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PubMed2024

Mitochondrial DNA control-region and coding-region data highlight geographically structured diversity and post-domestication population dynamics in worldwide donkeys.

Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000-7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide.

Animals↗
PubMed2026

Rgg144/SHP144-controlled streptolancidin D mediates intra-species competition in Streptococcus pneumoniae with cumulative effect from other bacteriocins and fratricide.

UNLABELLED: Streptococcus pneumoniae is a major colonizer of the human nasopharynx, where inter- and intra-strain competition plays a critical role in shaping population structure and influencing vaccine outcomes. Bacteriocins are key mediators of intra-species competition, yet many of their functions and regulatory mechanisms remain poorly understood. Here, we identify and characterize streptolancidin D, a previously uncharacterized bacteriocin encoded by the sldA-T locus, and demonstrate its contribution to pneumococcal competition. Using isogenic streptolancidin-producing and non-producing variants of a naturally colonizing strain, we show that sldA-T contributes to the inhibition of competitor strains in in vitro biofilms and during murine co-colonization. Importantly, streptolancidin D also inhibited in vitro a subset of genetically diverse pneumococcal isolates representing multiple serotypes, whereas non-producing variants showed no activity. This indicates that its effect is broad and not restricted to isogenic interactions. Genomic analysis of over 7,500 pneumococcal genomes revealed that sldA-T is present in ~12% of isolates, with lineage-associated distribution patterns, and is consistently encoded downstream of the Rgg144/SHP144 quorum sensing system. We further demonstrate that sldA-T is regulated by this system, with sldA-T promoter activity abolished in a SHP-deficient background and partially restored by exogenous peptide stimulation. Finally, we show that streptolancidin D acts in concert with other bacteriocin systems and competence-mediated fratricide, highlighting a multifactorial antimicrobial strategy that enhances pneumococcal competitiveness. Overall, our findings identify a quorum sensing-regulated bacteriocin that contributes to pneumococcal competition and helps shape population dynamics. IMPORTANCE: Bacteriocins are central to bacterial competition and niche occupation, particularly in structured environments like the human nasopharynx. While several pneumococcal bacteriocins have been characterized, the functions of many remain unknown, limiting our understanding of how these systems shape strain fitness and population dynamics. We characterize streptolancidin D, a bacteriocin that enhances intraspecies competitiveness in vitro and in vivo and contributes to the inhibition of genetically diverse pneumococcal strains. We demonstrate that its expression is tightly regulated by the conserved Rgg144/SHP144 quorum sensing system and that the locus is distributed and shows synteny across multiple pneumococcal lineages. Our findings reveal that streptolancidin D operates within a broader network of bacteriocins and competence-associated mechanisms that collectively shape competitive interactions. By integrating genomic, functional, and regulatory analyses, this work expands the known repertoire of pneumococcal antimicrobial systems and provides new insights into the mechanisms underpinning competition and population structure in S. pneumoniae.

Bacteriocins↗
PubMed2026

Bacteriocin-mediated intraspecies competition driven by acquired Bac41 operon in epidemic Enterococcus faecalis ST179.

Enterococcus faecalis is a common gut commensal and an opportunistic pathogen causing hospital-acquired infections. Despite its clinical importance, comprehensive global genomic and epidemiological data remain limited. Here, we analyzed 5,895 E. faecalis genomes collected between 2000 and 2020 and identified ST179, a human-derived single-operon variant of the high-risk CC16 clonal complex, as an emerging epidemic clone in China. Spot-killing assays revealed that ST179 strongly inhibited other clinical E. faecalis sequence types. Biochemical purification and proteomic analyses identified BacL1 as a key effector associated with this species-specific antibacterial activity. Functional assays confirmed its inhibitory phenotype, providing ST179 with a lineage-specific, bacteriocin-mediated competitive advantage. The high prevalence of the Bac41 operon likely contributed to the epidemiological success and ecological fitness of ST179. These findings highlight the role of bacteriocin-mediated intraspecies competition in shaping E. faecalis population dynamics and suggest that ST179 might become an emerging high-risk lineage in China.IMPORTANCEEnterococcus faecalis is a common gut bacterium and an opportunistic pathogen. We identify ST179 as an emerging epidemic clone in China and show that it outcompetes other strains via the bacteriocin Bac41. This competitive advantage helps explain its rapid spread. Our findings highlight how bacterial competition shapes population dynamics and provide insights into the emergence of high-risk E. faecalis lineages, informing strategies for monitoring and infection control.

Enterococcus faecalis↗
PubMed2026

Viral tags as keys to advancing invasion genomics.

Invasion genetics and genomics have greatly advanced the study of biological invasions, yet they often fail to resolve population dynamics at the fine spatiotemporal scales characteristic of most invasions. We propose shifting the focus away from the higher-order target species towards their viral symbionts, harnessing these as high-resolution 'genetic tags' to overcome many of these limitations. Owing to their comparably smaller genomes, shorter generation times, and higher mutation rates, most viruses evolve on timescales comparable to the invasion dynamics of their higher-order hosts, potentially better proxying and revealing recent dispersal patterns. We present a conceptual framework outlining how virus evolution may shed light on the contemporary spread of their non-native hosts, opening new avenues for invasion genetics, genomics, and management.

Genomics↗
PubMed2026

Weathering the storm: Most maternal and environmental drivers of individual reproductive success do not scale up to population recruitment in a large herbivore.

Population growth depends upon individual survival and reproduction, but do drivers of individual reproductive success scale up to population recruitment? Factors affecting individuals may have little effect on population dynamics if individuals within a population experience different conditions. When seasonal resource availability is unpredictable and breeding season long, average conditions over a breeding cycle may poorly reflect the environment experienced by many individuals. We compared the drivers of individual reproductive success and population recruitment in an asynchronously breeding large herbivore, the eastern grey kangaroo (Macropus giganteus). We analysed 18 years of individual-based data using multivariate hierarchical Bayesian models to first identify the causal mechanisms relating population density, environmental conditions and maternal traits to individual success. We then assessed whether the drivers of individual reproductive success scaled up to determine population recruitment. Most maternal and environmental covariates strongly influenced individual reproductive success, with distinct effects on juvenile survival before and after pouch exit. Maternal traits had a greater influence in the pouch, whereas environmental conditions became increasingly important once young exited the pouch. Most drivers of individual reproductive success did not affect population recruitment. Recruitment increased with population density and mean body condition of adult females. Weather harshness had a weak positive effect on recruitment, which appeared independent of female age structure, previous recruitment or forage. Most drivers of individual reproductive success did not scale up to population recruitment. Birth asynchrony could buffer population recruitment against environmental variation such that variables affecting individual reproduction have little impact at the population level. Large herbivores that reproduce asynchronously may therefore be more resilient to environmental variability than synchronous breeders.

Bayesian modelling↗
PubMed2025

Habitat Specialisation Impacts Clownfish Demographic Resilience to Pleistocene Sea-Level Fluctuations.

Habitat fragmentation and loss are key threats to biodiversity, yet their impacts on marine species remain poorly understood. Clownfishes, which rely on sea anemones for shelter and reproduction, provide an interesting model to explore how ecological specialisation mediates species responses to habitat perturbations. We used whole-genome data from 382 individuals across 10 species with varying host specialisations to reconstruct demographic histories and infer spatial genetic structure to assess the impact of Pleistocene sea-level fluctuations. Generalist species, associated with multiple hosts, maintained stable effective population sizes () and population connectivity during habitat fragmentation, reflecting resilience to environmental instability. In contrast, specialists experienced severedeclines and genetic structuring, driven by their dependence on specific hosts, without signs of population recovery following habitat reconnection. Spatial genomic analyses identified the Indonesian Through-Flow as a key dispersal corridor and the Coral Triangle as a critical hub of genetic diversity, while continental shelves and extensive open ocean regions appeared as barriers to gene flow. Our findings reveal how host specialisation shapes clownfish population dynamics, emphasising the importance of incorporating ecological dependencies into conservation assessments and deepening our understanding of species responses to ecological constraints and environmental changes over evolutionary timescales.

Animals↗
PubMed2025

Peruvian Population Genomics: Unraveling the Genetic Landscape and Admixture Dynamics of Urban Populations.

Latin American populations exhibit high genetic and phenotypic diversity shaped by complex admixture histories, yet remain underrepresented in genomic research. Here, we analyze genome-wide data from 432 urban individuals across 13 regions of Peru, including 346 newly genotyped from the Peruvian Genome Project. We revealed fine-scale population structure and demographic patterns shaped by both ancient and recent events. Indigenous American ancestries in urban individuals trace back to ancient north-south interactions consisted with archaeological records, while admixture events occurring within the last 8-10 generations involved sources already admixed between distinct ancestral lineages. Identity-by-descent analyses reveal sustained gene flow in southern Peru, while effective population size trends highlight demographic stability in Lima over the past 25 generations. Sex-biased admixture patterns suggest Indigenous ancestry contribution preferentially mediated by females. These findings offer a comprehensive view of Peru's genetic heritage, advancing our understanding of human genetic diversity and historical demographic processes in Latin America.

Admixture↗
PubMed2026

Single-cell RNA sequencing provides further insights into the immunostimulatory action of freeze-dried Lactiplantibacillus plantarum on Penaeus vannamei shrimp.

Immunostimulation through dietary interventions opened new avenues in developing disease control and prevention tools for shrimp aquaculture. We have previously shown that feeding with freeze-dried Lactiplantibacillus plantarum (LAB) increased disease resistance of Penaeus vannamei against both Vibrio parahaemolyticus and white spot syndrome virus (WSSV) based on bulk RNA sequencing of shrimp gills. This tissue participates in ion transport and serves as a first line of defense against environmental stressors and pathogenic infections. However, characterization of their cell composition and functions remains limited. Here, we implemented a single-cell RNA sequencing approach to further gather insights into how feeding with freeze-dried LAB modulates host immunity which may not be evident with bulk RNA sequencing approach. A total of five clusters with unique transcriptional signatures were identified, corresponding to pillar cells, septal cells, and sessile hemocytes. Pseudo-bulk analyses at global- and cluster-levels showed differential expression of genes related to host immunity and metabolism. We further revealed how overall transcriptomic changes are not exclusively caused by gene expression changes but may also be driven by cell population dynamics. This study highlighted how single-cell RNA sequencing approach may shed light on the mechanisms of action of immunostimulants which may be masked in bulk transcriptome analyses.

Animals↗
PubMed2025

Whole-genome sequencing, strain composition, and predicted antimicrobial resistance of Streptococcus pneumoniae causing invasive disease in England in 2017-20: a prospective national surveillance study.

BACKGROUND: Surveillance of the invasive disease burden caused by Streptococcus pneumoniae in England is performed by the UK Health Security Agency (UKHSA). In 2017, UKHSA switched from phenotypic methods to whole-genome sequencing (WGS) approaches for pneumococcal surveillance. Here, we present the first results of national WGS surveillance, up to the start of the COVID-19 pandemic, with the aim of describing the population genomics of this important pathogen. METHODS: We examined prospective national surveillance data from England, using bacterial isolates from cases of invasive pneumococcal disease (IPD) submitted to the national reference laboratory at UKHSA. A bioinformatic pipeline was developed to quality control WGS data and routinely report species and serotype. We assembled isolate data, assigned global pneumococcal sequencing clusters (GPSCs), and predicted antimicrobial resistance (AMR) profiles for isolates that passed further quality control. We collected additional data on patient outcomes and characteristics using enhanced surveillance questionnaires completed by patients' general practitioners. We used logistic regression analysis to assess the effects of various genomic and patient characteristics on the outcomes of IPD. FINDINGS: In England, between July 1, 2017, and Feb 29, 2020, there were 15 400 cases of IPD. From these cases, 13 749 (89·3%) isolates were sequenced, passed quality control, and were included in analyses. Serotype diversity was high during the study period, with 2751 (20%) isolates serotyped as 13-valent pneumococcal conjugate vaccine (PCV13) types, whereas serotype 8 was the most prevalent serotype (n=3074 [22·4%]) overall. There were 157 GPSCs within the collection, with GSPC3 the most common, encompassing 98·7% (3033 of 3074) of serotype 8 isolates. Most isolates (n=10 198 [74·2%]) did not contain AMR-associated genes. Resistance to co-trimoxazole was the most frequently predicted resistance (n=2331 [17%]), followed by resistance to tetracycline (n=1199 [8·7%]) and β-lactams (n=1149 [8·4%]). Logistic regression analysis found the presence of AMR-associated genes significantly increased the odds of patient death (odds ratio 1·18, 95% CI 1·01-1·38). Some GPSCs were also associated with a significant increase in the odds of patient death, such as GPSC12 (1·88, 1·48-2·38). Isolates from 2018 were associated with a significant increase in the odds of patient death (1·12, 1·00-1·25), whereas younger patient age was significantly associated with a reduction in the odds of patient death compared with being aged 85 years or older. INTERPRETATION: WGS-based surveillance has allowed us to interrogate country-wide population dynamics driving changes in pneumococcal serotype frequency. Here, we observe a stable but diverse population before the COVID-19 pandemic restrictions were enforced in England, with low rates of AMR. These findings will provide the baseline for pandemic and post-pandemic data, to collectively inform implementation and development of the vaccination programme within the country. FUNDING: None.

Streptococcus pneumoniae↗
PubMed2026

Fine-Scale Population Genomics Reveals Genetic Differentiation in the Brooding Amphipod Cheirimedon femoratus Across the South Shetland Islands, Antarctica.

Antarctic marine ecosystems are sensitive to environmental change, and impacts on processes such as population connectivity will play a fundamental role in future population dynamics and persistence, affecting short-term demography and long-term evolution. We investigated the population genomics of the common benthic brooding Antarctic amphipod Cheirimedon femoratus (Pfeffer, 1888), using 8837 high-quality single-nucleotide polymorphisms (SNPs) from 87 individuals collected at 4 sites in the South Shetland Islands, separated by up to 200 km: Deception Island, King George Island, Livingston Island, and Snow Island. While Admixture, F ST, principal component analysis (PCA), and demographic (Ne) analyses revealed a generally weak population genetic structure, Livingston Island emerged as a distinct population, especially compared to King George Island. All populations showed a heterozygote deficit with positive inbreeding coefficients (F IS), particularly high in the Snow Island population (~0.55). Tajima's D test suggested overall neutral evolution, although slight variation was observed among sites. Despite the limited dispersal potential of this brooding species, the observed connectivity may be maintained through passive dispersal, likely via floating macroalgae or ice-rafted debris, facilitated by prevailing regional ocean currents. This may enhance the population resilience of Antarctic benthic communities under environmental change, including regional warming and shifts in ocean circulation, compared to more isolated populations. Our findings underscore the complex interplay between passive connectivity and fine-scale differentiation in shaping Antarctic benthic invertebrate diversity.

Amphipoda↗
PubMed2026

Large language models in bioinformatics: a comprehensive survey.

The emergence of foundation models with trillion-level parameters has redefined the landscape of artificial intelligence. Various fields are developing their own large-scale models, which can solve many problems within the field and improve work efficiency. Biological large-scale models are a cross-disciplinary research field that combines mathematics, computer science, and biology, aiming to simulate and understand the structure, function, and dynamic changes of biological systems through the establishment of complex computational models. This field covers multiple levels such as biological pathways, population dynamics, protein folding, etc., providing us with tools for deep exploration of the mysteries of life and applications in medicine, ecology, and other fields. This article reviews the background and research status of biological large-scale models, and discusses future directions. Large language models (LLMs) and other large-scale foundation models have rapidly advanced in recent years, enabling powerful representation learning and generation across text, sequences, and multimodal data. In bioinformatics and biomedicine, these models are increasingly used to analyze genomic sequences, infer protein properties and structures, support drug discovery, and integrate heterogeneous biomedical evidence. This survey reviews the basic principles of LLMs and summarizes representative applications in (i) gene and genome sequence analysis, (ii) protein structure and function prediction, and (iii) drug design, including virtual screening and personalized medicine. We also discuss emerging multi-model modeling approaches, as well as key challenges such as data quality and privacy, interpretability, generalization to new organisms and tasks, and responsible deployment in health-related settings. Finally, we outline future directions for developing reliable, scalable, and explainable bioinformatics foundation models.

bioinformatics↗
PubMed2026

EV-B 3D polymerase remodels viral populations through 5'UTR recombination to subvert cardiac antiviral innate immunity.

Viral myocarditis, a leading cause of morbidity in young populations, is strongly linked to Coxsackievirus B (CV-B) infections harboring dominant 5'-terminally deleted (5'TD) and minor full-length (FL) CV-B RNA populations in cardiac tissues. Here, we demonstrate how viral RNA-dependent RNA polymerase (3Dpol)-driven recombination in the 5'UTR orchestrates viral RNA populations dynamics and subverts type I interferon responses. In primary human cardiomyocytes (HCMs), 3Dpol-mediated copy-choice recombination enhances 5'TD RNA replication while suppressing FL populations. Infection of immunocompetent mice with recombination-deficient CV-B3 (3Dpol Y276H) shifted 5'TD populations ratios toward immune-sensing viral RNAs, elevating cardiac IFN-β/ISG15 and accelerating viral clearance. Transfection experiments confirmed that 50-nt 5'TD RNAs (TD50) evade innate immunity, whereas shorter deletions (9-36-nt, TD15) restore type I interferon responses in HCMs. Our findings establish 3Dpol-driven recombination as a critical mechanism sustaining pathogenic 5'TD RNAs that subvert antiviral innate immunity, highlighting recombination inhibition as a promising therapeutic strategy against CV-B myocarditis.

Animals↗
PubMed2026

Precision Engineering of Evolution-Resilient Rice against Bacterial Blight.

The persistent conflict between rice and Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight, exemplifies a dynamic genetic arms race in agriculture. The cyclical deployment and erosion of major resistance (R) genes highlight the high adaptive potential of Xoo and the need for strategies that are durable rather than absolute. This review synthesizes a paradigm shift from reactive, single R-gene deployment toward proactive engineering of evolution-resilient resistance. We explore the molecular-genetic basis of Xoo adaptability, including TAL effector diversification, non-TAL virulence functions, genome variation, and immune suppression mechanisms. In response, we propose a framework for durable disease management with three connected components: precision disarmament through editing of susceptibility-gene effector-binding elements and executor/decoy designs; smart induction through targeted delivery and immune priming; and ecological fortification through protective microbiomes. We also discuss the limits, trade-offs, and field-validation requirements of these approaches. Integrating frontier technologies with evolutionary genetics, predictive genomics, and pathogen population dynamics can help develop rice varieties and deployment systems that are more difficult for Xoo populations to overcome.

CRISPR↗
PubMed2025

Integrating multiscale mathematical modeling and multidimensional data reveals the effects of epigenetic instability on acquired drug resistance in cancer.

Biological and dynamic mechanisms by which Drug-tolerant persister (DTP) cells contribute to the development of acquired drug resistance have not been fully elucidated. Here, by integrating multidimensional data from drug-treated PC9 cells, we developed a novel multiscale mathematical model from an evolutionary perspective that encompasses epigenetic and cellular population dynamics. By coupling stochastic simulation with quantitative analysis, we identified epigenetic instability as the most prominent kinetic feature related to the emergence of DTP cell subpopulations and the effectiveness of intermittent treatment. Moreover, we revealed the optimal schedule for intermittent treatment, including the optimal area for therapeutic time and drug holidays. By leveraging single-cell RNA-seq data characterizing the drug tolerance of lung cancer, we validated the predictions made by our model and further revealed previously unrecognized biological features of DTP cells, such as cell autophagy and migration, as well as new biomarker genes of therapeutic tolerance. Our work not only provides a paradigm for the integration of multiscale mathematical models with newly emerging genomics data but also improves our understanding of the crucial roles of DTP cells and offers guidance for developing new intermittent treatment strategies against acquired drug resistance in cancer.

Drug Resistance, Neoplasm↗
PubMed2026

Persistent spread of carbapenemase-producing Klebsiella pneumoniae in acute care hospitals in 36 European countries (the CCRE survey): a prospective, multicentre, cross-sectional, epidemiological, microbiological, and genomic surveillance study.

BACKGROUND: Carbapenem-resistant Enterobacterales pose a substantial threat to patients and health-care systems. We conducted a survey of carbapenem-resistant and/or colistin-resistant Enterobacterales (CCRE survey) in 37 European countries to describe their occurrence, geographical distribution, and population dynamics and inform control policies. We report the results of Klebsiella pneumoniae species complex isolates in this study. METHODS: In this cross-sectional, epidemiological, microbiological, and genomic study conducted in all EU, European Economic Area and EU candidate countries as of 2019, hospital microbiology laboratories were selected on the basis of population coverage. Participating laboratories collected, from patient samples, the first ten successive isolates of carbapenem-resistant or carbapenem-susceptible increased exposure (carbapenem-R/I) K pneumoniae species complex or Escherichia coli, and carbapenem-susceptible (carbapenem-S) comparator isolates of the same species, accompanied by patient epidemiological and clinical information. Isolate collection started in 2019, with three possible starting dates-ie, March 1, April 1, or May 1, 2019, and ended after collection of ten carbapenem-R/I and carbapenem-S isolates or a maximum period of 6 months. Isolates were tested for phenotypic susceptibility to 16 antimicrobial agents of relevance to K pneumoniae species complex. Whole-genome sequencing was performed centrally using Illumina technology. Isolates from the CCRE survey were compared with those from the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) study. FINDINGS: 1566 carbapenem-R/I and 1407 carbapenem-S K pneumoniae species complex isolates collected from patients in 302 hospitals in 36 countries (one country did not send isolates) were analysed in this study. The high-risk lineages identified during a previous similar survey in 2013-14 (EuSCAPE) were found to continue to circulate across European hospitals in 2019 (ST11, ST15, ST101, and ST258/512). Moreover, concerning shifts in the pathogen population were observed. First, a higher proportion of carbapenem-R/I isolates was found to carry a carbapenemase gene in the CCRE survey (1398 [89·3%] of 1566) than in EuSCAPE (657 [69·6%] of 944), mainly related to increased acquisition of carbapenemase genes by high-risk lineages. Of note, among ST307 isolates from all hospitals, the proportion of carbapenem-R/I isolates carrying a carbapenemase gene increased from 14 (60·9%) of 23 in EuSCAPE to 164 (91·1%) of 180 in the CCRE survey. Second, an expansion of emerging multidrug-resistant lineages (ST147, ST307, and ST39) was also noted: Among 113 hospitals that contributed K pneumoniae species complex isolates to both EuSCAPE and the CCRE survey, the proportion of ST147 increased from 16 (3·4%) of 476 in EuSCAPE to 49 (7·4%) of 662 carbapenem-R/I isolates in the CCRE survey, that of ST307 increased from 15 (3·2%) of 476 to 88 (13·3%) of 662, and that of ST39 increased from 3 (0·6%) of 476 to 10 (1·5%) of 662. Third, there was an increased spread of isolates harbouring acquired virulence loci: isolates with the highest Kleborate virulence score of five increased from 7 (0·4%) of 1717 in EuSCAPE to 40 (1·3%) of 2973 in the CCRE survey. Notably, the increase was mainly observed in the carbapenem-S-group. INTERPRETATION: The survey findings portray an escalating epidemiological situation and suggest that control measures have not been able to interrupt transmission of high-risk lineages of carbapenemase-producing K pneumoniae in European hospitals. The heterogeneous and evolving situation with regards to circulating lineages and dominant carbapenemase genes requires strengthening and continuous adaptation of diagnostic, treatment, and control measures guided by genomic surveillance. FUNDING: European Centre for Disease Prevention and Control and Centre for Genomic Pathogen Surveillance.

Humans↗
PubMed2025

Multiomic Analyses Reveal the Molecular Mechanisms of Arid Adaptation in a Desert Rodent Species.

Organisms living in desert habitats face multiple simultaneous pressures, such as high temperatures and arid, and the population dynamics and community diversity of small rodents are strongly affected by climate extremes. However, the potential mechanisms by which desert rodents adapt to arid remain largely unexplored. Here, we assembled a 3.18 Gb genome, including 25,812 protein-encoding genes, for Orientallactaga sibirica, which is widely distributed across both arid and semihumid environments in Eurasia. Orientallactaga sibirica has longer ears and hind limbs to enhance heat dissipation, which may be related to the positively selected genes, such as Fgf10, Fgf11, Hoxc4, Hoxd1, and Bmp4. The renal transcriptome revealed increased fat and carbohydrate metabolism for metabolic water production in O. sibirica residing in arid habitats. Pathways such as material metabolism, oxidative stress response, osmoregulation, and water and salt reabsorption were enriched in candidate genes, such as Avp, Ang, and Ace, under positive selection in O. sibirica. Moreover, amino acid replacement was observed in the protein sequences of seven candidate genes, including Aldh7a1, Lnpep, Wnk4, C1qc, and Awat2, and these specific amino acid replacements of genes such as Umod and Scnn1a were related to unique osmoregulation, osmotic protection, and water retention compensation mechanisms. Water deprivation under laboratory conditions induced the upregulation of Umod and Aldh7a1 expression, further supporting the results observed in the wild population. These findings demonstrate that the positively selected genes related to limb development and specific amino acid replacements in the genes Umod and Scnn1a for unique osmoregulation in the renal vascular system may contribute to arid adaptation in the desert rodent species O. sibirica. This study provides novel insights into the adaptive evolution of desert small mammals and can serve as a reference for future research on renal damage-related diseases, such as human kidney stones and salt-sensitive hypertension.

Animals↗
PubMed2026

Natural occurrence of a slow lytic pseudomonas phage in a Pediatric case of multidrug-resistant P. aeruginosa severe pneumonia.

Pseudomonas aeruginosa (P. aeruginosa) is widely distributed in the environment. As an opportunistic pathogen, it commonly causes infections in immunocompromised individuals, including respiratory tract infections and burn wound infections. P. aeruginosa possesses multiple antibiotic resistance mechanisms, including efflux pumps, resistance genes, and population dynamics. Phage therapy is a potential approach for addressing drug-resistant P. aeruginosa infections; however, clinical experience and standardized guidelines for its application in severe pneumonia remain limited. A 14-month-old infant was hospitalized for pneumonia. Four days later, he developed acute pneumonia and was sent to the ICU for 38 days of antibiotic therapy; nonetheless, P. aeruginosa remained detectable in the patient's respiratory secretions. During the clinical course, phage zjk6 was detected from a longitudinal P. aeruginosa isolate in the absence of phage therapy. This finding documents the coexistence of a naturally detected phage and MDR P. aeruginosa during prolonged pneumonia, but does not establish that the phage mediated bacterial clearance or clinical recovery. We performed whole-genome sequencing on P. aeruginosa isolates from patients to ascertain if they were infected by the same infection and assessed their antibiotic resistance using drug sensitivity testing. We isolated phages using the drip technique and double-layer plate method, examined their appearance by transmission electron microscopy, and assessed their biological properties through one-step growth curve analysis and lysis spectrum detection. Genome sequencing and comparative genomic analyses were performed to characterize phage zjk6 and representative bacterial isolates and to evaluate phage-host genomic relatedness. P. aeruginosa was isolated repeatedly during 49 days of treatment. Comparative genomic analysis of representative longitudinal isolates revealed multiple strain backgrounds, including distinct ST508 and ST266 lineages and a closely related ST836 lineage. Phage zjk6 was isolated from the fifth clinical isolate, which served as the propagation/reference host. This phage possesses an elongated tail and a limited lysis spectrum, which is capable of gradually lysing the fifth isolated P. aeruginosa strain. Genomic analysis showed that zjk6 formed plaques and displayed slow lytic behavior under the tested conditions, while also carrying lysogeny-associated regulatory modules, indicating temperate potential rather than a strictly lytic lifestyle. A naturally detected slow lytic Pseudomonas phage may coexist with MDR P. aeruginosa during prolonged infection. These findings support further study of phage-bacterium interactions in clinical infections, while the therapeutic significance of zjk6 requires additional validation.

Antibiotic resistance↗
PubMed2026

Genomics and social practices at Mogou and other Gansu sites during prehistoric trans-Eurasian exchange.

Beginning approximately 4,000 years ago, southwest-Asian-originating domesticated crops and livestock began appearing in Gansu, a key crossroads in northwestern China, yet the population dynamics and social practices underlying these historically transformative events in the region have not been fully explored. Despite the adoption of western domesticates, genome sequences of 149 individuals from the large Mogou cemetery and ten other sites in Gansu, dating between 4,700 and 3,000 years ago, revealed migrations within East Asian regions but no detectable evidence of genetic influence from western or central Eurasia, suggesting that early agricultural dispersals may have followed a model distinct from that documented in Europe and Central Asia. The Mogou cemetery represents a continuous community that interacted with surrounding regions but does not exhibit clear matrilocal or patrilocal residential patterns. We found no strong evidence that co-buried individuals represented biological relatives. Non-local ancestry appears to be linked to lower-status burial practices.

Humans↗