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Journal articleBroshkevitch CJ, Zhou S, Greifinger A, et al., 2025,
Sequencing HIV diagnostic samples to detect genetic clusters and assess sequence coverage gaps
, Open Forum Infectious Diseases<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>HIV molecular cluster detection in the United States relies on HIV sequences obtained from drug resistance testing during clinical care (“routine care sequences”). This approach misses people who are not linked to care or who receive care but have uncollected or unreported sequences.</jats:p> </jats:sec> <jats:sec> <jats:title>Methods</jats:title> <jats:p>We collected “HIV test sequences” from remnant serum samples of people testing newly positive from 2018 through 2021 by a large public health laboratory in North Carolina. We incorporated the HIV test sequences into a statewide molecular cluster analysis and assessed impact on “active cluster” detection (≥5 members newly diagnosed). We described data gaps filled by HIV test sequences, comparing extent of care sequence missingness due to gaps in care linkage versus sequence collection or reporting, and characteristics of people with an HIV test sequence who had a care sequence, care but no care sequence, or no evidence of care.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>Of 19,770 people included in the cluster analysis, 847 had an HIV test sequence, one-third of whom had no routine care sequence. We identified 13 additional active clusters (a 33% relative increase) and 40 larger active clusters after incorporating HIV test sequences. Most people with an HIV test sequence but no care sequence (78%) had another care indicator, suggesting sequence undercollection or underreporting, but a fifth (22%) had no evidence of care.</jats:p> </jats:sec> <j
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Journal articleSlavinska A, Jauneikaite E, Meškytė U, et al., 2025,
Genomic characterization of Listeria monocytogenes isolated from normally sterile human body fluids in Lithuania from 2016 to 2021
, Microbial Genomics, Vol: 11, ISSN: 2057-5858Listeria monocytogenes is a saprophytic gram-positive bacterium and opportunistic foodborne pathogen that can cause listeriosis in humans. The incidence of listeriosis has been rising globally and, despite antimicrobial treatment, the mortality rates associated with the most severe forms of listeriosis such as sepsis, meningitis and meningoencephalitis remain high. The notification of listeriosis in humans is mandatory in Lithuania, and up to 20 cases are reported annually. However, no studies have described the detailed virulence and antimicrobial susceptibility profiles of any clinical L. monocytogenes strains in Lithuania. Accordingly, this study aimed to describe the antibiotic susceptibility of invasive L. monocytogenes and perform in-depth characterization of strains isolated from patients with neuroinfections through whole-genome sequencing. A total of 70 isolates were collected, mostly from infected patients aged 65 or older, between 2016 and 2021 : 41 (58.6%) from blood, 19 (27.1%) from cerebrospinal fluid, 5 (7.1%) from wounds, 1 (1.4%) from pleural fluid and 1 (1.4%) from a brain abscess. Two phylogenetic lineages were identified—I (n = 16/70, 22.9%) and II (n = 54/70, 77.1%)—along with three serogroups—IIa (n = 53/70, 75.7%), IVb (n = 16/70, 22.9%), and IIc (n = 1/70, 1.4%). Genomic analysis of 20 isolates showed a high level of diversity with seven genotypes: ST6 (n = 6), ST155 (n = 5), ST8 (n = 4), ST504 (n = 2) and singletons for ST37, ST451 and ST2. Phylogenetic analysis clustered these isolates into two clades defined by serogroups IVb and IIa. Notably, five isolates were clustered tightly together (difference of 6–48 core SNPs from reference and 0, 4 or 44 SNPs from each other) with ST155, previously reported in a European outbreak. Comparison with publicly available L. monocytogenes genomes did not identify unique clusters or genotypes. No acquired antimicrobial resistance genes were identified. Our study highlights
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Journal articleCluver L, Makangila G, Hillis S, et al., 2025,
Protecting Africa's children from extreme risk: a runway of sustainability for PEPFAR programmes
, Lancet, Vol: 405, Pages: 1700-1712, ISSN: 0140-6736PEPFAR (President's Emergency Plan for AIDS Relief), a landmark US foreign health policy, is recognised for saving 26 million lives from HIV. PEPFAR investments have also had life-saving impacts for children across sub-Saharan Africa through childhood HIV prevention, care, and treatment, ensuring 7·8 million babies were born HIV-free, supporting 13 million orphaned and vulnerable children, and protecting 10·3 million girls from sexual abuse. In this Health Policy, we review data from UNAIDS, UNICEF, World Bank, Violence Against Children Surveys, SPECTRUM model data, and Population-based HIV Impact Assessments; synthesise PEPFAR reports; conduct in-depth interviews; search PubMed for programme effectiveness evidence; and review economic reports. PEPFAR support is associated with substantial collateral benefits for the USA and Africa, including a four-fold increase in export of US goods to Africa, and US$71·6 billion in total goods trade between the USA and Africa in 2024. PEPFAR-supported countries in Africa are committed to ownership of HIV responses by 2030—overall, PEPFAR-supported countries in sub-Saharan Africa have progressively increased their co-financing of their health systems through domestic government and private expenditure from $13·7 billion per year in 2004 to $42·6 billion per year in 2021. The feasibility of a 5-year transition to country-led sustainability is supported by evidence of innovative cost-saving models of delivery, including through faith-based and community-based organisations, and high return-on-investment for PEPFAR programmes. There are also collateral benefits of PEPFAR for US and Africa national security and health security, for example, reducing forced migration and increasing capacity to control emerging transborder infectious disease threats. Risks in sub-Saharan Africa remain acute: one in five girls (younger than 18 years) experience rape or sexual assault; one in ten children (younger
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Journal articleRomanello M, Beggs PJ, Cai W, et al., 2025,
From crisis to opportunity: a united response to Trump's attacks on climate action
, Lancet, Vol: 405, Pages: 1647-1650, ISSN: 0140-6736 -
Journal articleMousa A, Cuomo-Dannenburg G, Thompson H, et al., 2025,
Impact of dhps mutations on sulfadoxine pyrimethamine protective efficacy and implications for malaria chemoprevention
, Nature Communications, Vol: 16, ISSN: 2041-1723Sulfadoxine-pyrimethamine (SP) is recommended for perennial malaria chemoprevention in young children in high burden areas across Africa. Mutations in the dihydropteroate synthase (dhps) gene (437 G/540E/581 G) associated with sulfadoxine resistance vary regionally, but their effect on SP protective efficacy is unclear. We retrospectively analyse time to microscopy and PCR-confirmed re-infection in seven efficacy trials including 1639 participants in 12 sites across Africa. We estimate the duration of SP protection against parasites with different genotypes using a Bayesian mathematical model that accounts for variation in transmission intensity and genotype frequencies. The longest duration of SP protection is >42 days against dhps sulfadoxine-susceptible parasites and 30.3 days (95%Credible Interval (CrI):17.1-45.1) against the West-African genotype dhps GKA (437G-K540-A581). A shorter duration of protection is estimated against parasites with additional mutations in the dhps gene, with 16.5 days (95%CrI:11.2-37.4) protection against parasites with the east-African genotype dhps GEA (437G-540E-A581) and 11.7 days (95%CrI:8.0-21.9) against highly resistant parasites carrying the dhps GEG (437G-540E−581G) genotype. Using these estimates and modelled genotype frequencies we map SP protection across Africa. This approach and our estimated parameters can be directly applied to any setting using local genomic surveillance data to inform decision-making on where to scale-up SP-based chemoprevention or consider alternatives.
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Journal articleRawson T, Morgenstern C, Knock E, et al., 2025,
A mathematical model of H5N1 influenza transmission in US dairy cattle
, Nature Communications, ISSN: 2041-1723 -
Journal articleLeng T, Whittles LK, Nikitin D, et al., 2025,
Modeling gonorrhea vaccination to find optimal targeting strategies that balance impact with cost-effectiveness
, npj Vaccines, ISSN: 2059-0105Vaccination for UK men-who-have-sex-with-men (MSM) at increased gonorrhea risk has been advised, but not yet implemented. Effective targeting is essential for cost-effectiveness, but previously-examined approacheshave disadvantages: Vaccination-on-Diagnosis has low coverage (limiting impact), and Vaccination-according-to-Risk requires asking about sexual behavior to identify at-risk individuals, which is not always feasible. Wedeveloped a transmission-dynamic model to evaluate novel strategies offering vaccination based on information readily-available to clinicians (diagnostic/vaccination history, if the patient is seeking care due to partner notification). Offering vaccination to MSM who are notified partners of gonorrhea cases or were diagnosed themselves in the past 2 years averts 1.6x more cases and is more cost-effective than Vaccination-on-Diagnosis. If vaccination provides 20% protection for 1.5 years after primary vaccination and 3 years after revaccination then at £18/dose administered, all considered strategies have ≥ 50% and ≥ 90% probabilities of positive net monetary benefit compared with no vaccination with a quality-adjusted life year valued at £20,000 and £30,000 respectively, thus meeting the UK criteria for cost-effectiveness. All novel strategies considered achieve greater impact than Vaccination-on-Diagnosis without the feasibility issues of Vaccination-according-to-Risk.
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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, ISSN: 1201-9712 -
Journal articleRawson TM, Al-Hassan M, Brzeska-Trafny I, et al., 2025,
Comment on: Resistance profiles of carbapenemase-producing Enterobacterales in a large centre in England: are we already losing cefiderocol?
, Journal of Antimicrobial Chemotherapy, Vol: 80, Pages: 1462-1464, ISSN: 0305-7453 -
Journal articleBurger R, Bell-Mandla N, Harper A, et al., 2025,
Does enhanced HIV prevention, diagnosis, and linkage to care reduce hospitalisation in high HIV-burden communities in Zambia and South Africa? findings from the HPTN 071 (PopART) randomised trial
, PLOS Global Public Health, Vol: 5The objective of this study is to explore if a community-based HIV combination prevention intervention reduced inpatient hospitalisations in Zambia and South Africa by diagnosing HIV and TB in earlier stages of disease progression, thereby preventing severe disease and new infections. As part of the HIV Prevention Trials Network (HPTN) 071 trial, hospitalisation data from a cohort of 16 968 consenting randomly sampled adults aged 18–44 years were collected between 28 November 2013 and 16 November 2018 across 21 communities in Zambia and South Africa across three study arms. Arm A included annual visits by Community HIV-care Providers (CHiPs) and universal linkage to care for ART initiation for all PLWH (irrespective of CD4 count); arm B included annual CHiPs visits and ART per local guidelines; control arm C received the standard of care provided at government clinics, including HIV testing and ART offered according to local guidelines. For this study, we used a cluster-level two-stage analysis and adjusted for covariates that were unbalanced across intervention arms. Covariates included in the models were the cluster’s baseline HIV prevalence and hospitalisation rate and data on the respondent’s gender, age, educational attainment, and socio-economic status. Out of the pooled sample of 13 964 responses from the three post-baseline surveys, 439 (3.14%) reported hospitalisation in the past 12 months – 234 (1.68%) when excluding hospital admissions for births or injury. Comparing hospitalisations in the intervention and control arm clusters, the estimated adjusted risk ratio was 1.03 [0.64–1.66] for the full sample and 0.82 [0.39–1.74] for PLWH. We find no compelling evidence of impact of the HPTN071 (PopART) community-wide combination HIV prevention intervention on in-patient hospitalisation among a general population sample.
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