Biology subjects

Liu, Q.

Publications and source records attributed to Liu, Q..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Senescence-associated KRAS upregulation in peripheral T cells links to premature coronary artery disease

Aims: Premature coronary artery disease (PCAD) lacks specific molecular drivers, and the role of immunosenescence is unclear. We investigated whether aging-related gene dysregulation in T cells contributes to PCAD. Methods: We combined bulk transcriptomics of PBMCs from 12 PCAD patients and 21 controls, single-cell RNA sequencing of PBMCs and human atherosclerotic plaques, weighted gene co-expression network analysis, gene perturbation network analysis, and molecular docking. Results: KRAS was identified as a hub gene intersecting PCAD-associated genes and aging-related genes. Single-cell analysis showed KRAS upregulation predominantly in effector CD8+ T cells, which exhibited the highest senescence scores that were further elevated in disease. Network perturbation of KRAS strongly impacted the cell killing pathway. KRAS-high effector CD8+ T cells were detected in coronary and carotid plaques, displaying enhanced cytotoxicity, exhaustion, and senescence features. Additionally, a candidate small molecule was computationally predicted to bind inactive KRAS. Conclusions: Elevated KRAS expression in senescent, cytotoxic CD8+ T cells is associated with PCAD, bridging immunosenescence and premature atherosclerosis. This finding provides a novel biomarker candidate and potential therapeutic entry point, awaiting further functional validation.

bioinformatics↗

bioRxiv2026

Polyketide synthase 12 is an in vivo essential source of novel mycolyl lipids in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) is a major pathogen worldwide that infects and transmits only among humans, yet nearly all in vivo virulence research occurs in non-human hosts. To overcome this central challenge in tuberculosis research, we leveraged a dataset of more than 50,000 sequenced isolates to identify Mtb genes that that are functionally preserved during natural infection, disease causation, and transmission between humans. This whole-genome ranking identified polyketide synthase 12 (pks12 ) as an exceptionally in vivo essential gene in human tuberculosis, which we validated in zebrafish and mouse models. Though Pks12 produces a mycoketide lipid in only trace amounts, pks12 deletion severely altered the host-facing surface and arabinoglycan architecture of Mtb. This amplified effect was explained through the discovery of mannosyl-{beta}-1-phosphomycoketide monomycolate (MPMMM), which is synthesized from the known Pks12 product at higher abundance by antigen 85 mycolyltransferases. Thus, we used a new host-facing genomic-metabolomic-phenotypic approach to discover the functions of an in vivo essential Mtb gene, which controls the physical structure of the Mtb-host interface.

microbiology↗

bioRxiv2026

MoTRUST: adaptive semantic protection for mosaic single-cell integration and molecular recovery

Single-cell multi-omics reveals complementary aspects of cellular identity, but heterogeneous assays produce incomplete modality combinations. Integrating these mosaic measurements while preserving biological structure and recovering missing molecular information remains challenging. We present MoTRUST, combining neural representations, adaptive semantic protection, molecular prediction and conditional residual diffusion. MoTRUST ranked first in overall integration across 30 tasks spanning six scenarios and surpassed the strongest evaluated controls on six of eleven development recovery endpoints. Conditional residual diffusion reduced aggregate marginal prediction scores by 4.4-5.1% across three ATAC-to-RNA data sources while preserving point predictions. Together, these capabilities enable accurate mosaic integration and molecular recovery for multimodal characterization of cellular heterogeneity.

bioinformatics↗

bioRxiv2026

An open imaging and AI resource enabling unbiased quantification of extrachromosomal DNA at scale

Quantitative imaging of extrachromosomal DNA (ecDNA) is increasingly important for studying cancer heterogeneity and adaptation, yet automated analysis has been limited by the absence of accessible imaging data, gold standard annotations and adaptable computational tools. Here we establish an open resource for computational ecDNA imaging, integrating 2,986 native-resolution metaphase FISH image sets with manual annotations, standardized benchmarks and open-source quantification frameworks. We use this resource to systematically compare existing and newly developed approaches spanning rule-based computer vision, deep-learning-based segmentation and probabilistic localization. This comparison reveals count-dependent underestimation that distorts ecDNA copy-number distributions and motivates ecCount, a probabilistic localization method developed here to preserve individual ecDNA signals and quantitative burden. ecCount achieves an object-level F1 score of 0.939 on held-out images with minimal count bias. Together, the images, annotations, retrainable models, evaluation tools and guided workflows provide community infrastructure for applying, adapting and improving automated ecDNA quantification across experimental systems.

genetics↗

bioRxiv2026

Protein hunger-driven nitrogen flow from phospholipids to amino acids inDrosophila

Protein is unique among macronutrients due to its nitrogen content and that its building blocks, essential amino acids, cannot be synthesized by animals. Additionally, animals lack specialized amino acid storage sites, necessitating a continuous dietary intake. In the face of insufficient dietary protein, how do animals manage nitrogen limitation? Using Drosophila, we reveal a previously undocumented nitrogen flow from phospholipids to amino acids, a process enhanced by protein deprivation. Protein restriction triggers the degradation of phosphatidylethanolamine (PE), releasing the nitrogen-containing headgroup, ethanolamine, which subsequently serves a dual function. Ethanolamine stimulates protein intake by activating protein hunger neurons and, remarkably, along with phosphoethanolamine, donates nitrogen for amino acid biosynthesis. This nitrogen transfer is mediated by the microbiome and ethanolamine-phosphate phospho-lyase (ETNPPL) pathway in fly cells. Together, our findings identify phospholipids as a hidden nitrogen reservoir and reveal an unrecognized metabolic plasticity that reallocates nitrogen to maintain protein homeostasis.

physiology↗

bioRxiv2026

Maleic acid adjuvates BCG to induce CD4+CD8+ T cells and sterilize tuberculosis

Anti-tuberculosis (TB) immunity typically emphasizes CD4+ T and CD8+ T cells that only provide limited protection against Mycobacterium tuberculosis (Mtb) infection. The anti-TB function of CD4+CD8+ T cells remains unexplored, mostly due to the dogma that ThPOK and Runx3 antagonize each other to block their development and their scarcity. Here, we show that immunization of BCG (Bacillus Calmette-Gu&eacuterin) with Complete Freund's Adjuvant (CFA) markedly induced CD4+CD8+ T cells through the gut microbiota Clostridium butyricum or its metabolite maleic acid. Mtb-specific CD4+CD8+ T cells exhibited a broad T-cell receptor repertoire and sterilized Mtb infection by inducing SLAMF1 and neutrophil responses. Mechanistically, maleic acid interacted with PAK2 to promote STAT5 phosphorylation at Ser127, thus upregulating Ets1 expression. Direct binding of Ets1 to the Runx3 and ThPOK promoters orchestrated their expression to redirect the CD8+ T cell differentiation towards the CD4+CD8+ lineage. Moreover, immunization of BCG plus Clostridium butyricum or maleic acid sterilized Mtb infection in mouse models. These findings establish CD4+CD8+ T cells as superior immune effectors against Mtb, a concept that could fundamentally redirect the current paradigm for anti-TB vaccine development.

microbiology↗

bioRxiv2026

Chemically induced USP21-KLHL12 association recruits USP21 to COPII assembly

Ubiquitin-specific protease 21 (USP21) is a deubiquitinase implicated in various biological processes and disease states, including cancer. To better understand USP21 protein interaction networks, we used biotin identification proximity labeling, and uncovered USP21 interactions with the cytoskeleton, endosomal, and transcriptional regulators. Notably, a subset of these interactions was modulated by the USP21 selective inhibitor BAY-805. In cells, BAY-805 promoted proximity between USP21 and Kelch like protein KLHL12, a component of the Cullin3 ligase complex. Structural modeling using AlphaFold3, together with hydrogen deuterium exchange mass spectrometry, identified an orthosteric BAY-805 binding site within USP21. Binding of BAY-805 functionally competes with ubiquitin at USP21, thereby enabling USP21 interaction with KLHL12. This BAY-805 induced proximity elicited relocalization of USP21 to KLHL12 containing coat protein complex II (COPII) vesicles. Induced USP21-KLHL12 association led to enlargement of COPII vesicles and impaired transport of large cargoes such as collagen. Overall, our findings reveal a novel chemically induced proximity mechanism in which the monovalent ligand BAY-805 outcompetes ubiquitin from USP21, thereby recruiting USP21 to KLHL12 associated protein complexes.

cell biology↗

bioRxiv2026

Deep reinforcement learning-driven discovery of a MsbA-targeted small-molecule antibiotic for the treatment of Acinetobacter baumannii infection

Antibiotics with new mechanisms are highly pursued to address the threat of infections caused by drug-resistant Gram-negative bacteria. Targeting MsbA, a key protein of the lipopolysaccharide biosynthesis pathway, represents a promising strategy to discover new classes of antibiotics. However, currently available MsbA-targeted molecules either lack sufficient potency or have unfavorable properties, necessitating expansion of chemical space. In this study, we chose the most promising cerastecin Cpd 4 as the template, and used two Artificial Intelligence (AI)-based tools, i.e. Link-INVENT and AutoMolDesigner for molecular design, performed chemical derivatization and antibacterial activity evaluation, which led to the discovery of Y-11 (MIC for A. baumannii: 0.5 g/mL). Encouragingly, Y-11 showed equivalent potency to Cpd4 for carbapenem-resistant A. baumannii, and less cytotoxicity and hemolysis as well as lower spontaneous resistance frequency. In vivo efficacy study demonstrated that Y-11 could effectively reduce bacterial loads in the mice infected by A. baumannii. The following mechanism study including molecular dynamics simulation, biochemical assay, and transmission electron microscope (TEM) analysis suggested that Y-11 inhibited the transport of lipooligosaccharide and impaired the formation of outer membrane, probably by competitively binding to the substrate binding site of MsbA and modulating ATPase activity. Taken together, we have discovered a MsbA-targeted small molecule Y-11 via AI-driven drug design, which provides a foundation for future antibiotic development.

biochemistry↗

bioRxiv2026

A virus co-opts vector's m⁶A machinery for adaptive compensation

Insect vectors harbor diverse viruses that threaten human health and agricultural production, yet the genetic basis of mutualistic virus-vector interactions remain elusive. This underscores a long-standing paradox in pest management: viruses that cause destructive diseases also facilitate vector adaptation in ways that benefit both parties. Here we show that the globally devastating tomato yellow leaf curl virus (TYLCV) acts as a Cooperative Partner, co-opting its vector's m6A epitranscriptomic machinery to offset the reproductive fitness costs of neonicotinoid resistance in the whitefly. In resistant vectors, TYLCV infection alleviates reproductive deficits via the m6A-dependent pathway, where the methyltransferase METTL14 and demethylase ALKBH4 coordinately stabilize vitellogenin (Vg) transcripts to boost female fecundity. Mechanistically, the viral C2 and CP proteins directly interact with METTL14 and ALKBH4, respectively, remodeling their RNA binding affinity to facilitate mA modification on Vg. Disrupting either of these viral-vector protein interactions restores a reproductive cost phenotype in viruliferous resistant vectors, offering novel targets for sustainable pest control. Our findings uncover a fundamental role of epigenetic marks in adaptive trait, reshaping beneficial virus-vector relationships and providing new insights for innovative public health and crop protection strategies to address global challenges.

microbiology↗

bioRxiv2026

Cell-state-dependent responses to PLK1 inhibition reveal a non-canonical microtubule-endolysosomal vulnerability in quiescent leukemia stem cells

Relapse in cancer is frequently driven by therapy-resistant quiescent cancer stem cells. Conventional chemotherapy has been designed to target proliferating tumor cells and is generally presumed to be ineffective against non-cycling cancer stem cells. Using acute myeloid leukemia (AML) as a model, we challenge this prevailing view by showing that inhibition of the mitotic master regulator Polo-like kinase 1 (PLK1), a kinase extensively pursued for antiproliferative cancer therapy, unexpectedly eradicates quiescent leukemia stem cells (LSC) through a mechanism distinct from its canonical mitotic function. In proliferating AML cells, PLK1 inhibition (PLK1i) induced G2/M arrest and mitotic catastrophe. In contrast, quiescent LSC underwent apoptosis independent of mitotic arrest, revealing a cell-state-dependent mode of drug action. Mechanistically, PLK1i initiated a multi-step process through disruption of a previously unrecognized, stem cell-specific interaction between PLK1 and MAP1A, resulting in perturbed vesicle trafficking and endolysosomal homeostasis characterized by altered receptor internalization, vesicle accumulation and lysosomal dysfunction, ultimately culminating in apoptotic cell death. Combinatorial pharmacologic perturbation studies established microtubule regulation as a critical determinant of quiescent LSC survival, while ex vivo and in vivo assays demonstrated depletion of functionally-defined LSC following PLK1i. These findings identify a previously unrecognized role for PLK1 in intracellular trafficking and establish MAP1A-dependent control of vesicle homeostasis as a mechanistic determinant of cancer stem cell survival. More broadly, this study demonstrates that classical antimitotic compounds, including microtubule-targeting agents and PLK1 inhibitors, can eradicate both cycling leukemic blasts and quiescent LSC through distinct, cell state-dependent mechanisms, challenging proliferation-centric models of chemotherapy action.

cancer biology↗

bioRxiv2026

MultiFlow: coupled flow matching for predicting single-cell multiomic perturbation responses in unseen cellular contexts

Predicting cellular responses to perturbation requires resolving coordinated changes across molecular layers, yet most single-cell perturbation models focus on transcriptional responses alone. Here we present MultiFlow, a coupled flow-matching framework that unifies generation and perturbation prediction of paired gene expression and chromatin accessibility. By learning coupled RNA-ATAC flows conditioned on perturbation and control-derived cellular-state representation, MultiFlow enables prediction of coordinated multiomic responses in unseen cellular contexts. Across multiomic generation benchmarks, MultiFlow accurately reproduced paired RNA-ATAC states and their population distributions. In multiomic perturbation benchmarks, MultiFlow achieved the strongest overall performance in predicting both gene-expression and chromatin-accessibility responses, outperforming competing modality-specific perturbation-prediction methods. Joint multiomic modeling further preserved perturbation-induced RNA-ATAC coordination, including concordant peak-gene effects and cross-modal cellular neighborhood structure. These results establish coupled flow matching as a unified generative framework for modeling paired multiomic states and predicting coordinated perturbation responses across cellular contexts. Code and tutorial for MultiFlow are available at https://github.com/liuq-lab/MultiFlow.

bioinformatics↗

bioRxiv2026

PC1-guided transcriptomic stratification reveals hepatic transcriptional heterogeneity and defines a myeloid-associated 20-gene signature

Hepatic lipid-associated inflammation contributes to metabolic liver disease and cardiometabolic complications. Treatment-based transcriptomic comparisons can obscure inter-individual heterogeneity when animals exposed to the same experimental condition show divergent molecular responses. In the public hyperlipidemic liver transcriptomic dataset GSE338111, conventional sex-adjusted comparison of Amlexanox versus DMSO identified only 21 differentially expressed genes at FDR < 0.05 and |log2FC| [≥] 1, and submission of this DEG set to Metascape yielded no GO Biological Process enrichment result. We therefore applied treatment-independent, PC1-guided transcriptomic stratification based on the 500 most variable genes. This analysis resolved three PC1-derived groups and enabled derivation of a myeloid-associated 20-gene signature from the G2-versus-G1 contrast. Independent bulk-transcriptomic cohorts supported responsiveness of the signature to dietary challenge and pharmacologic intervention, while single-cell analysis localized its expression predominantly to hepatic myeloid populations. Human cis-eQTL Mendelian randomization and colocalization further identified TAGLN2 as the signature gene with the strongest genetic support for coronary heart disease. Together, these findings show that PC1-guided stratification can improve resolution of heterogeneous hepatic transcriptional responses and provide a cross-cohort molecular signature for subsequent mechanistic and translational evaluation.

genomics↗

bioRxiv2026

Logic-Gated Fluorogenic RNA Reporters for Multiplexed Live-Cell Imaging

Multiplexed imaging of biomolecular networks in living cells is limited by the small number of spectral separable fluorophores and the need to monitor dynamic processes in real time. Here, we present logicFRIES, a fluorogenic RNA (FR)-based platform that enables eight-plex live-cell imaging through programmable, logic-gated activation coupled with sequential fluorescence imaging. By integrating small-molecule-binding RNA aptamers into dye-activating fluorogenic RNAs, we engineered trigger-responsive FR reporters. This design implements an AND-gated mechanism in which fluorescence activation requires both a cognate trigger molecule and its corresponding fluorogenic dye, thereby expanding multiplexing capacity without adding new fluorophores. Using three membrane-permeable triggers, tetracycline, ASP2905, and guanine, we generated three distinct trigger-defined activation states for each engineered Broccoli and Pepper FR. Combined with orthogonal Corn/DFHO and DNB/TMR-DN reporter pairs, logicFRIES supports eight-plex imaging through sequential trigger/dye addition, imaging, and wash-based stripping cycles. We demonstrate robust, specific, and reversible fluorescence switching of these multiplexed FR reporters in living HEK293T and SKBR3 cells. Overall, logicFRIES extends live-cell imaging beyond conventional spectral limitations and provides a modular foundation for potentially developing multiplexed sensors targeting endogenous RNAs, proteins, and small molecules in complex cellular systems.

molecular biology↗

bioRxiv2026

RegFM: an interpretable context-aware foundation model for human transcriptional regulation

Transcriptional regulation is governed by interactions between cis-regulatory elements (CREs) and trans-acting regulators in a context-specific manner. Although DNA and single-cell foundation models have enabled modeling regulatory biology at scale, most represent either sequence or cellular state alone, limiting their ability to capture context-dependent gene regulation. Here we present RegFM, a context-aware foundation model for human transcriptional regulation. RegFM treats transcriptional regulation as a dialogue between cis-regulatory sequences (e.g., CREs) and trans-acting regulators (e.g., transcription factors (TFs) and chromatin regulators (CRs)) by coupling long-range CRE representations with TFs and CRs activity. Trained on large-scale ENCODE and CELLxGENE transcriptomic profiles, RegFM learns gene-centered regulatory representations that generalize across unseen cellular contexts. In a wide range of tasks, including gene expression prediction, cis-regulatory element annotation, bivalent promoter and dosage-sensitivity classification, and perturbation-response prediction, RegFM consistently improves over existing methods. RegFM emerges as a scalable and interpretable framework for modeling human transcriptional regulation and provides insights into context-dependent gene regulatory programs.

genomics↗

bioRxiv2026

Spatially-restricted metabolic delivery of auxin for selective adventitious root induction

Auxin impacts on nearly every aspect of plant growth and development. Its exogenous application therefore results in pleiotropic growth responses. Exploiting this activity for plant propagation requires avoiding or minimizing such off-target effects and is generally achieved as a trade-off between toxicity and organogenetic efficacity. We recently identified the compound HYSPARIN (HYS) with potent, and uniquely selective adventitious root inductive activity. Unlike other root-inducing compounds, HYS preferentially activates auxin responses in the shoot via an unknown mechanism. Here, we show that HYS acts as a shoot-specific proauxin. Rather than acting through auxin homeostasis, we found that HYS is hydrolysed in planta independently of ILR1/ILL amidohydrolases to release the synthetic auxin MCPA. Structure-activity relationship analysis confirmed a strong dependence on its MCPA moiety for activating auxin responses, and identified its promoiety as a determinant of shoot-specificity and activity. Selective application of MCPA also potently induces AR is consistent with a model in which HYS metabolism produces a spatially restricted, AR inductive auxin signal. The activation mechanism of HYS thus provides a conceptual framework for tissue-specific metabolic delivery of auxin and may enable the programmable delivery of other xenobiotics in plants.

plant biology↗

bioRxiv2026

Functional profiling of ESKAPE viromes uncovers resistance-limiting phage-host dynamics

ESKAPE pathogens drive clinical antibiotic resistance and intractable infections, severely compromising antimicrobial therapies. Bacteriophages are promising alternatives to antibiotics, yet their diversity, function and ecological impacts in ESKAPE pathogens remain poorly defined, hindering phage therapy translation. Here, we integrated 11,947 high-quality ESKAPE genomes with global metagenomic viral data to construct a comprehensive non-redundant virome of 14,496 ESKAPE-associated viruses, including four unreported viral clades. We found pervasive competition among mobile genetic elements (MGEs) in the ESKAPE mobilome, where nested MGE architectures empower low-mobility antibiotic resistance genes (ARGs) with horizontal transfer ability to fuel resistance dissemination. Unlike ARG-rich MGEs, ESKAPE phages carry minimal ARGs and antagonize plasmids to constrain ARG propagation, confirming their biosafety for therapy. We further revealed distinct phage-host arms races, typically virulent phages enrich anti-defense genes to evade bacterial immunity, and novel viruses hijack host methyltransferases targeted by CRISPR-Cas systems. This study establishes a systematic ESKAPE virome resource, demonstrates phages dual roles in targeting resistant pathogens and curbing resistance spread, and provides mechanistic support for phage therapy clinical application.

microbiology↗

bioRxiv2026

The aphid effector CathB6 suppresses EDS1-dependentimmunity and rewires MORF2-GUN1-GLK signalling tosustain host cellular homeostasis in Arabidopsis

Aphids use stylet mouthparts to probe plant tissues and deliver oral secretions into host cells, modulating immunity to establish long-term phloem feeding sites in sieve elements. This feeding behaviour make aphids efficient vectors of plant pathogens. We previously showed that Myzus persicae cathepsin B (CathB) effectors promote aphid colonization, accumulate in dynamic cytoplasmic processing bodies (p-bodies), bind the key Arabidopsis thaliana immune regulator EDS1, and recruit EDS1 together with its signalling partners PAD4 and ADR1 to p-bodies. However, the extent to which CathB effectors suppress EDS1-regulated immunity remains unclear. Here, we show that CathB6-expressing Arabidopsis lines exhibit substantial transcriptomic overlap with the eds1-2 mutant, consistent with CathB6 suppression of EDS1-dependent immunity. However, CathB6 also induces broader transcriptional reprogramming beyond that explained by loss of EDS1 function. A yeast two-hybrid screen identified the transcription factors GLK1 and GLK2, as well as several MORF proteins, as CathB6 interactors. CathB6-expressing plants recapitulated GLK- and MORF-regulated transcriptional changes, suppressing GUN1-associated activity while maintaining GLK-mediated expression of photosynthesis-associated nuclear genes (PhANGs). We found that GLKs promotes CathB6 nuclear accumulation and reduces its p-body association. TurboID proximity labelling further linked CathB6 to PhANG-associated proteins, known MORF2- and GUN1-interacting factors, p-body components, and actin-tubulin/myosin machinery, the latter being consistent with the highly dynamic behaviour of CathB6-associated p-bodies. Together, these data indicate that, beyond suppressing EDS1-mediated defenses, CathB6 interferes with the MORF2-GUN1-GLK signalling pathway, modulating plant defense responses while sustaining GLK-mediated PhANG expression to maintain cellular homeostasis during aphid attack. SIGNIFICANCE STATEMENTAphids damage crops and spread plant diseases while feeding. We discovered how a protein in aphid saliva, CathB6, helps these pests establish themselves on plants. CathB6 weakens a major immune pathway and alters communication between chloroplasts and the cell nucleus. This allows the aphid to reduce plant defences while maintaining photosynthesis and normal cell function. These findings reveal a sophisticated survival strategy and may identify ways to develop crops that are more resistant to aphids.

plant biology↗

bioRxiv2026

Transferable IncX3-blaNDM-15 in an uncommon ST580 Klebsiella pneumoniae recovered during paediatric intensive-care surveillance

Objective: Carbapenem-resistant Klebsiella pneumoniae harboring blaNDM poses a serious threat to public health; however, blaNDM-15 remains poorly characterized outside the dominant epidemic lineages. Methods: We characterized K. pneumoniae strain ETFK6090, isolated from a perianal surveillance swab of an 11-month-old immunocompromised child in a paediatric intensive care unit. Investigations included antimicrobial susceptibility testing, broth conjugation, S1 nuclease PFGE with Southern blotting, complete genome sequencing, and comparative genomic analysis against 465 curated blaNDM-positive K. pneumoniae genomes from 37 countries. Results: ETFK6090 belonged to ST580 and exhibited resistance to carbapenems, ceftazidime-avibactam, broad-spectrum cephalosporins, fluoroquinolones, gentamicin, chloramphenicol and trimethoprim-sulfamethoxazole; amikacin and fosfomycin retained low MICs. The complete genome comprised one chromosome and five plasmids, blaNDM-15 was localized on a 46,161-bp IncX3 plasmid, confirmed by Southern blotting. Conjugation into Escherichia coli EC600 transferred carbapenem and cephalosporin resistance, confirming in vitro mobility. The blaNDM-15 genetic environment retained a conserved blaNDM module, with IS-mediated rearrangements at the downstream boundary. In the global comparison, blaNDM-1 and blaNDM-5 predominated, the ST580-blaNDM-15 combination was exceedingly rare, and ETFK6090 constituted a distinct branch apart from major epidemic lineages. Conclusions: A transferable IncX3-blaNDM-15 plasmid can emerge in an uncommon ST580 background, underscoring the necessity to extend genomic surveillance of carbapenem-resistant K. pneumoniae beyond dominant epidemic clones, particularly in high-risk paediatric and intensive-care settings.

microbiology↗