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Integrating hotspot dynamics and centers of diversity: a review of Indo-Australian Archipelago biogeographic evolution and conservation.

The Indo-Australian Archipelago (IAA) is the world's preeminent marine biodiversity hotspot, distinguished by its exceptional species richness in tropical shallow waters. This biodiversity has spurred extensive research into its evolutionary and biogeographic origins. Two prominent theoretical frameworks dominate explanations for the IAA's biodiversity: the "centers-of hypotheses" and the "hopping hotspot hypothesis". The "centers-of hypotheses" posits that specific regions serve as key sources of IAA biodiversity, either through the accumulation and overlap of species from external areas or via elevated rates of local speciation. In contrast, the "hopping hotspot hypothesis" asserts that biodiversity hotspots are dynamic, shifting across geological timescales in response to tectonic and environmental changes. This review synthesizes these contrasting perspectives into an integrated framework, the "Dynamic Centers Hypothesis," which proposes that as biodiversity hotspots migrate over time, the IAA's role in generating and sustaining biodiversity has evolved, with varying contributions from different sources dominating distinct historical phases. By synthesizing the evidence for both hypotheses and incorporating recent findings, including fossil and phylogeography data, we propose the "Dynamic Centers Hypothesis" as a comprehensive and unifying explanation for the IAA's biodiversity. The review further explores biogeographic delineation, aligning tropical marine realms with the IAA's evolutionary trajectory, from its Tethyan roots to its modern Indo-West Pacific dominance. Looking forward, advances in DNA barcoding and genomics are uncovering vast cryptic diversity, revolutionizing our comprehension of IAA phylogeographic history. These discoveries underscore the imperative for a multidimensional conservation framework, integrating phylogenetic, and functional diversity, to preserve this biodiversity hotspot amid escalating global change.

Biogeography

Comprehensive In Vitro, Genomic, Microbiota, and Subacute Toxicological Safety Characterization of Lactiplantibacillus plantarum ATA-LPC98052.

BACKGROUND: Lactiplantibacillus plantarum is a widely studied probiotic species; however, probiotic characteristics and safety profiles are strain-specific, requiring independent evaluation. This study characterized Lactiplantibacillus plantarum ATA-LPC98052 as a candidate probiotic raw material. METHODS: ATA-LPC98052 was evaluated for hemolysis, acid/bile tolerance, Caco-2 adhesion, cytotoxicity, and storage stability. Subacute oral safety was assessed in Wistar rats by gavage for 28 days at 1.2 × 1011 CFU/kg/day; the study design incorporated selected principles of OECD Test Guideline 407. Clinical, hematological, biochemical, organ-weight, and macroscopic endpoints were evaluated. Fecal microbiota was analyzed by 16S rRNA sequencing; WGS was used for taxonomic confirmation and genomic safety screening. RESULTS: ATA-LPC98052 was γ-hemolytic and maintained 60% viability at pH 1.5 and 96% at pH 5.0, while viability ranged from 74% to 82% across 0.1-0.5% bile salt concentrations. Caco-2 cell viability was 99%, adhesion exceeded 90%, and the lyophilized preparation remained stable for 15 months, maintaining 9.6 log10 CFU/g. Repeated oral administration caused no mortality or consistent treatment-related toxicological pattern. Longitudinal microbiota analysis showed no significant treatment × time effects on alpha diversity or Bray-Curtis community structure, and no genus-level MaAsLin2 association was FDR-significant. WGS confirmed L. plantarum identity and no contamination; ResFinder detected no acquired antimicrobial resistance determinants meeting specified thresholds, whereas CARD/RGI identified low-identity qacJ and vanY homologs requiring cautious interpretation. CONCLUSION: ATA-LPC98052 demonstrated favorable in vitro probiotic characteristics, technological stability, gut microbiota-modulating potential, and a favorable subacute safety profile under the tested conditions; however, microbiota findings were exploratory, and phenotypic MIC testing remains warranted.

Animals

Oral bacteriome in pediatric patients with malignancies prior to chemotherapy: a pilot study using full-length 16S rRNA sequencing.

OBJECTIVE: To characterize the composition, diversity, and ecological features of the oral bacteriome in pediatric patients with malignancies prior to chemotherapy initiation. METHODS: In this prospective pilot study,supragingival plaque samples were collected from 10 pediatric cancer patients prior to the initiation of chemotherapy. Bacterial genomic DNA was extracted from each sample, and the full-length 16S rRNA gene was amplified and sequenced on the PacBio Sequel II platform using circular consensus sequencing (CCS). Raw CCS reads were quality-filtered and denoised into amplicon sequence variants (ASVs) using DADA2, and taxonomic assignment was performed against the SILVA 138 reference database. Alpha diversity was assessed using the Chao1, Shannon, Simpson, and Faith's phylogenetic diversity (PD whole tree) indices, while beta diversity was evaluated through principal coordinate analysis (PCoA), and non-metric multidimensional scaling (NMDS). Microbial co-occurrence networks were constructed to characterize bacterial interactions, and functional potential was predicted using PICRUSt2, and BugBase. RESULTS: A total of 614,473 high-quality CCS reads were generated, yielding 1,697 ASVs. Alpha diversity analysis revealed substantial inter-individual variation in microbial richness and diversity among the pediatric cancer patients. The bacterial community was dominated by the phyla Firmicutes, Proteobacteria, Bacteroidota, Actinobacteriota. At the genus level, Streptococcus, Prevotella, Neisseria, and Haemophilus were the most abundant taxa. Beta diversity analysis revealed distinct clustering patterns, indicating highly individualized microbial profiles. Co-occurrence network analysis identified several keystone taxa and potential pathogenic associations within the supragingival plaque community. Functional prediction indicated that the dominant metabolic pathways were related to amino acid metabolism, carbohydrate metabolism, and membrane transport. CONCLUSION: These preliminary findings reveal a taxonomically diverse, highly individualized pre-chemotherapy oral bacteriome, providing foundational baseline profiles to guide future longitudinal investigations of chemotherapy-induced dysbiosis and personalized interventions.

Humans

Pregnancy diet based on ancestral patterns increases growth in subcortical fetal brain regions.

Evidence on the biological basis for maternal nutrition effects on fetal and newborn neurodevelopment remains limited. This randomized controlled trial in Ecuador tested a maternal dietary pattern-derived from empirical studies of nutrition in human evolution and adapted locally-on offspring growth and brain development. Pregnant women (n = 215) in their first trimester were randomized to: 1) control (n = 104); or 2) Mikhuna ("nourish" in Kichwa) intervention (n = 111). The intervention, from 12 wk gestation to birth, consisted of a weekly food delivery (8 eggs, 500 g fish, and a variety of sustainably sourced fruits and vegetables) and a behavior change communication strategy encouraging diet diversity and limiting highly processed foods. Longitudinal data collection occurred at 12 wk, 21 wk, 35 wk gestation, and 2 wk postpartum, and included ultrasound imaging of fetal bone and brain parameters, maternal dietary intakes, anthropometry, socioeconomic and demographic variables, and other biomarkers. At close of intervention, a significantly higher percentage of women met the minimum dietary diversity threshold in Mikhuna (74.5%) vs. control groups (55.8%) (P = 0.004). Generalized linear regression models showed significant differences in Mikhuna compared to control for: corpus callosum length 0.19 cm (95% CI [0.02, 0.35]), gangliothalamic ovoid height 0.15 cm (95% CI [0.03 to 0.26]), and femur length -0.10 cm (95% CI [-0.19, -0.02]) from 21 wk to 35 wk; and corpus callosum Z 0.56 (95% CI [0.03, 1.09]) and femur length Z -0.21 (95% CI [-0.42, 0.00]) at 35 wk. The Mikhuna intervention increased the growth of subcortical fetal brain structures, which have established roles in motor control, cognition, and signal transmission.

Female

Delayed maturation of the milk microbiome in women with type 1 diabetes.

AIMS/HYPOTHESIS: The breastmilk microbiome plays a crucial role in gut microbial colonisation and immune development, but little is known about how it is influenced by type 1 diabetes. METHODS: We conducted a longitudinal 16S rRNA gene sequencing study of milk from women with type 1 diabetes (n=69 pregnancies; 174 samples) and women who did not have type 1 diabetes (n=49 pregnancies; 123 samples), collected at seven timepoints from birth to 15 months postpartum. Alpha diversity (richness, inverse Simpson evenness) was analysed by generalised linear mixed models, beta diversity was analysed by Bray-Curtis dissimilarities and PERMANOVA, and differential abundance was analysed by limma. Additionally, we examined associations with maternal genetic risk score (GRS), maternal HLA type, glycaemic management (HbA1c) and breastmilk secretory IgA (sIgA), and performed a parallel analysis for the infant stool microbiome. RESULTS: A significant interaction between type 1 diabetes status and timepoint was observed for alpha diversity, both richness (p=0.01) and inverse Simpson diversity (p=0.003), indicating distinct temporal trajectories between women with and without type 1 diabetes. In those without type 1 diabetes, richness increased significantly between birth and 1 week postpartum, but this early increase was delayed in women with type 1 diabetes to between 1 week and 3 months postpartum (p=0.002). Beta diversity analysis revealed earlier and more extensive compositional shifts in women without type 1 diabetes compared to those with type 1 diabetes. These differences persisted after adjusting for Caesarean delivery, BMI, parity and infant sex, and were not attributable to a delay in initiating breastfeeding. Taxa with delayed enrichment in women with type 1 diabetes included Streptococcus spp. and Rothia mucilaginosa, which metabolise human milk oligosaccharides to short-chain fatty acids to promote development of the infant's gut barrier and immune system. Maternal GRS, HLA, HbA1c or sIgA were not associated with milk microbiota diversity trajectories. In infant stool samples, alpha diversity did not differ between exposure groups, and showed no evidence of delayed maturation. Beta diversity revealed an early compositional shift between birth and 1 week postpartum only in infants born to women without type 1 diabetes. Similarly, significant taxonomic changes between birth and 1 week postpartum were detected only in infants born to women without type 1 diabetes, but with some taxa differing between exposure groups at 1 week. CONCLUSIONS/INTERPRETATION: Maternal type 1 diabetes is associated with delayed early maturation of the breastmilk microbiome. Early compositional differences in microbiota restructuring were also observed in the infant gut, partially mirroring the pattern in the milk microbiome; however, sustained differences in infant gut microbiota diversity were not detected. Further investigation could determine whether these changes affect development of the infant's gut and immune system.

Humans

Five decades of pneumococcal meningitis in Spain: a single-centre, clinical and genomic, retrospective, observational study.

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&#xb7;8-15&#xb7;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&#xb7;2-58&#xb7;1; p<0&#xb7;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&#xb7;0-15&#xb7;6) and broader serotype diversity. The introduction of PCV7 and PCV13 resulted in declines in vaccine-targeted serotypes and &#x3b2;-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 &#x3b2;-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 Investigaci&#xf3;n Biom&#xe9;dica en Red de Enfermedades Respiratorias, and the Centro de Investigaci&#xf3;n Biom&#xe9;dica en Red de Enfermedades Infecciosas, both at the Instituto de Salud Carlos III.

Journal Article

Eikenella corrodens in human oral and non-oral infections: a review.

There is substantial evidence in support of the existence of distinct clinical forms of human periodontal disease. Moreover, these different forms of periodontal disease may be associated with relatively distinct subgingival microflora, often involving microaerophilic or anaerobic Gram-negative bacterial species. Eikenella corrodens is a facultative Gram-negative bacillus which is a common inhabitant of the oral cavity and the intestinal and genital tracts. Its primary ecologic niche within the oral cavity appears to be dental plaque, both in periodontally healthy individuals and in periodontitis patients. However, E. corrodens is recognized as an infrequent human pathogen capable of causing extraoral infections, either as the sole infectious agent or as part of a mixed infection, its potential role in the etiology of periodontal disease is not well understood. E. corrodens is often present in the supra- and subgingival plaque of periodontally healthy subjects. On the basis of cross-sectional and longitudinal studies, E. corrodens appears to be somewhat more prevalent in subgingival plaque samples of periodontitis subjects than periodontally healthy individuals. However, the percentage of E. corrodens in the total cultivable microflora did not vary between the two groups. Microbiologic studies attempting to define the relationship between E. corrodens and periodontal disease assume that this species is essentially homogeneous and that all strains exhibit comparable pathogenic potential. However, E. corrodens exhibits 1) variable colony morphology, biochemical and serologic reactivity; 2) marked phenotypic diversity with respect to outer membrane protein and lipopolysaccharide structure; and 3) marked diversity in the restriction patterns of total genomic DNA. Thus, it is possible that a limited number of clones of E. corrodens may be associated with periodontal disease and/or extraoral infection, while other strains are relatively harmless commensals. Additional studies, possibly employing strain-specific nucleic acid probes, may be required to define the role of E. corrodens as a human periodontal pathogen.

Animals

Large-scale multiethnic electronic health record resource for diabetes complications research: the North West London Diabetes Cohort (NWLDC) - cohort profile.

PURPOSE: The North West London Diabetes Cohort is established to provide systematic characterisation of a large diabetes population as a foundation for complications research and prognostic modelling. Many predictive modelling studies neglect the essential descriptive characterisation of underlying cohorts, focusing narrowly on model accuracy. This cohort profile addresses this gap by comprehensively describing the demographic composition, clinical characteristics and complication incidence patterns. The notably diverse, multiethnic population enables examination of ethnic disparities and supports future development of reliable prognostic models and evidence-based prevention strategies for diabetes complications. PARTICIPANTS: At baseline, 337&#x2009;271&#x2009;patients with diabetes were identified. It includes 279&#x2009;067&#x2009;patients with type 2 diabetes, 17&#x2009;638 with type 1 diabetes, 33&#x2009;590 with gestational diabetes and 6916 with unspecified diabetes. The earliest diabetes diagnosis dates to January 1932, with data updated to 27 May 2025. FINDINGS TO DATE: This cohort profile describes baseline characteristics of patients with comprehensive data collected on demographics (age, sex, Deprivation Index, ethnicity), clinical measures (glycated haemoglobin, body mass index, blood pressure, lipids and estimated glomerular filtration rate) and 14 major diabetes complications tracked longitudinally. Key findings for patients with type 2 diabetes reveal diabetic retinopathy as the most common complication (74.6 per 1000 person-years), followed by hypertension (51.0) and kidney disease (31.4). Cumulative incidence analyses using the Aalen-Johansen estimator, which accounts for mortality as a competing risk, demonstrated significant ethnic disparities, with black, Asian, mixed and other ethnic groups showing elevated risk compared with white patients. Time-varying Cox models identified strong clustering between cardiovascular and renal complications, confirming a cardiometabolic-renal syndrome. Mental health conditions (depression and anxiety) were prevalent throughout the disease timeline, occurring both before and after diabetes diagnosis. FUTURE PLANS: This cohort will be used as a platform for developing and validating prognostic models for diabetes complications, enabling risk stratification and targeted interventions. Future work will incorporate medication data to refine diabetes type classification, examine the effectiveness of antidiabetic medications in preventing different complications and address demographic differences in prognostic model performance and prediction accuracy. To better characterise lifestyle, further interrogation of electronic health record data will examine recording of advice given, including dietary advice, referral to weight management schemes and presence of alcohol consumption codes.

Humans

The COVID-19 pandemic influenced the temporal dynamics of antimicrobial resistance markers and bacterial community across urban wastewater treatment plants.

Urban wastewater systems represent important interfaces between human activity and the environmental occurrence of antimicrobial resistance (AMR) markers. We assessed the temporal dynamics of intI1, ermB, and the 16&#xa0;S rRNA gene by quantitative PCR across three wastewater systems (EPC, CJC, and JW) in Fortaleza, Brazil, from November 2021 to November 2023. Bacterial communities were additionally characterized by 16&#xa0;S rRNA gene metabarcoding in 18 samples collected in December 2021 and January 2022. A synchronized decline in 16&#xa0;S rRNA gene and intI1 concentrations beginning in late 2022 was observed across all three wastewater systems, suggesting a shift toward lower microbial abundance. The ermB gene showed higher and more variable concentrations during part of the pandemic period, followed by convergence toward lower levels; however, the absence of antimicrobial-consumption data precluded attribution of this pattern to changes in macrolide selective pressure. Normalized antimicrobial resistance marker abundances were comparatively stable at EPC and JW but more variable at CJC. EPC exhibited the highest ASV richness, whereas CJC and JW showed greater diversity according to Shannon and inverse Simpson indices. Beta-diversity analyses identified wastewater system as the principal factor associated with bacterial community structure, while the effect of sampling period was smaller and metric-dependent. Neither ermB nor intI1 was individually associated with community composition, although intI1 showed a limited effect after adjustment for wastewater system in one model. Physicochemical parameters were not significantly associated with normalized marker abundances in the exploratory paired analysis. Arcobacter, Acinetobacter, and other potentially relevant genera were detected, but no direct associations between these taxa and the monitored AMR markers could be established. These findings highlight the value of integrating longitudinal qPCR, microbiome profiling, and environmental characterization to improve the interpretation of targeted AMR markers in One Health wastewater surveillance.

Wastewater

Evolution of tumor subclones and T-cell dynamics underlie variable ibrutinib responses in Waldenstr&#xf6;m macroglobulinemia.

To elucidate the molecular basis underlying differential responses and resistance to ibrutinib in Waldenstr&#xf6;m macroglobulinemia (WM), we conducted a prospective phase 2 trial of ibrutinib monotherapy in treatment-na&#xef;ve patients. A total of 74 sequential bone marrow (BM) aspirates from 17 patients, collected from baseline through 48 treatment cycles, were profiled using single-cell multiomics. BM cells were segregated primarily into B-cell/plasma cell and T-cell compartments. Longitudinal clonal tracking of malignant B cells/plasma cells identified 3 distinct evolutionary patterns: evolution (early clone contraction with late clone expansion and increasing genomic complexity), devolution (early clone expansion with late clone contraction and genomic simplification), and no evolution (stable clonal architecture). The evolution pattern was strongly associated with disease progression, whereas devolution correlated with durable clinical response. Transcriptomic profiling of resistant clones enabled development and validation of the Waldenstr&#xf6;m ibrutinib prediction (WIP) score, which predicted treatment response at baseline. Within the WIP signature, LYN emerged as a key regulator; LYN knockdown or inhibition significantly increased WM cell sensitivity to ibrutinib, suggesting a rational combination strategy. In parallel, GZMB+ CD8+ effector-memory T cells expanded after treatment in patients with progressive disease and coexisted with tumor evolution. These cells exhibited persistently impaired cytotoxic programs (eg, GNLY), a dedifferentiated memory-like state, elevated PDCD1 expression, and reduced T-cell receptor diversity. Together, this study provides, to our knowledge, the first single-cell framework of tumor clonal evolution and T-cell dysfunction under ibrutinib in WM, introduces the WIP score as a predictive biomarker for treatment response, and identifies actionable tumor-intrinsic and immune mechanisms driving resistance. This trial was registered at www.ClinicalTrials.gov as NCT02604511.

Aged

Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.

BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings. METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types. RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types&#xa0;and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r&#x2009;=&#x2009;0.76), siblings (r&#x2009;=&#x2009;0.61) and infants (r&#x2009;=&#x2009;0.54), while co-occurrence analysis found a higher likelihood (Pr&#x2009;>&#x2009;0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings. CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.

Animals

Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study.

BACKGROUND: Defining the temporal dynamics of invasive Streptococcus pyogenes (group A Streptococcus) and differences between hyperendemic and lower-incidence regions provides crucial insights into pathogen evolution and, in turn, informs preventive measures. We aimed to examine the clinical and temporal lineage dynamics of S pyogenes across different disease settings in Australia to improve understanding of drivers of pathogen diversity. METHODS: In this retrospective, multicentre, clinical and genomic epidemiology study, we identified cases of invasive S pyogenes infection from normally sterile sites between Jan 1, 2011, and Feb 28, 2023. Data were collected from five hospital networks across low-incidence regions in temperate southeast Australia and the hyperendemic, tropical, and largely remote Top End of the Northern Territory of Australia. The crude incidence rate ratio (IRR) of bloodstream S pyogenes infection comparing the Top End and southeast Australia and in First Nations people compared with non-First Nations people was estimated by quasi-Poisson regression. We estimated odds ratios (ORs) of intensive care unit (ICU) admission, in-hospital mortality, and 30-day mortality for the Top End versus southeast Australia using logistic regression. Retrieved and successfully sequenced isolates were assigned lineages at whole-genome resolution. Temporal trends in the composition of co-circulating lineages were compared between the two regions. We used an S&#x2009;pyogenes-specific multistrain simulated transmission model to examine the relationship between host population-specific parameters and observed pathogen lineage dynamics. The prevalence of accessory genes (those present in 5-95% of all genomes) was compared across geographies and temporal periods to investigate genomic drivers of diversity. FINDINGS: We identified 500 cases of invasive S pyogenes infection in patients in the Top End and 495 cases in patients in southeast Australia. The crude IRR of bloodstream infection for the Top End compared with southeast Australia was 5&#xb7;97 (95% CI 4&#xb7;61-7&#xb7;73) across the entire study period; in the Top End, infection disproportionately affected First Nations people compared with non-First Nations people (5&#xb7;41, 4&#xb7;28-6&#xb7;89). The odds of in-hospital mortality (OR 0&#xb7;43, 95% CI 0&#xb7;26-0&#xb7;70), 30-day mortality (0&#xb7;38, 0&#xb7;23-0&#xb7;63), and ICU admission (0&#xb7;42, 0&#xb7;30-0&#xb7;59) were lower in the Top End than in southeast Australia. Longitudinal lineage analysis of 642 S pyogenes genomes identified waves of replacement with distinct lineages in the Top End, whereas southeast Australia had a small number of dominant lineages that persisted and cycled in frequency. The transmission model qualitatively reproduced a similar pattern of replacement with distinct lineages when using a high transmission rate, small population size, and high levels of human movement-characteristics similar to those of communities in the hyperendemic Top End. Using a lower transmission rate, larger population size, and lower levels of migration similar to those of communities in urbanised southeast Australia, the transmission model qualitatively reproduced a pattern of dominant lineages that cycled in frequency. Despite distinct circulating lineages, the prevalence of accessory genes in the bacterial population was maintained across geographies and temporal periods. INTERPRETATION: In a hyperendemic setting, the replacement of distinct S pyogenes lineages occurred in waves, which could be linked to the disproportionate burden of disease and sparse human population in this setting. The maintenance of bacterial gene frequency could be consistent with multilocus selection. These findings suggest that lineage-specific interventions-such as vaccines under development-should consider disease setting and, without broad cross-protection, might lead to lineage replacement. FUNDING: National Health and Medical Research Council, and Leducq Foundation.

Humans

Distinct modes of evolution drive HIV escape from two broadly neutralizing antibodies.

Broadly neutralizing antibodies (bNAbs) show promise for HIV treatment and prevention, but are vulnerable to resistance evolution. Comprehensively understanding in vivo viral escape from individual bNAbs is necessary to design bNAb combinations that will provide durable responses. We characterize viral escape from two such bNAbs, 10-1074 and 3BNC117, using deep, longitudinal sequencing of full length HIV envelope (env) genes from study participants treated with bNAb monotherapy. Improved sequencing depth and computational evolutionary analyses permit us to identify in vivo routes and parallelism underlying HIV escape from each bNAb, providing new insights into this evolutionary process: 10-1074 escape is restricted to a small number of previously documented pathways, but these escape mutations 1) pre-exist in intra-host viral populations before therapy, 2) are not all equally preferred, and 3) emerge with a high degree of genetic parallelism within and across viral populations. In contrast, 3BNC117 escape follows background-specific patterns in which specific escape mutations present in one population rarely emerge or spread in other populations, but often still exhibit parallel evolutionary responses within their host. That bNAbs elicit starkly different in vivo escape profiles depending on their Env target exposes the limitations of generalizing escape patterns across therapies and highlights the substantial challenges in predicting a viral population's bNAb susceptibility from genetic diversity alone.

Journal Article

Longitudinal whole-genome analysis of bluetongue virus identifies conserved serotype-specific genomes and distinct genomic constellations within a Colorado sheep flock (2021-2023).

Bluetongue virus (BTV) is a segmented double-stranded RNA virus of ruminants transmitted by Culicoides spp. biting midges. Although the genome consists of ten segments, classification into serotypes is primarily based on genome segment 2. However, reassortment among genomic segments is a major driver of BTV evolution and diversity. This study used longitudinal whole-genome sequencing to characterize BTV genomes collected from 2021 to 2023 within a single sheep flock in Colorado, where multiple serotypes co-circulate. Whole-genome sequences were generated from fourteen blood samples representing four serotypes: BTV-6, -11, -13, and -17. Longitudinal sampling identified multiple BTV serotypes within individual sheep across consecutive years. Tanglegram analysis comparing segment phylogenies to the segment 2 tree demonstrated incongruent topologies across all genomic segments, suggestive of reassortment or the circulation of distinct genomic constellations. Nucleotide-level comparisons revealed high sequence homology among same-serotype samples from the same year, while the greatest genetic divergence was observed among BTV-17 genomes collected in different years. Additionally, all BTV-13 genomes contained a previously undescribed nonsynonymous substitution in segment 10 predicted to extend the encoded protein by three amino acids. Together, these findings demonstrate that highly conserved BTV genomes and distinct genomic constellations can be detected at the flock level across multiple years. This longitudinal whole-genome approach reveals the genetic complexity of endemic BTV populations, including novel variants and genomic patterns consistent with reassortment that are lost with conventional serotyped-based approaches, highlighting the need to integrate whole-genome characterization into endemic BTV monitoring programs.

Animals

Novel Mycoparasitic Mechanisms and Colonization Patterns on Poplar Revealed by GFP Tagging of the Biocontrol Fungus Clonostachys reniana.

Clonostachys rosea has long been the primary model for studying mycoparasitism within its genus; however, the potential of other species remains largely unexplored. In this study, we established a PEG-CaCl2-mediated protoplast transformation system for Clonostachys reniana. Our results demonstrate for the first time that this species is amenable to genetic manipulation and produces transformants with genetic stability, providing a reliable platform for functional genomic research in this fungus. Using green fluorescent protein tagging, we achieved stable transformants that retained wild-type physiological traits. Crucially, our data indicated that C. reniana utilizes a distinct mycoparasitic mechanism, which differs from the well-established sequential process of adhesion, coiling, and lysis seen in C. rosea. Confocal and scanning electron microscopy revealed that C. reniana, following initial coiling and invasive structure formation, penetrates the host hyphae of Botryosphaeria dothidea. It then grows longitudinally within the hyphal lumen, absorbing nutrients and eliminating the pathogen from the inside. Furthermore, C. reniana hyphae can colonize the intercellular spaces of the stem periderm in 84K poplar (Populus alba &#xd7; P. glandulosa) while displaying a distinct tissue-specific behavior in the roots by forming a mantle on the root surface resembling that of ectomycorrhizae. These findings establish C. reniana as a highly promising secondary model species within the Clonostachys genus. By uncovering a novel "internal-consumption" mycoparasitic mode, this study expands our understanding of the ecological diversity of biocontrol fungi and provides a powerful genetic toolset for future functional genomic research.

Clonostachys reniana

Patterns and implications of co-use between vaping and hallucinogens: a systematic review and meta-analysis.

BACKGROUND: The co-occurrence use of e-cigarettes and hallucinogens has become increasingly common, particularly among youth and young adults. However, evidence regarding the association between these behaviors remains limited and fragmented. This systematic review and meta-analysis aimed to synthesize current evidence, examining the correlation between hallucinogen use and the likelihood of being an e-cigarette user. METHODS: A comprehensive search was conducted in PubMed, Scopus, Web of Science, EMBASE, and Cochrane CENTRAL up to June 2025. Eligible studies measured both hallucinogen and e-cigarette use and reported quantitative associations between these behaviors. Data extraction and risk-of-bias assessments were performed independently by three reviewers using the Newcastle-Ottawa Scale. Pooled effect sizes were calculated using a random-effects model (REML). Certainty of evidence was evaluated with the GRADE approach. RESULTS: Eleven studies met the inclusion criteria (n&#xa0;=&#xa0;247,904), and seven were included in the meta-analysis (n&#xa0;=&#xa0;217,478). The pooled analysis demonstrated that hallucinogen users had 4.47 times higher odds of being e-cigarette users (OR: 4.47, 95% CI 2.72 to 7.34; p&#xa0;<&#xa0;0.001; I2&#xa0;=&#xa0;95.7%, n&#xa0;=&#xa0;7). The certainty of evidence was rated as low. CONCLUSIONS: Hallucinogen use is directionally and strongly associated with e-cigarette use across diverse populations. Although the direction of association was consistent across studies, the magnitude of effect was heterogeneous. These behaviors likely share psychosocial and environmental determinants, although alternative explanations, including shared genetic liability, recall bias, and residual confounding, cannot be excluded. Further longitudinal studies are needed to clarify the underlying mechanisms of this association and establish temporality. The findings also support integrating hallucinogen-use screening into e-cigarette prevention and harm-reduction programs targeting youth and young adults.

Humans

From glycosylation to inflammation: insights from NMR-Derived GlycA and GlycB.

Post-translational modifications (PTMs) play a crucial role in increasing proteomic diversity. N-linked glycosylation acts as a key regulatory layer that influences protein stability, trafficking, circulation, and immune responses. Unlike conventional inflammatory biomarkers that measure individual proteins, nuclear magnetic resonance (NMR) spectroscopy identifies the combined signals GlycA and GlycB from glycoproteins, offering an overall view of systemic glycoprotein changes. These signals represent the N-glycosylation patterns of several abundant acute-phase proteins (APPs), giving detailed molecular insights. This review offers a detailed assessment of GlycA and GlycB as mechanistically grounded indicators of liver glycoprotein remodeling and systemic inflammation. GlycA mainly indicates the levels and structural complexity of N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine (GalNAc) residues linked to acute-phase glycoproteins and glycan branching. In contrast, GlycB reflects changes in terminal sialylation, which influences glycoprotein half-life, immune recognition via lectins, and inflammatory signaling. Collectively, these biomarkers combine measurements of hepatic APP production with variations in glycan structure, offering mechanistically anchored reporters of hepatic glycoprotein remodeling. We explore the enzymatic pathways responsible for N-glycan branching, fucosylation, and sialylation, as well as the roles of major APP scaffolds in the GlycA and GlycB resonances. We also highlight the emerging clinical significance of these signals across infectious, autoimmune, cardiovascular, metabolic, neurodegenerative, and cancer-related diseases. Rather than serving simply as markers of inflammation, GlycA and GlycB provide mechanistically interpretable readouts of cytokine-driven hepatic glycoprotein remodeling and systemic immune activation, supporting their application in disease risk stratification, longitudinal monitoring, therapeutic response assessment, and precision medicine.

GlycA

Distinct cochlear cell types associated with genetic susceptibility to sensory and metabolic hearing loss in older adults.

Hearing loss is a heterogeneous condition that can be classified into different subtypes with diverse genetic and cellular components. To investigate the cochlear cell types underlying the genetic basis of sensory and metabolic components of age-related hearing loss (ARHL), we integrated human genome-wide association study data with mouse cochlear single-cell RNA sequencing data using the single-cell disease relevance score tool. These analyses revealed that genes associated with the sensory component of ARHL were most highly expressed in hair cells, while genes associated with the metabolic component of ARHL were most highly expressed in spiral ganglion neurons. We also investigated whether ARHL-associated gene expression patterns differed across subpopulations of the same cell type. Sensory hearing loss-associated genes showed differential expression across supporting cell subpopulations in younger mice, whereas metabolic hearing loss-associated genes exhibited differences across intermediate cell subpopulations of the stria vascularis in older mice. These findings provide evidence for the role of distinct genetic and cellular risk profiles for different ARHL subtypes, suggesting that prevention and therapeutic strategies may require targeting specific cell populations at different life stages.

ARHL