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Professor Arjen Dondorp and colleagues are inching their way across the fringes of five Southeast Asian countries to test a triple combination therapy of antimalarial drugs.
Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK.
Plasmids enable the dissemination of antimicrobial resistance (AMR) in common Enterobacterales pathogens, representing a major public health challenge. However, the extent of plasmid sharing and evolution between Enterobacterales causing human infections and other niches remains unclear, including the emergence of resistance plasmids. Dense, unselected sampling is essential to developing our understanding of plasmid epidemiology and designing appropriate interventions to limit the emergence and dissemination of plasmid-associated AMR. We established a geographically and temporally restricted collection of human bloodstream infection (BSI)-associated, livestock-associated (cattle, pig, poultry, and sheep faeces, farm soils) and wastewater treatment work (WwTW)-associated (influent, effluent, waterways upstream/downstream of effluent outlets) Enterobacterales. Isolates were collected between 2008 and 2020 from sites <60 km apart in Oxfordshire, UK. Pangenome analysis of plasmid clusters revealed shared 'backbones', with phylogenies suggesting an intertwined ecology where well-conserved plasmid backbones carry diverse accessory functions, including AMR genes. Many plasmid 'backbones' were seen across species and niches, raising the possibility that plasmid movement between these followed by rapid accessory gene change could be relatively common. Overall, the signature of identical plasmid sharing is likely to be a highly transient one, implying that plasmid movement might be occurring at greater rates than previously estimated, raising a challenge for future genomic One Health studies.
Prevalence of resistance-associated viral variants to the HIV-specific broadly neutralising antibody 10-1074 in a UK bNAb-naïve population
Broadly neutralising antibodies (bNAbs) targeting HIV show promise for both prevention of infection and treatment. Among these, 10-1074 has shown potential in neutralising a wide range of HIV strains. However, resistant viruses may limit the clinical efficacy of 10-1074. The prevalence of both de novo and emergent 10-1074 resistance will determine its use at a population level both to protect against HIV transmission and as an option for treatment. To help understand this further, we report the prevalence of pre-existing mutations associated with 10-1074 resistance in a bNAb-naive population of 157 individuals presenting to UK HIV centres with primary HIV infection, predominantly B clade, receiving antiretroviral treatment. Single genome analysis of HIV proviral envelope sequences showed that 29% of participants’ viruses tested had at least one sequence with 10-1074 resistance-associated mutations. Mutations interfering with the glycan binding site at HIV Env position 332 accounted for 95% of all observed mutations. Subsequent analysis of a larger historic dataset of 2425 B-clade envelope sequences sampled from 1983 to 2019 revealed an increase of these mutations within the population over time. Clinical studies have shown that the presence of pre-existing bNAb mutations may predict diminished therapeutic effectiveness of 10-1074. Therefore, we emphasise the importance of screening for these mutations before initiating 10-1074 therapy, and to consider the implications of pre-existing resistance when designing prevention strategies.
The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies
AbstractPlasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative ‘backbone’ of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.
Journeys Through Genomics: Co-Producing Visual Resources to Communicate Patient Experiences
Journeys through Genomics is a series of illustrations co-produced with patients and families to communicate their experiences of seeking genomic explanations for a health condition and the wider impact on their lives. The resources are embedded within qualitative longitudinal research exploring patient’s experiences of genomic medicine. This research takes place as genomic medicine becomes an integral part of mainstream care within the UK healthcare system. The depiction of genomic medicine often focuses on its technological components and the speed by which genetic code can be analysed, but here, we present a dynamic and situated understanding of the challenges genomic testing presents for patients and families. We describe the process of working with research participants and an artist to co-produce visual resources that illustrate the complexity of participant’s journeys, situating genomic testing within the broader context of their lives. These resources are designed to help future patients, families, and healthcare professionals understand the process, opportunities, and challenges they may face.
The hidden emotional labour behind ensuring the social value of research: Experiences of frontline health policy and systems researchers based in Kenya during COVID-19.
Health policy and systems research (HPSR) is a multi-disciplinary, largely applied field of research aimed at understanding and strengthening the performance of health systems, often with an emphasis on power, policy and equity. The value of embedded and participatory HPSR specifically in facilitating the collection of rich data that is relevant to addressing real-world challenges is increasingly recognised. However, the potential contributions and challenges of HPSR in the context of shocks and crises are not well documented, with a particular gap in the literature being the experiences and coping strategies of the HPSR researchers who are embedded in health systems in resource constrained settings. In this paper, we draw on two sets of group discussions held among a group of approximately 15 HPSR researchers based in Nairobi, Kenya, who were conducting a range of embedded HPSR studies throughout the COVID-19 pandemic. The researchers, including many of the authors, were employed by the KEMRI-Wellcome Trust Research Programme (KWTRP), which is a long-standing multi-disciplinary partnership between the Kenya Medical Research Institute and the Wellcome Trust with a central goal of contributing to national and international health policy and practice. We share our findings in relation to three inter-related themes: 1) Ensuring the continued social value of our HPSR work in the face of changing priorities; 2) Responding to shifting ethical procedures and processes at institutional and national levels; and 3) Protecting our own and front-line colleagues' well-being, including clinical colleagues. Our experiences highlight that in navigating research work and responsibilities to colleagues, patients and participants through the pandemic, many embedded HPSR staff faced difficult emotional and ethical challenges, including heightened forms of moral distress, which may have been better prevented and supported. We draw on our findings and the wider literature to discuss considerations for funders and research leads with an eye to strengthening support for embedded HPSR staff, not only in crises such as the on-going COVID-19 pandemic, but also more generally.
Budget monitoring, accountability practices and their influence on the efficiency of county health systems in Kenya.
Public Finance Management (PFM) practices influence the attainment of health system goals. PFM processes are implemented within the budget cycle which entails the formulation, execution, and monitoring of government budgets. Budget monitoring and accountability actors, structures, and processes are important in improving the efficiency of health systems. This study examined how the budget monitoring and accountability processes influence the efficiency of county health systems in KenyaWe conducted a qualitative case study of four counties in Kenya selected based on their relative technical efficiency. We collected data using in-depth interviews with health and finance stakeholders (n = 70), and document reviews. We analyzed data using a thematic approach, informed by our study conceptual framework. We found that weak budget monitoring and accountability mechanisms compromised county health system efficiency by a) weakening the effective implementation of the budget formulation and execution steps of the budget cycle, b) enabling the misappropriation of public resources, and c) limiting evidence-informed decision-making by weakening feedback that would be provided by effective monitoring and accountability. Devolution meant that accountability actors were closer to implementation actors which promoted timely problem solving and the relevance of solutions. Internal audit practices were supportive and provided useful feedback to health system managers that facilitated improvements in budget formulation and execution. The efficiency of county health systems can be improved by strengthening the budget monitoring and accountability processes. This can be achieved by increasing the population's budget literacy, supporting participatory budgeting, synchronizing performance and financial accountability, implementing the existent budget monitoring and accountability mechanisms, rewarding efficiency, and sanctioning inefficiency.
Examining health sector stakeholder perceptions on the efficiency of county health systems in Kenya.
Efficiency gains is a potential strategy to expand Kenya's fiscal space for health. We explored health sector stakeholders' understanding of efficiency and their perceptions of the factors that influence the efficiency of county health systems in Kenya. We conducted a qualitative cross-sectional study and collected data using three focus group discussions during a stakeholder engagement workshop. Workshop participants included health sector stakeholders from the national ministry of health and 10 (out 47) county health departments, and non-state actors in Kenya. A total of 25 health sector stakeholders participated. We analysed data using a thematic approach. Health sector stakeholders indicated the need for the outputs and outcomes of a health system to be aligned to community health needs. They felt that both hardware aspects of the system (such as the financial resources, infrastructure, human resources for health) and software aspects of the system (such as health sector policies, public finance management systems, actor relationships) should be considered as inputs in the analysis of county health system efficiency. They also felt that while traditional indicators of health system performance such as intervention coverage or outcomes for infectious diseases, and reproductive, maternal, neonatal and child health are still relevant, emerging epidemiological trends such as an increase in the burden of non-communicable diseases should also be considered. The stakeholders identified public finance management, human resources for health, political interests, corruption, management capacity, and poor coordination as factors that influence the efficiency of county health systems. An in-depth examination of the factors that influence the efficiency of county health systems could illuminate potential policy levers for generating efficiency gains. Mixed methods approaches could facilitate the study of both hardware and software factors that are considered inputs, outputs or factors that influence health system efficiency. County health system efficiency in Kenya could be enhanced by improving the timeliness of financial flows to counties and health facilities, giving health facilities financial autonomy, improving the number, skill mix, and motivation of healthcare staff, managing political interests, enhancing anticorruption strategies, strengthening management capacity and coordination in the health sector.
Full-length MSP1 is a major target of protective immunity after controlled human malaria infection.
The merozoite surface protein 1 (MSP1) is the most abundant protein on the surface of the invasive merozoite stages of Plasmodium falciparum and has long been considered a key target of protective immunity. We used samples from a single controlled human malaria challenge study to test whether the full-length version of MSP1 (MSP1FL) induced antibodies that mediated Fc-IgG functional activity in five independent assays. We found that anti-MSP1FL antibodies induced complement fixation via C1q, monocyte-mediated phagocytosis, neutrophil respiratory burst, and natural killer cell degranulation as well as IFNγ production. Activity in each of these assays was strongly associated with protection. The breadth of MSP1-specific Fc-mediated effector functions was more strongly associated with protection than the individual measures and closely mirrored what we have previously reported using the same assays against merozoites. Our findings suggest that MSP1FL is an important target of functional antibodies that contribute to a protective immune response against malaria.
Breadth of Fc-mediated effector function correlates with clinical immunity following human malaria challenge.
Malaria is a life-threatening disease of global health importance, particularly in sub-Saharan Africa. The growth inhibition assay (GIA) is routinely used to evaluate, prioritize, and quantify the efficacy of malaria blood-stage vaccine candidates but does not reliably predict either naturally acquired or vaccine-induced protection. Controlled human malaria challenge studies in semi-immune volunteers provide an unparalleled opportunity to robustly identify mechanistic correlates of protection. We leveraged this platform to undertake a head-to-head comparison of seven functional antibody assays that are relevant to immunity against the erythrocytic merozoite stage of Plasmodium falciparum. Fc-mediated effector functions were strongly associated with protection from clinical symptoms of malaria and exponential parasite multiplication, while the gold standard GIA was not. The breadth of Fc-mediated effector function discriminated clinical immunity following the challenge. These findings present a shift in the understanding of the mechanisms that underpin immunity to malaria and have important implications for vaccine development.
Diabetes and risk of hospitalisation due to infection in northeastern Thailand: Retrospective cohort study using population-based healthcare service data.
BackgroundPopulation-based studies describing the association between diabetes and increased risk of infection have largely been based in high-income countries. There is limited information describing the burden of infectious disease attributable to diabetes in low and middle-income countries. This study aimed to describe the burden and risk of infectious disease hospitalisation in people with diabetes compared to those without diabetes in northeastern Thailand.MethodsIn a retrospective cohort study using electronic health record data for 2012-2018 for 3.8 million people aged ≥20 years in northeastern Thailand, hospitalisation rates for any infectious diseases (ICD-10 codes A00-B99) were estimated and negative binomial regression used to estimate rate ratios (RR) for the association between diabetes and infectious disease hospitalisation adjusted for age, sex and area of residence.ResultsIn this study, 164,177 people had a diagnosis of diabetes mellitus at any point over the study period. Infectious disease hospitalisation rates per 1000 person-years (95%CI) were 71.8 (70.9, 72.8), 27.7 (27.1, 28.3) and 7.5 (7.5, 7.5) for people with prevalent diabetes, incident diabetes and those without diabetes respectively. Diabetes was associated with a 4.6-fold higher risk of infectious disease hospitalisation (RR (95% CI) 4.59 (4.52, 4.66)). RRs for infectious disease hospitalisation were 3.38 (3.29, 3.47) for people with diabetes managed by lifestyle alone and 5.29 (5.20, 5.39) for people receiving prescriptions for diabetes drugs.ConclusionsIn this Thai population, diabetes was associated with substantially increased risk of hospitalisation due to infectious diseases and people with diabetes who were on pharmacological treatment had a higher risk than those receiving lifestyle modification advice alone.
Association of Indoleamine 2,3-Dioxygenase (IDO) Activity with Outcome after Cardiac Surgery in Adult Patients
Indoleamine 2,3-deoxygenase (IDO) plays an important role in the catabolism of the amino acid tryptophan. Tryptophan and its metabolites are key immune modulators. Increased IDO activity has been observed in various diseases and is associated with worse clinical outcomes. However, comprehensive research regarding its role in cardiac surgery remains limited. Therefore, we aimed to investigate perioperative changes in IDO activity and pathway metabolites, along with their impact on clinical outcomes in adult patients undergoing cardiac surgery. As an observational cohort study conducted at the Inselspital in Bern from January to December 2019, we retrospectively analyzed the data of prospectively collected biobank samples of patients undergoing cardiac surgery with the use of cardiopulmonary bypass. IDO pathway metabolite analysis was conducted by mass spectrometry. Perioperative dynamics were descriptively assessed and associated with pre-defined clinical outcome measures (30-day mortality, 1-year mortality, incidence of stroke and myocardial infarction, and length of hospital stay) through a multi-step exploratory regression analysis. A cohort of 192 adult patients undergoing cardiac surgery with the use of cardiopulmonary bypass were included (median age 67.0, IQR 60.0–73.0, 75.5% male). A significant perioperative decrease in the kynurenine/tryptophan (Kyn/Trp) ratio (−2.298, 95% CI −4.028 to −596, p = 0.009) and significant perioperative dynamics in the associated metabolites was observed. No association of perioperative changes in IDO activity and pathway metabolites with clinical outcomes was found. A significant decrease in the Kyn/Trp ratio among adult patients undergoing cardiac surgery indicates a perioperative downregulation of IDO, which stands in contrast to other pro-inflammatory conditions. Further studies are needed to investigate IDO in the setting of perioperative immunomodulation, which is a key driver of postoperative complications in cardiac surgery patients.
Transforming Rapid Diagnostic Tests for Precision Public Health: Open Guidelines for Manufacturers and Users.
Precision public health (PPH) can maximize impact by targeting surveillance and interventions by temporal, spatial, and epidemiological characteristics. Although rapid diagnostic tests (RDTs) have enabled ubiquitous point-of-care testing in low-resource settings, their impact has been less than anticipated, owing in part to lack of features to streamline data capture and analysis. We aimed to transform the RDT into a tool for PPH by defining information and data axioms and an information utilization index (IUI); identifying design features to maximize the IUI; and producing open guidelines (OGs) for modular RDT features that enable links with digital health tools to create an RDT-OG system. We reviewed published papers and conducted a survey with experts or users of RDTs in the sectors of technology, manufacturing, and deployment to define features and axioms for information utilization. We developed an IUI, ranging from 0% to 100%, and calculated this index for 33 World Health Organization-prequalified RDTs. RDT-OG specifications were developed to maximize the IUI; the feasibility and specifications were assessed through developing malaria and COVID-19 RDTs based on OGs for use in Kenya and Indonesia. The survey respondents (n=33) included 16 researchers, 7 technologists, 3 manufacturers, 2 doctors or nurses, and 5 other users. They were most concerned about the proper use of RDTs (30/33, 91%), their interpretation (28/33, 85%), and reliability (26/33, 79%), and were confident that smartphone-based RDT readers could address some reliability concerns (28/33, 85%), and that readers were more important for complex or multiplex RDTs (33/33, 100%). The IUI of prequalified RDTs ranged from 13% to 75% (median 33%). In contrast, the IUI for an RDT-OG prototype was 91%. The RDT open guideline system that was developed was shown to be feasible by (1) creating a reference RDT-OG prototype; (2) implementing its features and capabilities on a smartphone RDT reader, cloud information system, and Fast Healthcare Interoperability Resources; and (3) analyzing the potential public health impact of RDT-OG integration with laboratory, surveillance, and vital statistics systems. Policy makers and manufacturers can define, adopt, and synergize with RDT-OGs and digital health initiatives. The RDT-OG approach could enable real-time diagnostic and epidemiological monitoring with adaptive interventions to facilitate control or elimination of current and emerging diseases through PPH.
Factors influencing meiotic recombination revealed by whole-genome sequencing of single sperm
Sequencing and the single sperm During meiosis, homologous chromosomes undergo doublestrand breaks in DNA that can cross over, shuffling genetic material. However, not every double-strand break resolves in a crossover event. Hinch et al. wanted to determine the rules governing DNA recombination. They developed a method to sequence individual mouse sperm and applied it to mice carrying two different alleles of a protein involved in mammalian crossovers. A high-resolution genetic map revealed the relationships between the distribution of crossovers, proteins involved in recombination, and specific factors determining whether a double-strand break becomes a crossover. Science , this issue p. eaau8861
Altering the Binding Properties of PRDM9 Partially Restores Fertility across the Species Boundary
Abstract Sterility or subfertility of male hybrid offspring is commonly observed. This phenomenon contributes to reproductive barriers between the parental populations, an early step in the process of speciation. One frequent cause of such infertility is a failure of proper chromosome pairing during male meiosis. In subspecies of the house mouse, the likelihood of successful chromosome synapsis is improved by the binding of the histone methyltransferase PRDM9 to both chromosome homologs at matching positions. Using genetic manipulation, we altered PRDM9 binding to occur more often at matched sites, and find that chromosome pairing defects can be rescued, not only in an intersubspecific cross, but also between distinct species. Using different engineered variants, we demonstrate a quantitative link between the degree of matched homolog binding, chromosome synapsis, and rescue of fertility in hybrids between Mus musculus and Mus spretus. The resulting partial restoration of fertility reveals additional mechanisms at play that act to lock-in the reproductive isolation between these two species.
ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair
During meiosis, homologous chromosomes pair and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, double-strand breaks (DSBs) initiate recombination within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have been identified. We identifiedZcwpw1, containing H3K4me3 and H3K36me3 recognition domains, as having highly correlated expression withPrdm9. Here, we show that ZCWPW1 has co-evolved with PRDM9 and, in human cells, is strongly and specifically recruited to PRDM9 binding sites, with higher affinity than sites possessing H3K4me3 alone. Surprisingly, ZCWPW1 also recognises CpG dinucleotides. MaleZcwpw1knockout mice show completely normal DSB positioning, but persistent DMC1 foci, severe DSB repair and synapsis defects, and downstream sterility. Our findings suggest ZCWPW1 recognition of PRDM9-bound sites at DSB hotspots is critical for synapsis, and hence fertility.