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Journal articlePapaiakovou M, Waeschenbach A, Ajibola O, et al., 2025,
Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets
, NATURE COMMUNICATIONS, Vol: 16- Cite
- Citations: 1
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Journal articlePapaiakovou M, Waeschenbach A, Anderson RM, et al., 2025,
Enrichment of Helminth Mitochondrial Genomes From Faecal Samples Using Hybridisation Capture
, MOLECULAR ECOLOGY RESOURCES, ISSN: 1755-098X -
Journal articleTroman C, Horsfield ST, Abraham D, et al., 2025,
Determining genotype and antimicrobial resistance of Salmonella Typhi in environmental samples by amplicon sequencing
, PLoS Neglected Tropical Diseases, Vol: 19, ISSN: 1935-2727BackgroundEstimates of the burden of typhoid fever due to Salmonella enterica serovar Typhi (S. Typhi) rely on data from clinical surveillance, which is rarely done in low income settings and is also limited by the poor sensitivity of the assays used and the reliance on health seeking by patients. Environmental surveillance for S. Typhi shed by symptomatic and asymptomatic individuals in wastewater offers a sensitive surveillance tool that could help to inform burden estimates. Sequencing S. Typhi direct from wastewater concentrates has the potential to identify circulating genotypes and associated antimicrobial resistance (AMR) genes, supporting public health interventions such as vaccination and antimicrobial usage.Methodology and principal findingsWe designed a multiplex targeted amplicon sequencing protocol for genotyping and determining AMR in S. Typhi from wastewater samples, targeting SNPs that identify genotypes of interest and both chromosomal and plasmid-borne AMR. PCR products were sequenced using the Oxford Nanopore Technologies (ONT) MinION, and genotypes and AMR identified using the GenoTyphi program.We tested this approach on samples from south India from both hospital outflow and wastewater collected from the community. All samples tested were suspected to be positive for S. Typhi following quantitative PCR for ttr, tviB, and staG gene targets. Out of 110 samples tested we were able to determine a genotype and/or AMR for 8. All samples that gave a genotype call suggested a genotype consistent with those found in clinical cases in India during the same time period and produced consensus sequences that clustered with S. Typhi when included in a phylogenetic tree.ConclusionsIn this study, we provide proof of concept data for amplicon sequencing of S. Typhi in wastewater which with further optimisation could be used to complement clinical surveillance data or provide data on S. Typhi presence in the absence of clinical surveillance. This information can
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Journal articleKwok WC, Pates K, Shah A, et al., 2025,
Antimicrobial resistance in chronic lung infection: the road to resistance
, Thorax, ISSN: 0040-6376Background Antimicrobial resistance (AMR) is a growing global health crisis and is particularly relevant to people living with chronic lung diseases such as bronchiectasis, cystic fibrosis and chronic obstructive pulmonary disease. These conditions frequently involve acute and chronic bacterial infections, requiring increased antibiotic usage and risk of AMR. Understanding the dynamics of AMR and emerging diagnostic and therapeutic strategies is crucial for optimising patient outcomes in this setting.Aims This review explores the interplay between AMR and chronic bacterial lung infections, examining current understanding of pathogen epidemiology, diagnostic strategies, clinical implications of resistance and the impact of treatments. Future directions in research and therapeutic innovation are also outlined.Narrative Key pathogens in chronic lung infections, such as Pseudomonas aeruginosa, Haemophilus influenzae, Staphylococcus aureus and Moraxella catarrhalis, exhibit diverse resistance mechanisms and AMR is linked to increased disease severity, exacerbation frequency and mortality, particularly with multidrug-resistant strains. Long-term antibiotic therapies, such as macrolides and inhaled agents, improve clinical outcomes but may drive resistance, necessitating ongoing efforts to understand how they can best be employed. Traditional diagnostic methods, such as culture-based antimicrobial susceptibility testing, often fail to capture the complexity of polymicrobial infections and resistomes. Although advanced techniques like next-generation sequencing and metagenomics are able to identify clinically relevant resistotypes, their development toward clinical utility is still in progress.Conclusions AMR in chronic lung infections represents a dynamic and multifaceted challenge. Novel antibiotics, precision medicine approaches and alternative therapies such as bacteriophages show promise but require further validation. Improved stewardship and individualised treatment
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Journal articleHung TM, Nguyen TN, Le MT, et al., 2025,
Non-medical costs incurred by critically ill patients with dengue, sepsis and tetanus within a major referral hospital in Southern Vietnam: a cost of illness study
, BMJ Public Health, Vol: 3, ISSN: 2753-4294Introduction Improving the knowledge of the costs of critical care is vital for informing health policy. However, cost data remain limited, particularly for low- and middle-income countries. The aim of this cross-sectional study is to describe the direct/indirect non-medical costs incurred by critically ill tetanus, sepsis and dengue patients and their families during their hospitalisation, using data from a major referral hospital in Vietnam.Methods This study was conducted within the Hospital for Tropical Diseases in Ho Chi Minh City, a tertiary referral hospital specialising in infectious diseases serving Southern Vietnam. Patients who were admitted to the intensive care unit (ICU) and diagnosed with either tetanus, dengue or sepsis were enrolled between April and November 2022. In total, 94 patients (and their caregivers) were interviewed. Structured questionnaires were used to estimate the direct non-medical costs and indirect costs (costs related to productivity/time losses) incurred during their hospitalisation by the patients and their caregivers (ie, the patients’ perspective).Results Overall, the estimated median total direct/indirect non-medical costs of the sample varied between US$511 and US$814 per patient, depending on the approach used to value the indirect costs. These total costs were broadly similar among sepsis and tetanus cases, but lower for dengue cases. The estimated indirect costs were highly sensitive to the approach used to monetise productivity losses and the valuation of informal care.Conclusion This study demonstrates that patients admitted to the ICU with a severe infection of these diseases can incur notable direct/indirect non-medical costs. These results highlight the importance of further research in this area. These findings are particularly relevant in the context of universal health coverage targets, as even with 100% coverage of medical costs, many families are still likely to suffer financial hardship.
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Journal articleMoorhouse L, Imai-Eaton J, Dadirai T, et al., 2025,
Measurement and interpretation of the Harare HIV combination prevention cascade in priority populations: A population survey of adolescent girls and young women and young men in Zimbabwe
, BMJ Public Health, Vol: 3, ISSN: 2753-4294Introduction HIV-negative adolescent girls and young women (AGYW), and men (ABYM), have disproportionately high HIV incidence in many African countries. We used a new HIV Prevention Cascade (HPC) approach to quantify levels of, and barriers to, prevention method use to guide interventions to increase effective uptake of primary HIV prevention.Methods Data from the Manicaland HPC pilot study (2018–19; n=9803) in Zimbabwe were used to measure levels of sexual risk behaviour and construct HPCs for male condom, pre-exposure prophylaxis (females), voluntary medical male circumcision (males) and combination prevention use by HIV-negative sexually active AGYW (15–24 years) and male partners (15–29 years).Results 19% of AGYW (n=1140) and 37% of ABYM (n=955) who had started sex reported one or more HIV risk behaviour and met the definition of the priority populations for HIV prevention. Of these, 63% of AGYW and 87% of ABYM were motivated to use an HIV prevention method, 28% and 63% had access to a method and 16% and 53% used a method. Male condoms were the most commonly used prevention method, accounting for 97% of use in AGYW and 55% in ABYM. Barriers to motivation, access and capacity to use were reported for all priority populations and methods. Some barriers were common across HPCs (eg, lack of risk perception, social unacceptability and lack of acceptable provision); others were specific to particular prevention methods or priority populations (eg, lack of availability).Conclusion HIV risk behaviours were commonly reported, but gaps in use of prevention methods exist among young people reporting these HIV risk behaviours in Manicaland. Population survey measurements of HPCs revealed large gaps in all steps in the cascade (lack of motivation, lack of access and lack of capacity to use prevention) and provided information on the reasons for these gaps that can aid in designing interventions that reduce new infections.
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Journal articleEllis J, Anderson R, 2025,
Pre-school age participation in mass drug administration: analysing the impact on community-wide schistosomiasis control
, International Journal of Infectious Diseases, Vol: 156, ISSN: 1201-9712ObjectivesSchistosome infection in childhood is common and can lead to morbidity. A formulation of praziquantel to treat preschool-aged children (PSAC) has been developed recently. This paper assesses the impact of including PSAC in mass drug administration (MDA) on transmission and morbidity at a community-wide level.MethodsWe used a model of schistosome transmission to simulate the probability of a community reaching elimination as a public health problem (EPHP) and the reduction in morbidity of children resulting from infections until the age of 5 years, measured by a “worm years” metric as a score of morbidity.ResultsIncluding PSAC in MDA will almost always lead to a reduction in morbidity. However, it does not necessarily result in a substantial increase in the probability of EPHP. The proportion of schistosome infections in each age group is a key factor in determining the effectiveness of MDA programs, which prioritize different age groups for treatment.ConclusionsPolicymakers should be aware that including PSAC in MDA may not help to reach the World Health Organization target of EPHP. However, a reduction in the average summed worm infection burden at the age children typically start attending school is highly desirable in increasing the long-term benefit of MDA in early childhood.
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Journal articleUlrich AK, Moua NM, Mack A, et al., 2025,
Meeting report on an integrated research agenda for mosquito-borne arboviruses
, Open Forum Infectious Diseases, Vol: 12, ISSN: 2328-8957The emergence and re-emergence of mosquito-borne arbovirus (MBV) diseases pose a rapidly expanding global health threat fueled by the convergence of multiple ecologic, economic, and social factors, including climate change, land use, poverty, deficiencies of water storage and sanitation, and limitations of vector control programs. On December 6, 2023, the Wellcome Trust and the University of Minnesota's Center for Infectious Disease Research and Policy held a meeting titled “An integrated approach to mosquito-borne arboviruses: a priority research agenda.” The meeting comprised presentations, panels, and facilitated discussions aimed at describing the state of the field, highlighting recent accomplishments, identifying novel strategies, and defining priority research goals and approaches for addressing MBV disease preparedness and response. This report summarizes meeting discussions in 3 key areas: the changing epidemiology of MBV disease, current and potential transmission- and disease-monitoring strategies, and evolutionary impacts on disease burden and transmission. It concludes with a list of priority strategies for research and investment in MBV disease prevention, preparedness, and control. To prepare for future epidemics of MBV diseases, research and policy will benefit from a multipathogen approach to MBVs. Building on existing knowledge and systems, these efforts must address social and ecological factors and connect with other global health agendas.
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Journal articleDelma FZ, Spruijtenburg B, Meis JF, et al., 2025,
Emergence of Flucytosine-Resistant Candida tropicalis Clade, the Netherlands
, Emerging Infectious Diseases, Vol: 31, Pages: 1354-1364, ISSN: 1080-6040Candida tropicalis is the second most virulent Candida species after C. albicans. Previous studies from the Netherlands and France reported a notable reduction in susceptibility to flucytosine (5-FC) in a substantial proportion of C. tropicalis isolates. We investigated epidemiologic patterns of C. tropicalis isolates in the Netherlands and the genetic mechanisms driving widespread non–wild-type (WT) 5-FC resistance. We conducted antifungal susceptibility testing and used advanced molecular techniques, including short tandem repeat genotyping and whole-genome sequencing paired with single-nucleotide polymorphism analysis, to analyze 250 C. tropicalis isolates collected across the Netherlands during 2012–2022. Our findings revealed the rapid emergence of a 5-FC–resistant, non-WT C. tropicalis clade, accounting for >40% of all C. tropicalis isolates by 2022. Genomic analysis identified a homozygous nonsense mutation in the FCY2 gene, which was exclusive to this non-WT population. Continued surveillance efforts are needed to detect and prevent the spread of drug-resistant Candida species.
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Journal articleStansfield SE, Moore M, Jamieson L, et al., 2025,
Estimated impact of long‐acting injectable PrEP in South Africa: a model comparison analysis
, Journal of the International AIDS Society, Vol: 28, ISSN: 1758-2652IntroductionLong-acting injectable cabotegravir (CAB-LA) demonstrated superiority to daily tenofovir disoproxil fumarate/emtricitabine (TDF/FTC) for human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) in two clinical trials. This analysis projects the impact of expanding PrEP coverage with CAB-LA in South Africa between 2022 and 2042.MethodsThree independently calibrated models of HIV transmission in South Africa (Synthesis, EMOD-HIV, Thembisa) projected HIV acquisitions and effective coverage (average PrEP coverage across exposure groups, weighted by HIV incidence in the absence of PrEP in each group) over 20 years under multiple scenarios of PrEP expansion compared to no PrEP expansion. PrEP expansion scenarios differed in targeted overall coverage, speed of expansion, coverage of high-exposure groups, and relative coverage of women and men.ResultsAchieving 5% PrEP coverage with CAB-LA by 2032 prioritizing high-exposure groups resulted in 49% (Synthesis), 18% (EMOD-HIV), and 8% (Thembisa) effective coverage and averted a median of 43%, 29% and 10% of new HIV acquisitions, respectively. Similar expansion with TDF/FTC resulted in lower impact by 19 percentage points (pp), 18pp and 3pp, respectively. Increasing CAB-LA coverage to 15% led to an additional 7pp, 12pp and 16pp, respectively, of HIV acquisitions averted. Achieving 5% CAB-LA coverage expanding to women only resulted in a lower impact by 16pp (Synthesis) and 13pp (EMOD-HIV), and a higher impact by 2pp (Thembisa). Scenarios with similar effective coverage resulted in comparable impact estimates across models.ConclusionsOffering CAB-LA in South Africa may substantially impact the HIV epidemic based on these projections. Effective coverage proved to be a good predictor of intervention effectiveness.
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