factors. RESULTS: Overall HIV prevalence was 5.6%, 5.3% in venues and 7.3% in nonvenues. Overall SW HIV prevalence was 2-fold higher than among participants engaged in nontransactional sex. After adjusting for age and individual-level risk factors, HIV prevalence was 2.72 times higher among venue-based SWs (95% confidence interval: 1.56 to 4.85) and 2.11 times higher among nonvenue AGYW not engaged in SW (95% confidence interval: 0.97 to 4.30) compared with venue-based AGYW not engaged in SW. CONCLUSION: AGYW who sell sex remain at high risk of HIV across types of hotspots. The residual pattern of elevated HIV burden by AGWY subgroup and hotspot type suggests that unmeasured, network-level factors underscore differential risks. As such, hotspots constitute a "place" to reach AGYW at high risk of HIV.
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Journal articleOgi-Gittins I, Hart WS, Song J, et al., 2024,
A simulation-based approach for estimating the time-dependent reproduction number from temporally aggregated disease incidence time series data
, Epidemics: the journal of infectious disease dynamics, Vol: 47, ISSN: 1755-4365Tracking pathogen transmissibility during infectious disease outbreaks is essential for assessing the effectiveness of public health measures and planning future control strategies. A key measure of transmissibility is the time-dependent reproduction number, which has been estimated in real-time during outbreaks of a range of pathogens from disease incidence time series data. While commonly used approaches for estimating the time-dependent reproduction number can be reliable when disease incidence is recorded frequently, such incidence data are often aggregated temporally (for example, numbers of cases may be reported weekly rather than daily). As we show, commonly used methods for estimating transmissibility can be unreliable when the timescale of transmission is shorter than the timescale of data recording. To address this, here we develop a simulation-based approach involving Approximate Bayesian Computation for estimating the time-dependent reproduction number from temporally aggregated disease incidence time series data. We first use a simulated dataset representative of a situation in which daily disease incidence data are unavailable and only weekly summary values are reported, demonstrating that our method provides accurate estimates of the time-dependent reproduction number under such circumstances. We then apply our method to two outbreak datasets consisting of weekly influenza case numbers in 2019–20 and 2022–23 in Wales (in the United Kingdom). Our simple-to-use approach will allow accurate estimates of time-dependent reproduction numbers to be obtained from temporally aggregated data during future infectious disease outbreaks.
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Journal articleVicco A, McCormack C, Pedrique B, et al., 2024,
A scoping literature review of global dengue age-stratified seroprevalence data: estimating dengue force of infection in endemic countries
, EBioMedicine, Vol: 104, ISSN: 2352-3964BackgroundDengue poses a significant burden worldwide, and a more comprehensive understanding of the heterogeneity in the intensity of dengue transmission within endemic countries is necessary to evaluate the potential impact of public health interventions.MethodsThis scoping literature review aimed to update a previous study of dengue transmission intensity by collating global age-stratified dengue seroprevalence data published in the Medline, Embase and Web of Science databases from 2014 to 2023. These data were then utilised to calibrate catalytic models and estimate the force of infection (FOI), which is the yearly per-capita risk of infection for a typical susceptible individual.FindingsWe found a total of 66 new publications containing 219 age-stratified seroprevalence datasets across 30 endemic countries. Together with the previously available average FOI estimates, there are now more than 250 dengue average FOI estimates obtained from seroprevalence studies from across the world.InterpretationThe results show large heterogeneities in average dengue FOI both across and within countries. These new estimates can be used to inform ongoing modelling efforts to improve our understanding of the drivers of the heterogeneity in dengue transmission globally, which in turn can help inform the optimal implementation of public health interventions.FundingUK Medical Research Council, Wellcome Trust, Community Jameel, Drugs for Neglected Disease initiative (DNDi) funded by the French Development Agency, Médecins Sans Frontières International; Swiss Agency for Development and Cooperation and UK aid.
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Journal articleCori A, 2024,
SIR… or MADAM? The impact of privilege on careers in epidemic modelling.
, Epidemics, Vol: 47As we emerge from what may be the largest global public health crises of our lives, our community of epidemic modellers is naturally reflecting. What role can modelling play in supporting decision making during epidemics? How could we more effectively interact with policy makers? How should we design future disease surveillance systems? All crucial questions. But who is going to be addressing them in 10 years' time? With high burnout and poor attrition rates in academia, both magnified in our field by our unprecedented efforts during the pandemic, and with low wages coinciding with inflation at its highest for decades, how do we retain talent? This is a multifaceted challenge, that I argue is underpinned by privilege. In this perspective, I introduce the notion of privilege and highlight how various aspects of privilege (namely gender, ethnicity, sexual orientation, language and caring responsibilities) may affect the ability of individuals to access to and progress within academic modelling careers. I propose actions that members of the epidemic modelling research community may take to mitigate these issues and ensure we have a more diverse and equitable workforce going forward.
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Journal articleMohan S, Mangal TD, Colbourn T, et al., 2024,
Factors associated with medical consumable availability in level 1 facilities in Malawi: a secondary analysis of a facility census
, The Lancet Global Health, Vol: 12, Pages: e1027-e1037, ISSN: 2214-109XBACKGROUND: Medical consumable stock-outs negatively affect health outcomes not only by impeding or delaying the effective delivery of services but also by discouraging patients from seeking care. Consequently, supply chain strengthening is being adopted as a key component of national health strategies. However, evidence on the factors associated with increased consumable availability is limited. METHODS: In this study, we used the 2018-19 Harmonised Health Facility Assessment data from Malawi to identify the factors associated with the availability of consumables in level 1 facilities, ie, rural hospitals or health centres with a small number of beds and a sparsely equipped operating room for minor procedures. We estimate a multilevel logistic regression model with a binary outcome variable representing consumable availability (of 130 consumables across 940 facilities) and explanatory variables chosen based on current evidence. Further subgroup analyses are carried out to assess the presence of effect modification by level of care, facility ownership, and a categorisation of consumables by public health or disease programme, Malawi's Essential Medicine List classification, whether the consumable is a drug or not, and level of average national availability. FINDINGS: Our results suggest that the following characteristics had a positive association with consumable availability-level 1b facilities or community hospitals had 64% (odds ratio [OR] 1·64, 95% CI 1·37-1·97) higher odds of consumable availability than level 1a facilities or health centres, Christian Health Association of Malawi and private-for-profit ownership had 63% (1·63, 1·40-1·89) and 49% (1·49, 1·24-1·80) higher odds respectively than government-owned facilities, the availability of a computer had 46% (1·46, 1·32-1·62) higher odds than in its absence, pharmacists managing drug orders had 85% (1·85, 1·40-2&
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