BACKGROUND:Pneumococcal meningitis remains a major threat, with high fatality rates and long-term sequelae, despite advances in vaccination and treatment. We aimed to examine the associations between pneumococcal serotypes, Global Pneumococcal Sequence Cluster (GPSC), antimicrobial resistance, source of infection, and clinical outcomes in adults with pneumococcal meningitis. METHODS:In this single-centre, clinical and genomic, retrospective, observational study, we analysed all laboratory-confirmed cases of adult pneumococcal meningitis recorded at Hospital Universitari de Bellvitge, Spain. Clinical data were obtained from a prospectively maintained clinical database and linked to microbiological and genomic data by unique patient identifiers. Clinical sources of infection were classified as cerebrospinal fluid leakage, acute otitis media, or haematogenous origin. Disease severity was defined as shock at presentation, sequelae as any persistent neurological deficit at discharge, and mortality as death within 30 days. Serotype data were available for 265 isolates, and whole-genome sequencing was done on 200 viable isolates. For outcome analyses, patients who did not receive dexamethasone were excluded. Serotype, GPSCs, antimicrobial susceptibility, phylogenetic, and genome-wide association study (GWAS) data were analysed to assess determinants of meningitis source, disease severity, sequelae, and 30-day mortality. FINDINGS:387 adult patients (median age 58 years [IQR 45-68]; 54% male) with pneumococcal meningitis were recorded between Jan 1, 1974, and Dec 31, 2023. Acute otitis media was the most frequent source of pneumococcal meningitis (174 [45%] of 387 cases) and was mainly caused by serotype 3 (pneumococcal conjugate vaccine [PCV]13; GPSC12). The 30-day case-fatality rate in this group was 17 (10%) of 174 (95% CI 5·8-15·2). Haematogenous episodes accounted for 104 (27%) of 387 cases and had a significantly higher 30-day case-fatality rate (50 [48%] of 104; 95% CI 38·2-58·1; p<0·0001) with a higher frequency of serotype 4. Cerebrospinal fluid leakage accounted for 105 (27%) of 387 cases and had the lowest 30-day case-fatality rate (nine [9%] of 105; 95% CI 4·0-15·6) and broader serotype diversity. The introduction of PCV7 and PCV13 resulted in declines in vaccine-targeted serotypes and β-lactam resistance. Whole-genome sequencing identified 60 distinct GPSCs. Among prevalent lineages, GPSC16 (20 [10%] of 200; serotypes 19A and 23F) and GPSC6 (18 [9%] of 200; serotypes 9V, 11A, and 14) were associated with β-lactam resistance. GWAS did not identify genetic variants significantly associated with severity, sequelae, or mortality. INTERPRETATION:This longitudinal study provides a comprehensive view of adult pneumococcal meningitis over five decades, revealing changes in sources of infection, serotype distribution, pneumococcal lineages, and antimicrobial resistance patterns over time. Lineage-level findings suggested variability in clinical outcomes, underscoring the importance of continued genomic surveillance and supporting consideration of broader vaccine targets. GPSC12 predominance and its association with mortality and more severe outcomes highlight the need for preventive measures against serotype 3, although these findings require confirmation in larger multicentre cohorts. FUNDING:Instituto de Salud Carlos III, cofunded by European Social Fund, and the Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, and the Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, both at the Instituto de Salud Carlos III.
Dengue, a mosquito-borne viral disease, is undergoing its largest surge in history, driven by climate and demographic changes. Expanding transmission has highlighted previously under-recognised populations at heightened risk of severe disease, including people with multimorbidity and immunosuppression, for whom live-attenuated vaccines are contraindicated or unlicensed. This evolving epidemiology underscores the urgent need for safe and effective treatments for dengue, particularly for those with complex risk profiles compounded by socioeconomic disadvantage. We examined ethical, regulatory, and implementation considerations to support WHO target product profile development for dengue therapeutics. Our analysis highlights the need for better characterisation of groups at risk through approaches such as enhanced surveillance; co-produced approaches for the inclusion of these groups in research prioritisation, trials, and care; and strategies to address key barriers to access for all, such as rapid diagnostics. This framework can potentially inform equitable development and delivery of countermeasures for other infectious disease threats to global health.
Dengue, an Aedes mosquito-borne viral infection, is on the rise with climate and demographic change. In 2023, WHO declared dengue its highest grade of emergency, following the largest number of cases and deaths in recorded history. This emergency highlighted the absence of safe and effective dengue-specific treatments as a gap in the product landscape for care for people with dengue. To accelerate development of dengue-specific treatments for wide implementation and access in all dengue-endemic countries, WHO conducted a landscape analysis of the dengue therapeutics pipeline and convened a global expert and public consultation to develop target product profiles for treatments for non-severe and severe dengue. These target product profiles provide strategic guidance for product developers, regulators, procurement agencies, and funders on the intended use, target populations, and key product characteristics of dengue-specific treatments required to meet public health needs, setting clear targets to drive development of dengue drugs accessible to those who need them the most.
Acute rheumatic fever is an immune-mediated sequela of Streptococcus pyogenes (group A Streptococcus) infection, presenting with fever, arthritis, chorea, rash, and, crucially, carditis. Without effective secondary prophylaxis and care, acute rheumatic fever can progress to chronic rheumatic heart disease, a leading yet under-recognised cause of cardiovascular morbidity and death that disproportionately affects children and young adults aged 5-24 years in low-resource settings. Robust evidence implicates the role of antigenic mimicry-particularly between streptococcal M protein and cardiac or myocardial matrix proteins-together with dysregulated immune control in driving valvular injury. In this Review, we discussed mechanisms of rheumatic heart disease immunopathogenesis, highlighting the roles of T-cell responses, chemokine-guided recruitment to valves, cytokine dysregulation, endothelial activation, and stromal remodelling. We also analysed limitations of existing data and delineate strategies to develop experimental models, identify biomarkers, and define immunomodulatory targets that can inform earlier diagnosis, enhanced secondary prevention, and rational therapeutic strategies.
BACKGROUND:The PhagoBurn trial compared the efficacy and tolerability of a cocktail of lytic anti-Pseudomonas aeruginosa bacteriophages with standard of care for patients with burns but did not meet its primary endpoint. In this follow-up study using samples from the PhagoBurn trial, we aimed to investigate non-canonical phage-bacterium interactions and longitudinal changes in the phenotypic and genotypic characteristics of P aeruginosa during phage therapy. METHODS:In this retrospective, observational, reverse translational study, we collected viable P aeruginosa isolates from the wound swabs of individuals who completed at least 7 days of treatment with the phage cocktail product (PP1131) in the multicentre PhagoBurn trial conducted in Switzerland, France, and Belgium. Isolates were subjected to longitudinal phenotypic screening for phage susceptibility using standard drop assays and reverse double-layer assays. Isolates with unique phage susceptibility profiles were selected for genomic characterisation. After the unexpected detection of PP1131-derived phage DNA in many bacterial isolates, non-canonical phage-bacterium interactions were assessed using double-layer agar lysis assays and ultrastructural assessments using electron microscopy. FINDINGS:Of the 27 individuals enrolled in the PhagoBurn trial, 13 received phage therapy; among them, ten individuals completed the therapy, and longitudinal P aeruginosa isolates from seven individuals were available for analysis. 184 (mean 26 [SD 21·9] isolates per individual) bacterial isolates were phenotypically assessed. Phage susceptibility varied substantially between and within individuals over time, with rapid emergence of resistance in some cases. 98 (53%) of 184 isolates (mean 14 [11·8] isolates per individual) had unique phage susceptibility profiles and were selected for genome sequencing. In these 98 isolates, mutations were detected in genes involved in virulence regulation, secretion and efflux, chemotaxis, and biosynthesis. Complete or partial phage genomes derived from PP1131 were detected in 41 (42%) of the 98 sequenced bacterial isolates; 16 (39%) of 41 phage-positive isolates continuously secreted infectious phage particles, consistent with a productive chronic infection phenotype. In 23 (56%) of 41 isolates, phage genomic DNA persisted without detectable phage release, suggesting non-productive chronic infection (including putative pseudolysogeny). These alternative infection states remained stable and detectable after serial passages in vitro and were observed in isolates from individuals with both favourable and unfavourable clinical outcomes. INTERPRETATION:Bacterial adaptation, phage adaptation, and non-canonical phage-bacterium interactions have been largely overlooked in clinical trial design and might contribute to variability in therapeutic outcomes and warrant further investigation. The non-canonical phage interactions (eg, chronic infection and pseudolysogeny) observed in this study highlight the need for protocols that account for the emergence of persistent non-lytic phage-bacterium interactions. FUNDING:Stiftung für die Forschung in Anästhesiologie und Intensivmedizin, Swiss National Science Foundation, and Placide Nicod Foundation.
Antimicrobial resistance (AMR) has made multidrug-resistant organisms (MDROs), particularly ESKAPE-E pathogens (including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp, and Escherichia coli), a major threat to modern medicine. Although novel antibiotics, antimicrobial stewardship, and infection prevention remain essential, such interventions are unlikely to offset projected AMR trends on their own. Vaccines can help to mitigate AMR by preventing infections and reducing antibiotic exposure. WHO estimates that vaccines targeting 23 pathogens (excluding Neisseria gonorrhoea) could reduce global antibiotic need by 22%, equivalent to 2·5 billion defined daily doses annually. In the mRNA era, modular vaccine platforms enable rapid design of protein antigens and multivalent constructs, with emerging preclinical proof of concept against selected bacterial pathogens. In this Personal View, we argue that mRNA vaccines should be considered enabling platforms for selected protein-based MDRO targets rather than universal solutions for antibacterial vaccine development. We propose a microbiome-informed framework that distinguishes systemic protection from mucosal decolonisation and aligns antigen selection, delivery route, and trial endpoints with colonisation dynamics, microbiome resilience, and AMR reduction goals.
BACKGROUND:Chikungunya fever is a mosquito-borne disease characterised by severe arthralgia and is caused by chikungunya virus (CHIKV), an alphavirus. The aim of this study was to establish a WHO International Standard for CHIKV-specific neutralising antibodies-a potential correlate of protection. METHODS:Two candidate International Standards (code numbers 1502/19 and 1504/19) were prepared: 1502/19 using plasma from a CHIKV-convalescent individual and 1504/19 using plasma from blood donors from a CHIKV-endemic region. Potencies of the two candidate International Standards were evaluated alongside samples from recovered individuals and donors previously infected with CHIKV, in an international study (2019-20), using a range of virus-neutralisation assays and immunoassays. Statistical analysis was used to estimate mean and relative potencies of the candidate International Standards. Participants included vaccine developers, arbovirus reference laboratories, and diagnostics manufacturers. FINDINGS:26 laboratories from 12 countries reported detection of anti-CHIKV antibodies and associated potencies. All participants consistently detected both 1502/19 and 1504/19. Overall mean potencies were near-identical for the two candidate International Standards (1502/19, 3·44 log10 and 1504/19, 3·48 log10). Intra-assay variation was considerably lower than inter-assay variation for the candidate International Standards, which varied by more than 100-fold; this variability was seen for all other anti-CHIKV-positive samples. Assay variability was substantially reduced when antibody titres from the panel of samples were expressed relative to 1502/19 or 1504/19. An agreement was reached to establish 1502/19 as the first WHO International Standard for anti-CHIKV neutralising antibodies, with an assigned unitage of 1000 International Unitage/mL. INTERPRETATION:The use of the candidate International Standards resulted in harmonisation of anti-CHIKV neutralisation titres, allowing for better comparison of results of neutralisation assays for anti-CHIKV antibodies, either as a consequence of natural infection or produced in response to different vaccines, and will be essential in estimating antibody titres associated with protection against CHIKV. FUNDING:German Ministry of Health (Bundesministerium für Gesundheit).
BACKGROUND:Melioidosis is a life-threatening infectious disease caused by Burkholderia pseudomallei, endemic to southeast Asia and northern Australia. Serological tests targeting haemolysin co-regulated protein 1 (Hcp1) and O-polysaccharide (OPS) antigens have shown promise for diagnosis and surveillance, but their interpretation is limited by an incomplete understanding of antibody persistence following infection. To address this gap, we aimed to characterise post-infection decay dynamics of Hcp1 and OPS-specific IgG and IgA antibodies to improve diagnostic interpretation and population-level seroepidemiological inference. METHODS:We conducted a retrospective cohort study using previously collected samples from two cohorts of patients with culture-confirmed B pseudomallei infection and healthy blood donors recruited from three tertiary hospitals in northeast Thailand (Mukdahan Hospital, Roi-Et Hospital, and Surin Hospital). Inclusion criteria were age 15 years or older for cohort 1 and 18 years or older for cohort 2, and hospitalisation history with microbiologically confirmed B pseudomallei infection from any clinical specimen. Exclusion criteria for both cohorts included pregnancy, receipt of palliative care, or incarceration. Whole blood samples were collected at enrolment and on days 5, 12, and 28 and at months 3 and 12. Clinical and demographic data were collected through medical record review and patient interviews. We measured IgA and IgG antibody responses to Hcp1 and OPS antigens using kinetic and endpoint ELISAs. Diagnostic accuracy was evaluated at enrolment and day 28 using receiver operating characteristic curves, with optimal cutoffs determined using Youden's J statistic. Joint cutoffs for antigen-isotype pairs were optimised by evaluating all pairwise threshold combinations and selecting those maximising balanced accuracy. Antibody dynamics were modelled using Bayesian hierarchical two-phase modified predator-prey models that captured the exponential rise during active infection and non-exponential decay following pathogen clearance, both in the overall cohort and in analyses stratified by diabetes status. FINDINGS:We tested 656 samples from 142 patients with melioidosis and 76 healthy blood donors enrolled between Dec 30, 2015, and July 13, 2022. The median patient age was 54 years (IQR 46-61); 99 (70%) of 142 patients were male, and 98 (69%) of 142 had diabetes. Areas under the receiver operating characteristic curves (AUCs) for each antigen-isotype combination at enrolment ranged from 0·89 to 0·98 and were comparable between kinetic and endpoint assays (difference ≤0·1 AUC); the kinetic ELISA provided a broader dynamic range at high antibody concentrations, where endpoint assay values reached saturation. Modelled median antibody responses remained above the Youden diagnostic threshold for more than 1 year for all antigen-isotype combinations. OPS IgG had the highest diagnostic accuracy at enrolment (AUC=0·93, 95% CI 0·90-0·96); however, modelled median antibody responses remained elevated above the Youden threshold for 902 days (approximately 2·5 years). A higher joint cutoff for OPS IgA and IgG improved accuracy and reduced the modelled duration of positivity to less than 1 year. People with diabetes had higher peak responses and slower decay rates across most antigen-isotype combinations. INTERPRETATION:Modelled OPS-specific and Hcp1-specific antibody responses show rapid increases following infection and gradual decay over the subsequent year; these dynamics can be used to estimate population-level incidence rates. Clinically, persistent antibody positivity may reduce diagnostic specificity in endemic settings by detecting past rather than recent infections. Joint antigen cutoffs might improve sensitivity and specificity at clinical presentation. FUNDING:US National Institutes of Health, Defense Threat Reduction Agency, and Wellcome Trust UK.
BACKGROUND:With the introduction of metagenomics in clinical diagnostics unfolding and the expanding role of pathogen genomics in national surveillance, conditions are favourable for the further maturation of these approaches in public health surveillance. In this study, we aimed to pilot the use of probe-based metagenomics for nationwide sentinel surveillance through general practitioner (GP) networks and for the genomic characterisation of both anticipated and emerging respiratory viruses in primary care. METHODS:This prospective, pilot study included patients with acute respiratory illness attending GP practices participating in nationwide sentinel virological surveillance in the Netherlands, from Jan 10, 2025, to April 25, 2025. On predefined selection days, 90-100 combined nasopharyngeal and oropharyngeal swab specimens were analysed through parallel metagenomic testing using probes targeting 15 488 strains of human and animal viruses. Results were compared with a standard two-tiered surveillance strategy comprising PCR targeting 17 viruses, followed by amplicon-based nanopore whole-genome sequencing of influenza viruses, SARS-CoV-2, and respiratory syncytial virus (RSV). The primary outcome was detection and in-depth genomic characterisation of viruses within and beyond the scope of standard screening. Sensitivity, specificity, positive and negative predictive values, and genome coverage were analysed. FINDINGS:93 patients were included, with a median age of 51 years (IQR 33-67); 55 (59%) were women and 38 (41%) were men. Overall, 74 (80%) specimens tested positive through standard PCR-based screening. Metagenomic surveillance detected viruses in 88 (95%) specimens, including DNA viruses known to establish latent infections. For viruses targeted by routine PCR, metagenomics showed a pooled sensitivity of 93·8% (95% CI 88·1-98·7), specificity of 99·8% (95% CI 99·5-100·0), positive predictive value of 96·2% (95% CI 91·8-100·0), and negative predictive value of 99·7% (95% CI 91·8-100·0), with a median genome coverage of 99·4% (IQR 96·9-99·9%). Metagenomic data enabled simultaneous full genomic characterisation of circulating viruses targeted by current amplicon-based surveillance, including influenza viruses (success rate 30 [86%] of 35 detections) and RSV (six [86%] of seven), and of viruses that were post hoc characterised by whole-genome sequencing in response to epidemiological findings during the study period (human metapneumoviruses [hMPV], five [50·0%] of ten), and non-targeted viruses such as adenoviruses. The data facilitated characterisation of a reassortant A(H3N2) influenza virus, potential vaccine escape mutants, markers of susceptibility to influenza antiviral drugs and RSV monoclonal antibodies, and a human A(H1N2)v influenza virus infection. INTERPRETATION:The technically robust and comprehensive performance across heterogeneous circulating viruses shown here supports evaluation in larger prospective studies in high-prevalence settings, where implementation might be most cost-efficient. Further optimisation of probe-based enrichment strategies could reduce turnaround time and facilitate integration into routine public health surveillance. FUNDING:The Netherlands Organisation for Health Research and Development (ZonMw), and the Ministry of Health, Welfare and Sport (VWS).
BACKGROUND:In sub-Saharan Africa, invasive antimicrobial-resistant infections often originate from community-level acquisition. In this study, we aimed to evaluate the effect of a cluster-level intervention on individual-level extended spectrum β-lactamase-producing Escherichia coli (ESBL-E) acquisition. We assessed whether a behavioural intervention bundle targeting suboptimal antibiotic use and hygiene practices reduced household-level acquisition of ESBL-E. METHODS:We conducted a cluster-randomised controlled trial in 22 village clusters in Nanoro district, Burkina Faso. We enrolled 12 randomly selected households per cluster to assess the intervention effect on ESBL-E household transmission. The intervention comprised three rounds delivered at 3-month intervals and combined WHO Access, Watch, Reserve-based educational and feedback sessions for formal and informal medicine providers with community health education campaigns. Consenting household members provided stool samples before, during, and after intervention rollout, alongside a pre-post household water, sanitation, and hygiene (WASH) survey. ESBL-E acquisition was defined as a transition from a negative to a positive stool sample between consecutive sampling visits, with transition hazards estimated using continuous-time Markov models. We estimated intervention effects on ESBL-E acquisition using Bayesian Markov models. Cox frailty models assessed associations between WASH exposures and acquisition. The study is registered with ClinicalTrials.gov (NCT05378880). FINDINGS:1203 individuals were enrolled between Oct 11, 2022, and Feb 19, 2024. At baseline, 346 (57%) of 604 individuals in the control household group and 291 (49%) of 599 individuals in the intervention household group tested positive for ESBL-E colonisation. Pre-intervention acquisition incidence rates were 3·8 per 100 person-days (95% credible interval [CrI] 2·0-9·9) in the intervention group and 3·5 per 100 person-days (95% CrI 1·8-9·6) in the control group. The intervention did not change the risk of ESBL-E acquisition in months 1-6 (hazard ratio [HR] 1·02 [95% CrI 0·78-1·31]) but was associated with a reduction in months 6-9 (HR 0·82 [95% CrI 0·56-1·14], probability of a reduction p[HR<1]=0·88). Acquisition risk was higher in the rainy season (peak HR 1·73 [95% CI 1·49-2·00]), whereas improved sanitation was associated with lower risk (HR 0·77 [95% CI 0·59-1·00]). INTERPRETATION:Findings, although inconclusive, were consistent with a modest intervention-related reduction in ESBL-E acquisition incidence. Higher acquisition rates associated with rainy seasons and poor sanitation highlight the need to tackle environmental drivers of antimicrobial resistance transmission in addition to antibiotic use in rural sub-Saharan Africa. FUNDING:EU Joint Programme Initiative on Antimicrobial Resistance CABU-EICO.
BACKGROUND:Non-sputum-based tuberculosis tests are a global priority because sputum-dependent diagnostics systematically miss populations at highest risk of disease, including people living with HIV. We evaluated the diagnostic accuracy of a next-generation urine lipoarabinomannan assay. METHODS:In this two-centre diagnostic accuracy study, we enrolled adults aged 18 years or older, regardless of their HIV status, with presumptive pulmonary tuberculosis, attending outpatient clinics in South Africa and Uganda. Participants who had received tuberculosis treatment within the previous 2 months or had an unknown treatment history were excluded. Demographic and clinical data, including HIV status and CD4 cell count, were collected alongside urine, blood, and sputum. We compared the diagnostic accuracy of the Biopromic lipoarabinomannan assay (BP-LAM; Biopromic TB LAM, Biopromic, Solna, Sweden) and WHO-recommended Determine TB LAM Ag assay (LF-LAM; Abbott, Santa Clara, CA, USA) against an extended microbiological reference standard (eMRS; sputum Xpert MTB/RIF Ultra [Ultra; Cepheid, Sunnyvale, CA, USA], culture, or both). Sputum induction was available in South Africa. Secondary outcomes were diagnostic yield and accuracy stratified by subgroups (HIV, CD4 cell count stratum, country, and sputum scarcity status), including design-locked and prototype assays. FINDINGS:We tested urine from 629 participants (282 from South Africa and 347 from Uganda) collected between Oct 5, 2018, and March 11, 2022. 315 individuals with tuberculosis and a random selection of 314 without tuberculosis underwent urine testing. 250 (40%) of 626 participants were female and 376 (60%) were male; the median age was 34 years (IQR 19-60). BP-LAM had higher sensitivity than LF-LAM (63% [95% CI 58-69] vs 22% [18-27]; p<0·0001) and similar specificity (93% [90-96] vs 89% [85-92]; p=0·067). BP-LAM sensitivity was similar regardless of HIV status (67% [58-76] for people with HIV vs 62% [55-69] for people who were HIV-negative; p=0·39) but was higher in people with HIV and CD4 counts less than or equal to 200 cells per μL (79% [63-90] vs 58% [44-72] for people with HIV and CD4 count >200 cells per μL; p=0·041). Specificity of BP-LAM was significantly lower in people with HIV than in individuals who were HIV-negative (90% [83-94] vs 96% [92-99]; p=0·016). The design-locked BP-LAM had better specificity than the prototype (93% [90-96] vs 85% [80-88]; p<0·0001). Diagnostic yield was significantly higher for Ultra (82% [78-86]), followed by culture (72% [68-77]) in comparison with BP-LAM (61% [56-66]; p<0·0001), and LF-LAM yield was significantly lower (29% [24-33]; p<0·0001), with similar patterns across HIV status. BP-LAM yield was similar to that of Ultra when sputum induction was unavailable (67% [55-79] vs 64% [49-78]; p=0·82). INTERPRETATION:BP-LAM showed higher sensitivity than LF-LAM, including in HIV-negative people, and identified a similar number of cases as sputum Ultra when sputum induction was unavailable. Further validation and implementation studies are warranted. FUNDING:Global Health Technology Fund (GHIT) programme and EDCTP2 programmes supported by the EU.
