The Journal of Infectious Diseases

BackgroundAfter the global deployment of pneumococcal conjugate vaccines (PCVs), serotype 12F has become the predominant serotype responsible for invasive pneumococcal disease (IPD) worldwide. As PCVs that include serotype 12F are gradually introduced, we aim to characterise the global population structure and genetic diversity of the 12F capsule locus using whole-genome sequencing. Capsule variants with vaccine evasion potential were further investigated by functional experiments. MethodsA global collection of pneumococcal serotype 12F genomes (n=806) from 37 countries across six continents were included in this study. To characterise the serotype 12F population, Global Pneumococcal Sequence Cluster (GPSC), in silico serotype, and antimicrobial resistance profile were inferred from whole-genome data for each isolate. The capsule biosynthesis (cps) locus was analysed for gene content variations that could alter polysaccharide capsule production or structure, thereby influencing recognition by vaccine-induced antibodies. These isolates were further investigated by assessing their capsule production using immunofluorescence assays and its susceptibility to vaccine-elicited antibody killing by opsonophagocytosis assays. FindingsThe global increase in serotype 12F was driven by both distinct pneumococcal lineages across different continents, and a globally-disseminated and multidrug-resistant lineage GPSC26. We identified six capsule variants in nine isolates that had disruptive mutations in cps genes including wze, wcil, wciJ and fnlA. Most (6/9) of the disruptive mutations were a result of strand-slippage mutations. A convergent strand-slippage mutation disrupting the glycosyltransferase gene wciJ was identified in four isolates from distinct lineages and countries. Despite the truncation, three of four isolates with available Quellung typing results still identified them as 12F, indicating the production of the capsule. We then created a genetically engineered lab strain with wciJ knockout and complemented with wciJ containing the strand-slipppage mutation. The knockout strain did not produce any capsule. In contrast, the lab strain with wciJ containing the strand-slippage mutation produced a mixed population of encapsulated and non-encapsulated pneumococci, even within the same chain of pneumococcal cells. This observation indicated encapsulated subpopulation possesses a functional WciJ and rapidly reversible strand-slippage mutation during replication. Opsonophagocytosis assays indicated that the clinical 12F strain with strand-slippage mutation in wciJ exhibited reduced susceptibility to vaccine-elicited serum killing, compared to a genetically closely related 12F clinical strain with an intact wciJ. However, substantial inter-individual antisera variation limits definitive interpretation. InterpretationOur work revealed the global rise of serotype 12F pneumococci has been driven by both regional-specific lineages, and a globally-disseminated and multidrug-resistant lineage GPSC26. We demonstrated that strand-slippage mutation is one of the major drivers of serotype 12F capsule variants and represents a novel mechanism enabling reversible on-off switching of capsule production. The ability to switch off capsule expression in a subpopulation may enable evasion of antibody-mediated killing but increase susceptibility to innate immune clearance. FundingBill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control and Prevention.

BackgroundUndetectable HIV-specific antibodies in early-treated children with confirmed infection correlate with low viral reservoir and may identify those eligible for future HIV remission strategies. The neonatal immune systems unique characteristics, combined with impairments resulting from exposure to maternal HIV and antiretroviral treatment (ART), may affect antibody responses to HIV. Yet immune competence remains understudied in the context of negative HIV serology. The ANRS-EP59-CLEAC study included 76 children and adolescents with HIV. We measured plasma HIV antibodies by enzyme immunoassay, other analytes by ELISA or multiplex assays, and blood cell phenotypes and functions by flow cytometry. We used Fishers and Mann-Whitneys tests and logistic regression to analyze variables associated with negative HIV serology. Nine participants tested negative for HIV-specific antibodies, eight children and one adolescent. Negative HIV serology occurred exclusively in participants who had initiated ART early and had HIV RNA < 50 copies/mL at evaluation. Among 17 early-treated children with sustained viral suppression, only 7 had negative HIV serology. In this subgroup, negative HIV serology associated with higher nadir CD4 counts, lower plasma IgM levels, higher frequencies of circulating follicular CD8 T lymphocytes, and higher expression of the costimulatory molecule CD86 on myeloid dendritic cells. We found no evidence of B or T lymphocyte deficits associated with negative HIV serology. Low antigenic exposure was necessary but insufficient to explain negative HIV serology. Beyond its association with low HIV reservoir, negative HIV serology correlated with less severe prior CD4 T-lymphocyte depletion and higher frequencies of follicular CD8 T lymphocytes. SummaryIn HIV-infected infants, starting antiretroviral therapy (ART) very early dramatically improves health outcomes. An important phenomenon observed in some of these children is that, despite being HIV-infected, they show no detectable antibodies against the virus -- a profile referred to as negative HIV serology. This feature could help identify patients most likely to benefit from future strategies aimed at achieving long-term virus control without treatment. To better understand this phenomenon, we studied HIV-infected children and adolescents enrolled in the ANRS-EP59-CLEAC trial, which compares the effects of ART initiated early (before 6 months of age) versus late (after 24 months). We showed that negative HIV serology is associated with early treatment, but also with a better-preserved immune system: less depletion of CD4 T cells, which are critical immune cells, and a higher abundance of specific T lymphocytes with potent antiviral activity. Importantly, we found no evidence of defects in the mechanisms responsible for antibody production. These findings suggest that negative HIV serology reflects a favorable immunological profile and could serve as a useful marker to select children as candidates for HIV remission trials.

Specific anaerobic species within the penile microbiome - Bacteria Associated with Seroconversion, Inflammation and Immune Cells (BASIC) - have been linked to increased HIV-1 susceptibility. These bacteria can directly disrupt epithelial integrity and are believed to increase local inflammation, resulting in an increased density of HIV-susceptible T cells in the inner foreskin. It is currently unknown whether other immune cells bearing the HIV entry receptors, CD4 and CCR5, are also elevated in individuals with a high abundance of BASIC species. Using inner foreskin tissues and penile swabs from males undergoing voluntary medical male circumcision, we performed a retrospective cross-sectional study to assess the relationship between BASIC species and the tissue density of such immune cells, including CD68+ macrophages, CD11c+ dendritic cells, and CD207+ Langerhans cells. The most abundant cells in the inner foreskin expressing the HIV co-receptors were CD11c+ dendritic cells (48.6% of CD4+/CCR5+ cells), followed by CD68+ macrophages (28.6%), CD3+ T cells (18.8%), and CD207+ Langerhans-like (8.8%) cells. The absolute abundance of BASIC species was associated with elevated tissue densities of both CD4+/CCR5+ T cells (as previously reported) and a heterogeneous population of CD3-/CD4+/CCR5+ cells of myeloid origin. In the dermis, BASIC species abundance was linked to elevated densities of cells expressing CD11c, CD68, and CD207, as well as those co-expressing CD11c and CD207; furthermore, CD11c+ and CD207+ cells were farther from the basement membrane in participants with a high abundance of BASIC species. Myeloid cells were not elevated in participants with a high abundance of control taxa. In an integrated analysis including previously published data from this same cohort, myeloid-cell densities clustered tightly together, positively correlated with BASIC species and pro-inflammatory cytokines, and had trends to negative correlations with control taxa (significant for CD207+ cell density). Overall, our findings suggest that BASIC species are associated with a broader foreskin immune phenotype marked by increased densities of HIV-susceptible myeloid and T cells, alongside epithelial disruption.

BackgroundHuman immunodeficiency virus (HIV) infection in pregnancy is associated with preterm birth (PTB), low birthweight (LBW), and perinatal death (PND). Although antiretroviral therapy (ART) suppresses viral load it does not prevent HIV-associated adverse pregnancy outcomes or resolve inflammation. As circulating maternal immune factors may not fully capture maternal-fetal interface immune dysregulation, this observational cohort study aimed to identify localized and systemic immune factors associated with PTB, LBW and PND in ART-treated pregnant people living with HIV (PPLWH). MethodsWe enrolled 118 PPLWH in Kinshasa, Democratic Republic of the Congo, during the second or third trimester. We collected maternal peripheral plasma (at enrollment, 1-3 days post-delivery, and postpartum) alongside umbilical cord and placental plasma at delivery. Concentrations of 45 immune factors were measured via LegendPlex and ELISAs and associations analyzed using Kruskal-Wallis tests with Dunns correction or Mann-Whitney tests. ResultsPlacental plasma exhibited the highest overall concentrations of immune factors, highlighting a distinct localized microenvironment. Among 118 pregnancies, 35 (30%) resulted in PTB, 10 (9%) in PND, and 9 (8%) in LBW. Compared to term births, PTB was associated with higher levels of the chemokines CCL20, CXCL9, and CXCL10 in cord and/or postdelivery plasma (p<0.01), while placental CCL20 levels were lower (p<0.05). Compared to live births, PND was associated with higher postdelivery CXCL1, cord IL-8, placental MPO and NGAL (p<0.05); higher postdelivery CXCL5 (p<0.01); and higher S100A8/A9 levels in cord and postdelivery plasma (p<0.01 and p<0.001, respectively). Finally, LBW was associated with higher enrollment IL-18 and S100A8/A9 levels (p<0.05 and p<0.01, respectively); as well as higher SAA levels in postdelivery and postpartum plasma (p<0.05). ConclusionsIn ART-treated PPLWH, distinct adverse birth outcomes are driven by time- and compartment-specific immune pathways. PTB is associated with localized T-cell chemokine responses, PND with neutrophil recruitment and activation, and LBW with pro-inflammatory cytokine and acute-phase protein responses. These pathways provide mechanistic insights into pregnancy complications in PPLWH and highlight potential compartment-specific biomarkers for risk stratification.

BackgroundMalaria transmission persists in Sahelian West Africa, with asymptomatic Plasmodium falciparum infections acting as a reservoir. Yet malaria epidemiology and research focus heavily on clinical cases. It remains unclear whether parasites causing clinical infections are genetically representative of the asymptomatic reservoir. MethodsA one-year cohort study (2021-2022) was conducted in four villages in the Kedougou district of Senegal and two villages in the Kati district of Mali, collecting 1,133 P. falciparum-positive samples from asymptomatic and clinical infections. Using parasite molecular barcodes and whole-genome sequencing, we estimated multiplicity of infection (MOI), runs of homozygosity (RoH), and identity-by-descent (IBD) to compare parasite populations between infection types and across age groups. ResultsA total of 226 whole genomes and 728 barcodes were analysed, representing 78.2% (570/729) of clinical cases and 21.7% (158/728) of asymptomatic infections. MOI was high, with over 50% of infections being polyclonal, and did not differ by age or infection status. IBD analysis revealed a highly diverse parasite population, with transmission clusters including both asymptomatic carriers and clinical cases. Drug resistance allele frequencies were similar between groups. ConclusionOverall, we found no evidence of genetic differentiation between parasites from clinical and asymptomatic infections, suggesting that clinical cases reflect the broader parasite population sustaining transmission. These findings provide a basis for linking genomic metrics with epidemiological factors and for monitoring the impact of future interventions on the parasite population.

ProblemThe anti-microbial protein granulysin is present in vaginal secretions during the follicular phase of the menstrual cycle but nearly disappears during the luteal phase. The reason for this change is unknown. Method of studyParticipants (n = 23) with regular menstrual cycles collected daily vaginal swabs for granulysin ELISAs. Endocervical cytobrushes, ectocervical biopsies, vaginal biopsies, and PBMC were collected across the cycle to enumerate granulysin-expressing cells by flow cytometry. Cycle phase was determined by daily urinary luteinizing hormone testing and confirmed by serum progesterone levels. ResultsGranulysin levels in secretions were up to 10,000 times higher during menstruation than during the luteal phase (menstruation, median 3,924 pg/mL [IQR 400-17,280]; luteal, median and IQR undetectable [<7.81 pg/mL]). In the endocervical canal, granulysin-expressing cells were much more abundant during menstruation than during the mid-follicular or mid-luteal phases. In contrast, the number of granulysin-expressing cells in the ectocervix and vagina remained stable during the cycle. The most abundant granulysin-expressing cell types in the mucosa were CD8 T cells and NK cells. In a minority of participants, granulysin was consistently detected in luteal-phase swabs; this phenomenon was associated with parity. ConclusionsGranulysin in vaginal secretions is associated with menstruation, which also drives a spike in granulysin-expressing cells in the endocervical canal. This result explains the much higher granulysin levels in secretions during the follicular than the luteal phase. In contrast, immune cells from ectocervical and vaginal biopsies express granulysin independently of the menstrual cycle, indicating their continuous ability to respond to microbial infection.

BackgroundProlonged SARS-CoV-2 infection in immunocompromised individuals may accelerate virus evolution within the host, raising concerns about the virus evading immunity, developing resistance, and forming novel variants of concern. However, the determinants and public health implications of within-host viral evolution in this population remain incompletely understood. MethodsWe performed longitudinal analyses of SARS-CoV-2 genomes from 91 patients with COVID-19 who were classified as being severely or moderately immunocompromised. Using serial measurements of viral RNA loads and infectious titers, we modeled the shedding dynamics of the virus and stratified the infected cases by upper respiratory virus shedding duration to assess associations with within-host evolutionary dynamics. ResultsShedding modeling identified two profiles of shedding duration: intermediate and long. The long shedding profile (shedding lasting >21 days) was found in 14.8% of moderately immunocompromised cases and 72.1% of severely immunocompromised cases. Frequent single-nucleotide variants accumulated specifically in severely immunocompromised individuals with the long shedding phenotype, correlating positively with shedding duration. By contrast, mutations remained limited in moderately immunocompromised individuals with the long shedding phenotype and in severely immunocompromised individuals with the intermediate shedding phenotype. We identified mutations in the spike receptor-binding domain associated with monoclonal antibody resistance; however, we found no fitness-enhancing mutations for inter-host transmission, and antiviral drug resistance mutations were rare. Instead, mutations were introduced frequently and randomly across the entire viral genome. ConclusionsProlonged upper respiratory virus shedding exceeding 21 days combined with severe immunocompromise is a risk factor of the accumulation of within-host SARS-CoV-2 mutations. Although no variants of concern emerged, the introduction of genome-wide random mutations suggests that the risk for novel variant generation cannot be excluded. These findings highlight the need for intensive antiviral strategies to limit shedding duration to less than 21 days in severely immunocompromised patients, and for immunological investigations to elucidate the host factors underlying residual shedding control in those who achieve clearance within this threshold.

BackgroundHigh-risk human papillomavirus (HPV) infection is necessary for cervical carcinogenesis, but HPV detection alone does not distinguish transient infection from lesions at greatest risk of progression. We evaluated whether HPV burden, vaginal microbiota structure, and host-context variables jointly characterize cervical intraepithelial neoplasia grade 3 (CIN3) in a Black/African American and White analytic cohort from the Vaginal Microbiome Health Project (VaMHP), integrating L1-based HPV typing, 16S rRNA vaginal microbiota profiling, and linked clinical metadata. ResultsAmong 1181 participants, 75 had CIN3. CIN3 was associated with HPV positivity (55/75, 73.3% vs 431/1106, 39.0%; odds ratio [OR] 4.31, 95% CI 2.55-7.29; Fisher exact p = 7.9 x 10^-9) and with multiple HPV infection among HPV-positive participants (35/55, 63.6% vs 176/431, 40.8%; OR 2.54, 95% CI 1.42-4.54; p = 0.0022). HPV communities in CIN3-positive samples showed higher Shannon diversity, greater observed strain richness, higher evenness, and significant beta-diversity separation. In vaginal microbiota analyses, alpha diversity did not differ by CIN3 status, but community composition did, and Lactobacillus crispatus was the only taxon depleted in CIN3 after multiple-testing correction. Race, age, and metronidazole exposure were central nodes in the host-factor network. In predictive modeling, a full integrated model combining metadata, HPV, and vaginal microbiota features (auROC = 0.745) outperformed both HPV + vaginal microbiota (auROC = 0.670) and HPV-only (auROC = 0.440) models. ConclusionsCIN3 in this cohort was associated with coordinated shifts in virologic burden, vaginal community structure, and host social-clinical context. The results support a structure-function interpretation in which loss of Lactobacillus crispatus-dominant states and enrichment of dysbiosis-associated communities define a host-microbiome context that is more permissive to HPV persistence and precancer. These findings move beyond descriptive omics by showing that microbiome and host-context features add nonredundant discriminatory signal beyond HPV-only models.

Background Tuberculosis remains the leading infectious cause of death worldwide. In the WHO African region, declining incidence has coincided with antiretroviral therapy (ART) scale-up, though whether this reflects reduced progression to disease or reduced transmission is unclear. We evaluated how ART and symptom status influence within-household Mycobacterium tuberculosis complex (MTBC) transmission risk. Methods We conducted a case-contact household study in rural South Africa, enrolling index adults with bacteriologically-confirmed pulmonary tuberculosis. MTBC immunoreactivity was measured in all child household contacts (aged 2-14 years) as a proxy measure of within-household transmission. We assessed the influence of index person ART status and symptom status, and explored effect-measure modification of the association between index person HIV status and transmission risk by sex. Results Among 755 child contacts of 296 index persons, effective ART was not associated with within-household MTBC transmission risk (risk ratio [RR], 1.07; 95% CI, 0.66-1.74). Among PLHIV engaged in ART care, WHO TB four-symptom screen (WHO4SS) status was not associated with transmission risk (RR, 0.80; 95% CI, 0.43-1.47), although absence of reported cough reduced risk (RR, 0.61; 95% CI, 0.38-0.96). A pronounced interaction between sex and HIV status was observed: HIV-negative women had the highest within-household MTBC transmission risk (30.5% vs. 14.3% in women with HIV) whereas risks were similar between HIV-positive and HIV-negative men. Conclusions We found no evidence that effective ART or WHO4SS status influenced within-household MTBC transmission risk, though confidence intervals were wide. Absence of reported cough was associated with lower risk, and transmission risk was highest among child contacts of HIV-negative women. These findings suggest reported cough is a useful marker of transmission risk and that routine tuberculosis screening within ART care may reduce transmission from PLHIV; intensified efforts are nonetheless needed to achieve earlier tuberculosis detection in HIV-negative individuals.

BackgroundThe female lower reproductive tract harbors a complex microbiome that plays a critical role in reproductive health. A vaginal microbiome dominated by Lactobacillus crispatus (LC; Community State Type (CST) I) supports vaginal health, whereas a microbiome enriched with anaerobic species, such as Gardnerella vaginalis (GV) and Mobiluncus mulieris (MM) (CST IV) is linked to bacterial vaginosis (BV) and adverse outcomes, including sexually transmitted infections, infertility, and preterm birth. Although antibiotics such as metronidazole and clindamycin are commonly prescribed to treat BV, recurrence rates remain high, and the impact of these treatments on bacterial extracellular vesicles (bEVs), critical mediators of host-microbe interactions, is poorly understood. ResultWe investigated how antibiotic treatment at a dose below minimum inhibitory concentration alters the production and immunomodulatory function of bEVs derived from GV, MM, and LC. Using nanoparticle tracking analysis, cytokine profiling, and TLR pathway analyses, we found that antibiotic treatment significantly enhanced the inflammatory properties of bEVs in a species- and antibiotic-specific manner. Notably, bEVs from antibiotic-exposed GV and MM cultures induced elevated cytokine responses in epithelial and immune cells, primarily through TLR2 activation for GV bEVs, and through both TLR2 and TLR5 activation for MM bEVs. While LC bEVs are typically non-inflammatory, exposure to metronidazole, even at a lower dose than what is used clinically, rendered them immunostimulatory, suggesting a potential unintended proinflammatory consequence of treatment on beneficial microbes. We also detected bEVs in human vaginal swabs, including vaginolysin-positive bEVs, even in CST I microbiomes, indicating that low-abundance microbes, including pathogens, remain transcriptionally active. ConclusionsThese findings suggest that antibiotics not only reduce microbial load but also reshape bacterial communication via bEVs, potentially contributing to inflammation, epithelial barrier disruption, persistent dysbiosis, and recurrent infections. This work underscores the need for precision antimicrobial strategies that eliminate pathogens while preserving beneficial bacteria and their functional bEVs. Future therapies may benefit from considering the ecosystem-wide effects of antibiotics on the vaginal microbiome and its bEV-mediated signaling network.

Summary Background Persistent transmission from relapsing Plasmodium vivax infections threatens malaria elimination programs in the Asia-Pacific and Americas. Tools to identify people at risk of relapse are urgently required. We aimed to validate a panel of eight P. vivax serological biomarkers for predicting future relapses. Methods In this observational study, soldiers returning from malaria-endemic Papua to non-endemic East Java, Indonesia, were screened at enrolment using antibody measurement (Luminex) and trained random forest classification algorithms, then followed for 6 months. Active case detection was performed fortnightly by microscopy. Algorithms classified soldiers as recently infected (last nine months) and thus at risk of relapse, based on anti-vivax antibody measurements at enrolment. Findings Between December 2018 and July 2022, 592 soldiers were enrolled, with 553 completing follow-up; 119 experienced a P. vivax relapse. Of these, 102 were correctly classified as at risk of relapse at enrolment, corresponding to 86% sensitivity and 86% specificity, with an AUC of 0.92. Interpretation P. vivax serological biomarkers can identify people at risk of relapse with high sensitivity and specificity and could be used as a novel public health intervention, P. vivax serological testing and treatment (PvSeroTAT), to reduce relapse-driven transmission.

Ganciclovir (GCV), and its orally available pro-drug valganciclovir (VGCV), are preferred therapies for treating congenital cytomegalovirus (cCMV), however, their use carries a significant risk of neutropenia for the child. This risk limits dosing and effectiveness of VGCV, particularly in the treatment of infants with cCMV infection, who are at increased risk for sensorineural hearing loss (SNHL). We hypothesized that an improved understanding of the pharmacokinetics (PK) and pharmacodynamics (PD) of VGCV in cCMV-infected infants at risk for SNHL would inform strategies for optimizing safe and effective VGCV dosing. Participants were enrolled in one of two clinical studies interrogating the PK, safety, and efficacy of VGCV treatment in cCMV-infected infants at risk for SNHL. GCV exhibited a short median half-life of 2.02 h and the median (range) area under the 24 h concentration-time curve (AUC24) was 60.8 (26.8, 99.4) g*h/mL. An AUC24 > 70 g*h/mL was associated with an elevated risk of neutropenia (Fisher's Exact p = 0.029). No associations between GCV PK and hearing outcomes were observed. Taken together, these results indicate vast inter-individual variability in GCV PK that is associated with dose-related toxicity, supporting the need for individualized dosing in the cCMV-infected population.

Background Artemisinin derivatives are central to first-line treatment of both uncomplicated and severe Plasmodium falciparum malaria. Emerging artemisinin partial resistance in East Africa threatens to spread across the continent. Methods In two cross-sectional studies in Zambia in 2024, we genotyped the artemisinin resistance-associated gene Pfkelch13. In Kaoma, western Zambia, we evaluated the percentage of patients with day-3 parasite positivity following treatment with artemisinin-based combination therapy, and ex vivo parasite susceptibility to dihydroartemisinin (the active metabolite of artemisinin). We also assessed longitudinal changes in Pfkelch13 mutation prevalence in Kaoma using isolates collected from 2018 through 2026. Results We identified a novel mutation, Pfkelch13 A724E, in 52% (113 of 217) of isolates from Western Province, 51% (94 of 184) of isolates from North-Western Province, and 11.7% (229 of 1,949) of isolates country-wide. In Kaoma, 28% (21 of 75) of patients carrying Pfkelch13 A724E mutant parasites before treatment were parasite positive on day 3, compared with 0% (0 of 23) of patients with the wild-type allele (P=0.003). Within day-3 positive patients, the proportion of A724E mutant parasites increased significantly after treatment (P = 0.013). The prevalence of Pfkelch13 A724E in Kaoma increased steadily from 0% (95% confidence interval [CI], 0 to 22%) in 2018 to 79% (95% CI, 73 to 85%) in 2026. Conclusions A novel Pfkelch13 mutation conferring partial resistance to artemisinin is spreading in Zambia. Additional clinical evaluations are urgently needed in the region. (Funded by the Gates Foundation, INV-048316).

Background: Malaria exposure has been hypothesized to alter immune responses to childhood vaccines, but evidence is inconsistent. We evaluated whether early-life malaria exposure and perennial malaria chemoprevention (PMC) modify antibody responses to the 10-valent pneumococcal conjugate vaccine (PCV-10) among infants in a high malaria transmission setting in eastern Uganda. Methods: This study was nested within the MIC-DroP trial (NCT04978272) whereby 202 infants were selected for inclusion. Serotype-specific IgG concentrations were measured using an in-house multiplex seroassay from samples obtained at 8 and 24 weeks of age. Immunogenicity was quantified as the log10 fold-change in IgG concentration between the 8 and 24-week timepoints, and seroconversion as [&ge;]0.35 g/mL at week 24 (i.e., seropositive). Generalized estimating equation models were used to assess associations of PCV-10 immunogenicity and seroconversion with malaria exposure, malaria chemoprevention and birth outcomes. Results: Among the 195 of 202 infants who completed the three-dose PCV-10 series, neither infant PMC nor malaria exposure from study enrollment to 14 weeks were associated with PCV-10 immunogenicity or seroconversion. In contrast, low birthweight (<2500g) was associated with lower immunogenicity (82% lower antibody fold-change, p=0.003) and reduced odds of seroconversion (OR=0.19, p=0.003); preterm birth (<37 weeks) showed similar associations (79% lower antibody fold-change, p=0.018; OR=0.181, p=0.009). Conclusion: In this malaria-endemic setting, early-life malaria exposure and chemoprevention did not measurably alter PCV-10 antibody responses. However, low birthweight and prematurity were associated with reduced vaccine immunogenicity.

Tuberculosis (TB) is a significant cause of morbidity and mortality in children and adolescents, causing 172,000 deaths in 2024 in children and adolescents worldwide. Diagnostic challenges are pronounced in pediatrics, in which collecting respiratory specimens is challenging and TB is often paucibacillary, leading to delayed diagnosis and increased mortality. We describe the protocol and methodology of the Pediatric TB Diagnostic (PDTBDx) cohort, a study with the primary aim of evaluating non-sputum-based TB diagnostics for diagnosis and treatment response in children. This is a prospective observational cohort study of >400 children recruited from inpatient and outpatient clinical sites in Nairobi, Kenya. Children <15 years presenting to study clinical sites with TB symptoms will be considered for enrollment as symptomatic participants. Enrolled participants will undergo rigorous clinical assessment and longitudinal follow-up to ensure appropriate diagnostic classification by NIH consensus statement guidelines for pediatric TB. Baseline evaluation includes symptom assessment, chest x-ray, HIV testing, respiratory TB culture and GeneXpert Ultra, and urine LAM. Subsequent visits occur at week 2, months 1, 2, 4, 6,12 and 24. Blood and urine specimens will be collected at baseline and at follow-up visits for storage for evaluation of novel diagnostic assays, including exosome-based and CRISPR-based TB biomarkers. This large, prospective cohort of pediatric participants with and without TB follows a consistent and rigorous protocol for diagnosing childhood TB, in concordance with internationally recognized guidelines. Assays evaluated in PDTBDx will guide improved diagnostic strategies for pediatric TB.

Klebsiella pneumoniae (KP) isolates belonging to multi-locus sequence type 258 (ST258) are a frequent cause of hospital-associated outbreaks and display extensive multidrug resistance. The KP ST258 lineage consists of two genetically distinct clades, called Clade 1 and Clade 2. These two clades are genetically related to one another, but are historically distinguished by having different capsular polysaccharide types. While bacteria belonging to both clades are isolated from clinical infections, Clade 2 is isolated more frequently compared to Clade 1. To investigate drivers of this difference in clade prevalence, we collected 172 clinical KP ST258 isolates from patients at a single medical center. Clinical review showed that patients infected with Clade 2 isolates were more acutely ill than Clade 1-infected patients, despite having fewer comorbidities. We also found that Clade 2 isolates were more resistant to killing by human serum, despite binding more complement protein C3 than Clade 1 isolates. Additionally, mice infected with a Clade 2 isolate had increased bacterial dissemination from the lungs to the liver and spleen than mice infected with a Clade 1 isolate, and this dissemination required an intact capsule locus. Increased dissemination in mice was not due to differential serum killing, as mouse serum was unable to kill isolates of either clade, but dissemination was associated with decreased macrophage uptake of the Clade 2 isolate. Taken together, these data suggest that KP ST258 Clade 2 is more virulent than Clade 1, though the specific mechanisms at play appear to differ between mice and humans.

PurposePatients with common variable immunodeficiency (CVID) frequently exhibit impaired antibody responses to vaccination, yet the dynamics of humoral and cellular immunity following mRNA immunisation remain incompletely defined. This study aimed to characterise the temporal evolution of anti-SARS-CoV-2 antibody and T cell responses across successive vaccine doses in a well-characterised CVID cohort, and to identify key determinants of vaccine responsiveness in this population. MethodsWe performed a longitudinal and cross-sectional analysis of serum and peripheral blood mononuclear cell (PBMC) samples collected from 88 CVID patients after two, three, or four doses of mRNA vaccine (Moderna/mRNA-1273 or Pfizer-BioNTech/BNT162b2). Anti-receptor-binding domain (RBD) IgG titers were quantified in relation to vaccine dose, time since last vaccination, and clinical characteristics. Vaccine-specific CD4+ and CD8+ T cell responses were assessed ex vivo using an activation-induced marker (AIM) assay by flow cytometry. ResultsThe proportion of patients with detectable anti-RBD IgG increased from 35% after two doses to more than 80% after four doses. Boosting-dependent increases in IgG titers were observed exclusively in samples collected more than three months after the last dose, and antibody levels correlated positively with time since vaccination, consistent with delayed but progressive humoral kinetics that stabilised after the third dose. In contrast, spike-specific CD4+ and CD8+ T cell responses were rapidly induced and remained stable across all timepoints. ConclusionVaccine-induced immunity in CVID is characterised by delayed humoral responses alongside preserved cellular immunity. Early post-vaccination serology may systematically underestimate vaccine responsiveness, and booster vaccination supports stabilisation of antibody responses in this population.

BackgroundWe assessed associations between antibody concentrations within 7 days of symptom onset and testing positive for influenza virus infection among outpatients enrolled in a test-negative study. MethodsFrom November 2018[boxh]May 2019, study sites in five states obtained serum and respiratory specimens from outpatients aged [&ge;]18 years presenting with acute respiratory illness. Respiratory specimens were tested for influenza virus, and viral clades were identified by genomic sequencing. We measured influenza antibody titers against vaccine and circulating viruses by hemagglutination inhibition (HI), microneutralization (MN) and neuraminidase inhibition (NAI) assays. Percent of patients with HI, MN and NAI titers [&ge;]10 and [&ge;]40 were compared among patients with and without influenza-associated illness, and reduction in odds of confirmed influenza at increasing HI, MN and NAI antibody titers was estimated using logistic regression adjusting for influenza vaccination status and time since beginning of influenza season. ResultsAmong 175 patients with confirmed influenza virus infection, including 112 with influenza A(H1N1)pdm09 and 63 with A(H3N2) (44 clade 3C.3a), and 130 test-negative control patients, higher antibody titers against influenza hemagglutinin or neuraminidase proteins at enrollment were associated with lower odds of influenza virus infection. HI and MN antibody titers against circulating viruses were more strongly associated with protection than titers against vaccine reference viruses. Odds of A(H1N1)pdm09 infection were 44% and 54% lower for each two-fold increase in A(H1N1)pdm09 HI or NAI titer, respectively. Odds of A(H3N2) infection were 46% and 30% lower, respectively, for each two-fold increase in MN or NAI titer against circulating A(H3N2) virus clade. NAI titers were independently associated with lower odds of influenza A(H1N1)pdm09 and A(H3N2) after controlling for HI titer. ConclusionHigher influenza antibody titers against circulating viruses were associated with lower likelihood of influenza virus infection among adult patients with acute respiratory illness. SUMMARYFrom November 2018[boxh]May 2019, we assessed the association between antibody concentrations during acute illness and laboratory-confirmed influenza among adult patients enrolled in a test-negative study in five US states. We found that higher influenza antibody titers were associated with lower likelihood of symptomatic influenza virus infection.

BackgroundTuberculosis (TB) incidence in the United States has remained elevated above pre-pandemic levels since 2021, with over 85% of cases resulting from reactivation of Mycobacterium tuberculosis (Mtb) infection. New vaccines that would prevent TB in adults are under development, but the potential health impact of a program prioritizing non-U.S.-born persons and persons with medical comorbidities, including persons living with HIV (PLWH), has not been evaluated. MethodsWe developed a deterministic compartmental transmission model that simulates Mtb infection, transmission, and progression to TB in the U.S., both in the general population and in key high-risk groups. We calibrated the model to 2024 U.S. TB surveillance data and estimated annual cases prevented, percent reduction in annual TB cases, and number needed to vaccinate (NNV, a measure of vaccine program efficiency) at equilibrium conditions for targeted vaccination strategies under optimistic and plausible scenarios, varying assumptions of vaccine efficacy, duration of protection, and achieved vaccination coverage in high-risk groups. FindingsUnder an optimistic scenario, vaccinating PLWH, non-U.S.-born persons, and persons with medical comorbidities (all high-risk groups) prevented 5,385 cases per year (51{middle dot}8% reduction, NNV = 366). Under a more conservative plausible scenario, the same strategy prevented 1,348 cases per year (13{middle dot}0% reduction, NNV = 510). The efficiency and impact of targeting strategies we considered were preserved across all sensitivity and uncertainty analyses. InterpretationTargeted vaccination of persons with Mtb infection in population subgroups recognized to be at high-risk for TB can reduce incidence substantially. Strategies that include non- U.S.-born persons and PLWH are most efficient and impactful. FundingAmerican Lung Association, U.S. National Institutes of Health, and the Ferguson Fellowship.

BackgroundBacterial vaginosis (BV) is a common and difficult-to-treat vaginal disorder, with significant implications for reproductive health, particularly in low and middle-income countries. Clinical cure based on symptom resolution or Nugent scores often do not correspond to restoration of healthy vaginal microbiome. Factors underlying treatment failure remain poorly defined, warranting the need for understanding post-treatment microbiome dynamics to improve long-term outcomes. ObjectivesTo delineate longitudinal vaginal bacteriome dynamics, integrating microbial composition, transition patterns, and clinical symptoms in a closely followed cohort of women with BV based on treatment outcome. MethodsVaginal swabs from reproductive-age women (18-45 years) were collected and classified as BV-positive ([&ge;]7) or healthy ([&le;]3) using Nugent scoring. BV cases were treated using single-dose secnidazole and followed for three months. Sociodemographic, clinical, and behavioral data were statistically analyzed across groups. Vaginal microbiome composition was assessed using 16S rRNA sequencing, evaluating taxonomic profiles, alpha and beta diversity, differential abundance, and co-occurrence networks. ResultsAntibiotic treatment reduced overall microbial diversity and shifted community composition toward healthy controls, though relapse samples retained higher diversity of BV-associated taxa such as Sneathia, Dialister, and Gardnerella, while no-relapse and control groups showed higher Lactobacillus abundance. Corynebacterium amycolatum appeared protective, while Mycoplasma and Fusobacterium played symptom-specific roles. Microbial network analysis showed denser and more persistent associations in baseline and relapse groups, with Sneathia remaining a central node. ConclusionShort-term symptom resolution in BV does not correspond to full microbial recovery; necessary for long-term remission. Functional traits of resilient taxa like Sneathia, Fannyhessea and Dialister may confer resilience and enable recolonization, undermining long term treatment efficacy.