Nature Microbiology

Plant-based dietary strategies may offer a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing autologous hematopoietic cell transplantation (auto-HCT) for multiple myeloma, a population in whom intestinal dysbiosis has been linked to infectious complications and inferior survival. We conducted a single-arm study to test the feasibility and biological activity of a high-fiber, plant-based, whole-food meal delivery intervention during the peri-tran...

BackgroundInfections are the leading cause of non-relapse mortality in pediatric hematopoietic cell transplant (HCT) recipients. Up to 90% of bacteremias in these patients originate from gut microbiome organisms. However, selection for resistance genes, such as Extended-spectrum {beta}-lactamase (ESBL), in these patients gut microbiomes remains poorly understood. MethodsStools were prospectively collected from pediatric HCT recipients at multiple centers (n=133 patients, five centers) on the da...

BackgroundEpstein-Barr virus (EBV) establishes latency in most adults and can be reactivated under conditions of co-infection and immune dysregulation. COVID-19 has been associated with EBV reactivation, primarily in hospitalized cohorts, but EBV shedding in the oral cavity and the extent to which these dynamics trigger a systemic anti-EBV antibody response during acute COVID-19 remain poorly understood. MethodsWe conducted a nested cohort study of 69 community-based participants including 56 S...

Abnormal respiratory microbiomes are reported in children with artificial airways, yet the timing and persistence of these disruptions have not been defined in infants following new tracheostomy placement. We conducted a prospective longitudinal study to characterize airway microbiome dynamics following new tracheostomy placement during early life, a critical period for microbiome development. Fifteen hospitalized infants <=12 months contributed 84 tracheal aspirate samples collected from day 1 ...

ObjectivesTo identify and validate plasma host-response protein biomarkers that improve discrimination of bacterial infection in febrile infants [&le;]90 days of age, and to assess whether novel biomarkers add value beyond established markers. MethodsSub-study of the prospective multicentre Febrile Infant Diagnostic Assessment and Outcome (FIDO) cohort. Novel biomarkers were identified through plasma proteomic profiling (Olink(R)) and combined with biomarkers and signatures from the literature ...

We examined whether the recent emergence of influenza A(H3N2) subclade K, associated with an unusually early influenza season in the Northern hemisphere, was accompanied by a reduction in human population immunity. Using virus neutralisation assays on pre-epidemic human sera collected in May 2025, we found evidence of moderate antigenic drift. Further, vaccines used in the 2024/2025 season induced cross-neutralising immunity. These findings provide timely insight for interpreting recent influenz...

The virulence of Plasmodium falciparum is closely linked to P. falciparum erythrocyte membrane protein 1 (PfEMP1), encoded by a diverse var gene family. PfEMP1 mediates parasite immune evasion and vascular adhesion of infected red blood cells, contributing to severe disease. While expression of group A or domain cassettes (DC8 and DC13)-containing var genes have been associated with severe malaria, comparisons between the severe malaria syndromes remain limited. Furthermore, interactions between...

BackgroundFailure of rapid diagnostic tests (RDTs) to detect Plasmodium parasites in peripheral blood of individuals is a major barrier to successful case management and control of malaria in Ethiopia. Characterizing factors contributing to RDT failure is essential if malaria control and elimination strategies are to succeed. MethodsWe consented and enrolled 148 individuals with suspected malaria presenting to health clinics in Mizan Aman, Ethiopia. We administered a clinical questionnaire, dia...

BackgroundRespiratory viruses are major contributors to population mortality, but cause-of-death coding undercounts their impact. Ecological regression models linking viral circulation to mortality fluctuations can address this limitation. AimTo estimate the population attributable fraction (PAF) of mortality associated with influenza A and B, respiratory syncytial virus (RSV), and SARS-CoV-2 in Ontario, Canada (1993-2024). MethodsWe analysed monthly all-cause mortality data with laboratory su...

AO_SCPLOWBSTRACTC_SCPLOWInfluenza A subclade K viruses caused high infection rates in the 2025/2026 Northern Hemisphere season, raising concerns about antigenic drift and reduced vaccine effectiveness. We measured antibody responses in matched human pre- and post-vaccination sera against a vaccine-like as well as subclade K isolates. Pre-existing immunity to subclade K variants was noted with seasonal influenza vaccination boosting titers two-fold against subclade K and three-fold against the va...

Biological fitness quantifies the efficiency and selective advantage of pathogens and hosts in their bilateral interaction. Key questions--such as how much more infectious an emerging variant is compared with its predecessor, or how much protection vaccination offers relative to no vaccination--require fitness to be measured systematically, in real time, and ideally beyond controlled laboratory settings. We propose an approach that infers biological fitness from mostly non-biological data on inf...

In November 2024, a highly divergent BA.3-related SARS-CoV-2 lineage, designated BA.3.2, was detected in South Africa, marking the first appearance of a BA.3-derived lineage in over two years. Phylogenetic reconstruction places BA.3.2 on an extended branch descending from ancestral BA.3, with no intermediate genomes detected, consistent with a prolonged period of unsampled or isolated evolution. Molecular clock analyses indicate accelerated divergence characteristic of a saltation event, while p...

RationaleSevere SARS-CoV-2 infection induces disrupted oropharyngeal and gut microbiota during acute disease which may persist and contribute to the development of post-acute pulmonary sequelae. To date, it is unclear whether dysbiosis following severe disease is linked to long-term pulmonary function impairment. ObjectivesTo determine associations between oropharyngeal and gut microbiota composition with lung function after severe COVID-19. Methods16S and internal transcribed spacer (ITS) rRN...

BackgroundAcute respiratory distress syndrome (ARDS) is a life-threatening lung condition that requires admission to an intensive care unit (ICU). Sepsis is one of the leading causes of ARDS and understanding protein regulation during sepsis could reveal key mechanisms that predispose patients to ARDS. We performed genome-wide association studies (GWAS) on ARDS biomarkers levels to identify protein quantitative trait loci (pQTLs) and genes which could be associated with ARDS risk. MethodsGWAS w...

Malaria remains a major public health concern in Cameroon, with Plasmodium falciparum responsible for most morbidity and mortality, particularly among children under five. In response to rising cases, Cameroon began implementing the RTS,S/AS01 malaria vaccine in early 2024. Given the vaccines strain-specific efficacy, understanding antigenic diversity and complexity of infection (COI) is critical for evaluating long-term impact. We analyzed 100 P. falciparum-positive dried blood spots collected ...

BackgroundPlasmodium vivax is the predominant cause of malaria in South Asia. P. vivax cases have fallen over the past decade, but cross-border transmission remains a major challenge to elimination. Genetic data can generate valuable insights into transmission; however, until now, only low-resolution data have been available from Nepal, Bhutan and Bangladesh. We piloted high-resolution genotyping using a new microhaplotype (multiallelic) assay to monitor P. vivax transmission across borders. Me...

Clostridioides difficile is a highly methylated organism within the gut microbiome that is responsible for Clostridioides difficile infection (CDI), a common disease that is mediated by toxins production from the bacterium. C. difficile infection is ten times more common in chemotherapy patients than the average patient, but the reasons for this disparity are unclear. Conditioning chemotherapy (CC), an integral part of cancer treatments, has the ability to induce methylation changes in many cell...

Linezolid is a critical last-resort antimicrobial for multidrug-resistant Enterococcus faecium, particularly against vancomycin-resistant lineages where therapeutic options are severely limited. While resistance has historically arisen through de novo chromosomal mutations, the global emergence of transferable resistance mechanisms threatens to render more infections untreatable. Here, we characterise a recent (2023-2024) hospital-associated outbreak of linezolid-resistant E. faecium in Queensla...

Ethiopian cutaneous leishmaniasis (CL) shows remarkably heterogeneous clinical presentations, but the underlying immunopathological mechanisms driving this heterogeneity in disease presentation remains poorly understood. To characterise the local immune response in Ethiopian CL, we performed spatial transcriptomics on paired lesional and non-lesional skin punch biopsies from five Ethiopian CL patients. We used reference-free deconvolution, morphology-guided regional analyses, and immunohistochem...

Cutaneous leishmaniasis (CL) is a skin disease caused by Leishmania infection, for which no licensed human vaccine exists. Protective immunity is largely T cell-mediated and depends on antigen presentation by MHC molecules, yet the naturally presented epitopes during human disease remain poorly defined. To address this gap, we performed mass spectrometry-based immunopeptidomics on lesional biopsies from 27 Ethiopian CL patients spanning the full clinical spectrum. We newly identified 333 MHC-I a...