搜索结果：read-only

In this study, we comparatively assessed short-read (Illumina), long-read (Oxford Nanopore Technologies, ONT), and hybrid (Illumina + ONT) sequencing strategies for bacterial genome analysis using the aquaculture-derived isolate 160P. Genomic DNA was extracted and sequenced on Illumina paired-end and ONT long-read platforms, and de novo assemblies were generated using SPAdes, Canu, Flye, and Unicycler under short-read-only, long-read-only, and hybrid workflows, followed by evaluation with QUAST assembly metrics. Among the tested approaches, the hybrid Unicycler assembly provided the highest contiguity, yielding seven contigs and a dominant 4.55 Mb contig consistent with near-complete chromosomal representation. Downstream analyses included functional genome annotation and in silico screening of antimicrobial resistance determinants (CARD), virulence-associated genes (VFDB), and secondary metabolite biosynthetic gene clusters (antiSMASH). Comparative genomic relatedness based on Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) indicated that 160P is most closely related to Aeromonas sobria CECT 4245T yet falls below commonly applied species-level thresholds, supporting its placement as a genomically distinct lineage warranting further taxonomic investigation. Collectively, these findings underscore the value of hybrid sequencing for improving assembly continuity, enhancing annotation completeness, and strengthening taxonomic resolution in bacterial pathogen genomics.

Experience plays a role in belief development. We present a method to evaluate the experiential basis of a belief and investigate whether belief-change interventions are more effective if the qualities of an intervention experience more closely match the experience that might have led to the belief. Psychology department research pool participants (total N = 1102) were in either a read-only or experience-based intervention for three beliefs: that they can detect stares from unseen others, that pyramids have remarkable powers of preservation, and that pyramids produce concentration benefits for people meditating under them. Stare detection and pyramid effects on concentration were diagnosed as experience-based beliefs and were both more strongly affected by experience-based interventions. Pyramid preservation power did not have the properties of an experience-based belief, and intervention type had no effect on that belief. Potential improvements in evaluating experience and implications for more consequential belief change research are discussed.

The pretesting effect suggests that attempting and failing to guess unknown information can improve memory compared to errorless study. A relevant question concerns the optimal timing for providing corrective feedback and administering the final test. This study explored two variables: (1) the timing of feedback after unsuccessful pretest attempts, either immediately or following a delay of 24 hours (Experiment 1) or 48 hours (Experiment 2); and (2) the timing of the final test after feedback, either immediately or after a 24-hour delay (Experiment 1). Recall accuracy was evaluated across these conditions and compared to an errorless (read-only) learning condition. The results showed that pretesting consistently yielded higher recall accuracy than the read-only condition. Immediate feedback was more effective than delayed feedback, and performance on the immediate test was superior to that of the delayed test. More importantly, the pretesting effect persisted even with delays in feedback and final testing. This flexibility in timing suggests practical applications, particularly in educational settings where immediate feedback or testing may not always be feasible.

Plant cells contain three genetically distinct DNA compartments-nuclear, chloroplast, and mitochondrial-and biologically meaningful sequence sharing among them is expected because organellar DNA can move into the nucleus and, in some cases, between organelles. This complicates alignment-free k-mer analysis, the interpretation of compartment-specific sequence vocabularies, and the evaluation of missing-sequence signals such as minimal absent words (MAWs). A reproducible workflow that treats these compartments explicitly is therefore useful both for plant genome analysis and for read-backed quality control. A fully scripted workflow was applied to a telomere-to-telomere-scale Arabidopsis thaliana nuclear reference (Col-CEN v1.2) and a chromosome-level Oryza sativa ssp. japonica reference (GCF_034140825.1), together with chloroplast, mitochondrial, and raw-read datasets. Distinct canonical k-mer types were counted for k = 11-31 and decomposed into mutually exclusive set-algebra categories. The same framework was then used for read-backed validation and for MAW/nullomer testing under Markov models with false-discovery-rate (FDR) control. The two plant species showed markedly different sharing landscapes. In Arabidopsis, chloroplast k-mers became largely compartment-specific by k = 31 (85.6% of the chloroplast set), whereas mitochondrial k-mers remained dominated by nuclear overlap (93.4% of the mitochondrial set at k = 31). In rice, chloroplast k-mers remained strongly shared with the nuclear genome across the entire range (88.6% of the chloroplast set at k = 31), whereas mitochondrial-nuclear sharing remained high but lower than that in Arabidopsis (77.5% at k = 31). Raw-read validation showed that assembly-derived k-mers were almost completely supported by reads in both species (> 99.7% at k = 31 and KMC3 -ci = 1), whereas the read-only fraction collapsed sharply as the minimum-occurrence threshold (-ci) increased from 1 to 10. Because one raw-read dataset was analyzed per species, these contrasts are best interpreted as species-specific workflow case studies rather than as a direct sequencing-platform benchmark. MAW lists derived from chloroplast, mitochondrial, nuclear, and raw-read datasets contained many candidates, but all FDR-adjusted runs returned zero significant nullomers, consistent with the corresponding sequence-based null models rather than with biologically exceptional absence. This workflow provides a reproducible framework for quantifying compartment-specific and shared plant sequence vocabularies, validating those vocabularies against raw reads, and testing absent-word candidates under explicit null models. The two-species application shows that chloroplast and mitochondrial compartments need not behave similarly and that raw-read-only vocabularies are highly sensitive to low-support k-mers. Together, these analyses provide a robust starting framework for plant compartment-aware k-mer interpretation, while locus-level explanations for shared or absent words remain a downstream task for follow-up analyses.

Young and older adults are often victimized by various forms of scams and fraud. However, little research has been conducted on how a scam prevention intervention may impact young and older adults' accuracy and confidence in determining the legitimacy of emails. The present study investigated young and older adults' accuracy and confidence, as well as potential contributing factors to scam susceptibility, before and after engaging with one of three intervention activities: control (no intervention), read-only (read common scam qualities), or interactive (interactively learned scam qualities in emails). Young and older adult participants were randomly assigned to one of the three conditions. Before and after the intervention, participants evaluated a series of legitimate and scam emails, indicating whether each email was legitimate or a scam. Participants also rated their confidence in their accuracy, the personal relevance of each email, and their curiosity about engaging further with the email. Both age groups showed no difference in sensitivity when determining the legitimacy of the emails before and after the interventions. Importantly, both age groups in the read-only and interactive conditions showed a bias toward labeling emails as scams, indicating a generally cautious approach. Although the interventions did not improve detection sensitivity, participants were more cautious when evaluating emails. This tendency may help reduce vulnerability to scams and fraud and suggests that interventions can encourage greater caution when evaluating suspicious emails across age groups.

A primary goal of research on associative recognition has been to identify the conditions that facilitate the formation of unitized representations of stimuli to be remembered, thereby enhancing familiarity-based associative recognition in recent years. In the present study, we sought to examine whether self-generation, as an active and internally driven form of relational processing, can support familiarity-based associative recognition by facilitating the formation of unitized representations. A total of 24 participants were recruited for this experiment. Participants studied triplets of Chinese single-character words. All words within a triplet formed a compound word with a fourth missing word. The missing word had to be produced before it was presented in the self-generation condition and was immediately presented in the read-only condition. In the test phase, participants had to discriminate between intact triplets that were repeated from the study phase and rearranged triplets, in which one or two words were exchanged with words from another studied triplet. The behavioral results revealed significantly higher Pr in the self-generation condition than in the read condition. The ERP results revealed a greater FN400 effect elicited in the self-generation condition than in the read condition. These findings demonstrate that self-generation enhances familiarity-based associative recognition to a significantly greater extent than the read-only condition.

Carbapenems are broad-spectrum antibiotics that are losing effectiveness against infections caused by multidrug-resistant Enterobacterales that have acquired carbapenemase genes. The New Delhi metallo-β-lactamase (bla NDM) is one of the most common carbapenemases in Canada and around the globe. These genes are frequently found on conjugative plasmids, which can disseminate through horizontal gene transfer. We applied whole-genome sequencing to characterize 1,032 bla NDM carbapenemase-producing Enterobacterales isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2023. Using a combination of short-read and long-read sequencing, we obtained 226 complete and circular bla NDM-encoding plasmids. Unlike other carbapenemases in Canada, we found that bla NDM plasmids were very diverse; there was a lack of dominant clusters identified using MOB-suite, and clustering methods were not able to accurately predict plasmid clusters for short-read-only data. The majority of bla NDM plasmids were IncF-type (69.0%, 156/226). Both bla NDM and bla OXA-48-type carbapenemase genes were found in 11.4% (118/1,032) of isolates, and we identified several instances of both carbapenemase genes co-harboured on the same plasmid replicon (n=9). Our findings highlight that plasmid transfer has not played a major role in bla NDM transmission across Canada and that long-read sequencing is essential for resolving bla NDM plasmid structure and cluster membership.

Contemporary language learning applications such as Duolingo and Rosetta Stone often introduce vocabulary through guessing-with-feedback exercises in which learners match words and pictures. We investigated whether that process might yield a pretesting effect-that is, the phenomenon where guessing with correct answer feedback (pretesting) enhances memory. Across four experiments, adult online learners engaged in multiple-choice pretesting to learn Spanish word translations shown in word-image (Experiments 1-2) or image-word (Experiments 3-4) format. Relative to a read-only condition, pretesting yielded statistically significant performance improvements on subsequent cued recall (Cohen's d = 0.18-0.40) and, in most cases, multiple-choice tests (d = 0.25-0.67), regardless of whether test formats were separately presented or intermixed. Participants also reported preferring pretesting over reading for learning second-language vocabulary, especially for word-image learning. Together, these findings extend the pretesting effect to visual and verbal materials, offering theoretical insights and substantiating word-image and image-word guessing-based approaches of language learning.

The best whole genome assemblies are currently built from a combination of highly accurate short-read sequencing data and long-read sequencing data that can bridge repetitive and problematic regions. Oxford Nanopore Technologies (ONT) produce long-read sequencing platforms and they are continually improving their technology to obtain higher quality read data that is approaching the quality obtained from short-read platforms such as Illumina. As these innovations continue, we evaluated how much ONT read coverage produced by the Rapid Barcoding Kit v14 (SQK-RBK114) is necessary to generate high-quality hybrid and long-read-only genome assemblies for a panel of carbapenemase-producing Enterobacterales bacterial isolates. We found that 30× long-read coverage is sufficient if Illumina data are available, and that more (at least 100× long-read coverage is recommended for long-read-only assemblies. Illumina polishing is still improving single nucleotide variants (SNVs) and INDELs in long-read-only assemblies. We also examined if antimicrobial resistance genes could be accurately identified in long-read-only data, and found that Flye assemblies regardless of ONT coverage detected >96% of resistance genes at 100% identity and length. Overall, the Rapid Barcoding Kit v14 and long-read-only assemblies can be an optimal sequencing strategy (i.e., plasmid characterization and AMR detection) but finer-scale analyses (i.e., SNV) still benefit from short-read data.

The development of affective computing and medical electronic technologies has led to the emergence of Artificial Intelligence (AI)-based methods for the early detection of depression. However, previous studies have often overlooked the necessity for the AI-assisted diagnosis system to be wearable and accessible in practical scenarios for depression recognition. In this work, we present an on-board executable multi-feature transfer-enhanced fusion model for our custom-designed wearable three-lead Electroencephalogram (EEG) sensor, based on EEG data collected from 73 depressed patients and 108 healthy controls. Experimental results show that the proposed model exhibits low-computational complexity (65.0 K parameters), promising Floating-Point Operations (FLOPs) performance (25.6 M), real-time processing (1.5 s/execution), and low power consumption (320.8 mW). Furthermore, it requires only 202.0 KB of Random Access Memory (RAM) and 279.6 KB of Read-Only Memory (ROM) when deployed on the EEG sensor. Despite its low computational and spatial complexity, the model achieves a notable classification accuracy of 95.2%, specificity of 94.0%, and sensitivity of 96.9% under independent test conditions. These results underscore the potential of deploying the model on the wearable three-lead EEG sensor for assisting in the diagnosis of depression.

The Comparative Pathology Workbench (CPW) is a web-browser-based visual analytics platform providing shared access to an interactive "spreadsheet" style presentation of image data and associated analysis data. The software was developed to enable pathologists and other clinical and research users to compare histopathological images of diseased and/or normal tissues between different samples of the same or different patients/species. The CPW provides a grid layout of cells in rows and columns so that images that correspond to matching data can be organized in the form of an image-enabled "spreadsheet". An individual workbench or bench can be shared with other users with read-only or full edit access as required. In addition, each bench cell or the whole bench itself has an associated discussion thread to allow collaborative analysis and consensual interpretation of the data. Here, we present the updated system based on 2 years of active use in the field that generated constructive feedback. The updates deliver new capabilities, including automated importation of entire image collections, sorting image collections, long running tasks, public benches, uploading miscellaneous image types, refining search facilities, enabling use of tags, and improving efficiency, speed, and user-friendliness.

Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio technologies have been applied to viral metagenomics, it is not known to what extent different technologies will impact the reconstruction of the viral community. Thus, we constructed a mock bacteriophage community of previously sequenced phage genomes and sequenced them using Illumina, Nanopore and PacBio sequencing technologies and tested a number of different assembly approaches. When using a single sequencing technology, Illumina assemblies were the best at recovering phage genomes. Nanopore- and PacBio-only assemblies performed poorly in comparison to Illumina in both genome recovery and error rates, which both varied with the assembler used. The best Nanopore assembly had errors that manifested as SNPs and INDELs at frequencies 41 and 157 % higher than found in Illumina only assemblies, respectively. While the best PacBio assemblies had SNPs at frequencies 12 and 78 % higher than found in Illumina-only assemblies, respectively. Despite high-read coverage, long-read-only assemblies recovered a maximum of one complete genome from any assembly, unless reads were down-sampled prior to assembly. Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short-read-only assemblies. When using a single technology, Illumina only was the best approach. The differences in genome recovery and error rates between technology and assembler had downstream impacts on gene prediction, viral prediction, and subsequent estimates of diversity within a sample. These findings will provide a starting point for others in the choice of reads and assembly algorithms for the analysis of viromes.

Head trauma is responsible for significant morbidity and mortality in the pediatric trauma population. There are validated guidelines which indicate the necessity for computed tomography of the head (CTH), but the indication for a dedicated CT of the facial bones (CTF) is less clear. We sought to identify our population of head trauma patients who would clinically benefit from the addition of CTF. Using the electronic medical record, pediatric trauma patients who underwent CTH and/or CTF from 2016 to 2021 were identified. We collected information on demographics, traumatic mechanism, subspecialty consultation, and operative and procedural interventions. 2117 pediatric patients were evaluated. A total of 372 patients received CTH and 173 patients received both CTH + CTF. Patients with CTH + CTF were older (P < 0.001), involved in high-velocity blunt trauma (P < 0.001), and had a longer length of stay (P < 0.001). There were no fractures identified in 73 (42.2%) patients with both CTH + CTF. Of patients with fractures, there were 204 fractures identified and 73.0% (149/204) of fractures were seen on both the CTH + CTF. There were 19.6% (40/204) read only on CTF and 10 patients (5.7%) had a fracture requiring intervention. 8 of the 10 fractures requiring operative intervention were mandibular bone fractures. Computed tomography of the head can be used as a screening tool for facial fractures. A negative CTH can eliminate the need for additional radiation from a CTF. Computed tomography of the facial bones will identify more fractures, but few requiring intervention. We suggest that CTF be limited to a subset of pediatric trauma patients with facial injury.

In this work, we present an optimized nanopore long-read only sequencing workflow for epidemiologic analysis of clonal outbreaks built with open-source tools. A set of unrelated clinical Pseudomonas aeruginosa isolates (n = 10) was chosen for workflow optimization, and sequencing libraries were prepared using a modified rapid barcoding strategy that incorporates temperature ramps to improve performance for high-GC content genomes. Sequencing data were used to benchmark the performance of the dorado suite (v0.9.1), including its basecaller, pre-assembly read error correction, and post-assembly polishing algorithms. All long-read assemblies and core genome multilocus sequence typing (cgMLST) were performed with Flye and pyMLST, respectively. Results were compared with a standard reference Illumina short-read approach, and discordant positions were determined at the core and whole-genome levels. Optimal performance was found with dorado sup@v5.0.0 basecalling with the inclusion of dorado error correction and dorado polish with its bacterial model. This workflow was then validated with four retrospective hospital outbreak isolate sets, including Klebsiella pneumoniae (n = 12), P. aeruginosa (n = 11), Enterococcus faecium (n = 10), and Staphylococcus aureus (n = 10). The nanopore-only assemblies obtained from the optimized pipeline demonstrated fully concordant cgMLST-based minimum spanning trees compared to the Illumina short-read reference. At the whole-genome level, high concordance was also observed, with as few as two discordant positions per genome compared to short-read assemblies. This optimized library preparation and open-source computational workflow enables nanopore-only clonality and outbreak analysis with performance comparable to that of Illumina short-read sequencing and will contribute critically to hospital infection control. For the past decade, bacterial whole-genome sequencing has been performed using high-accuracy short-read sequencing. More recently, long-read sequencing with Oxford Nanopore Technologies (ONT) instruments has emerged as a potential alternative based on multiple advantages, including lower costs, portability, and speed. However, this platform has suffered from basecall error rates that were too high for many applications in clinical microbiology, including outbreak tracing. With the release of new flow cell chemistries and basecall algorithms, the accuracy has improved dramatically, making this approach feasible for outbreak investigations. In this work, we optimize a streamlined nanopore-only workflow for epidemiologic analysis of bacterial pathogens. The workflow was validated with isolates from four previously identified clinical outbreaks with varying GC content and demonstrated fully concordant cgMLST clustering as compared to short-read references. This workflow will facilitate the broader implementation of ONT-only genomes and cgMLST analysis to assist in hospital outbreaks worldwide.

Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry. In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role. Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.

A widely accepted view is that errorless learning is essential for supporting new learning in people with anterograde amnesia, but findings are mixed for those with a broader range of memory impairments. People at a chronic stage of recovery from brain injury (BI) with impaired memory and executive function (N&#x2009;=&#x2009;26) were compared with adults in a comparison group without any known risks to brain function (N&#x2009;=&#x2009;25). Learning techniques were compared using a "Generate-and-correct" and "Read-only" condition when learning novel word pairs. At test, both groups scored above chance and showed benefits of Generate-and-correct (errorful learning). Poor learners in the BI group were classified from "flat" learning slopes extracted from an independent word-pair learning task. Critically, poor learners showed no benefit, but also no decrement to learning, using the Generate-and-correct method. No group was harmed by errorful learning; all, except the poorest learners, benefitted from errorful learning. This study indicates, that in some rehabilitation settings, encouraging clients to guess the meaning of unfamiliar material (e.g., from cards, magazines, newspapers) and then correct their errors, could have benefits for recognition memory. Determining when and how errorful learning benefits learning is a key aim for future research.

Versatile memory is strongly desired for end users, to protect their information in the information era. In particular, bit-level switchable memory that can be switched from rewritable to read-only function would allow end users to prevent important data being tampered with. However, no such switchable memory has been reported. We demonstrate that the rewritable function can be converted into read-only function by applying a sufficiently large current pulse in a U-shaped domain-wall memory, which comprises an asymmetric Pt/Co/Ru/AlOx heterostructure with strong Dzyaloshinskii-Moriya interaction. Wafer-scale switchable magnetic domain-wall memory arrays on 4-inch Si/SiO2 substrate are demonstrated. Furthermore, we confirm that the information can be stored in rewritable or read-only states at bit level according to the security needs of end users. Our work not only provides a solution for personal confidential data, but also paves the way for developing multifunctional spintronic devices.

Delivering optimal care to patients with seizures and epilepsy requires all EEGs to be interpreted accurately and reliably. This study investigated neurology professionals' opinions on the ideal standards for EEG in clinical care. We developed an anonymous e-survey targeting practicing and trainee neurologists focused on participants' demographics, clinical practice characteristics, and views on optimal EEG standards of care-including whether an EEG certification test is needed and whether postresidency/fellowship training in EEG/epilepsy is necessary for neurologists who interpret outpatient/routine EEGs in practice. The survey was hosted by the Neurology Clinical Practice-Practice Current, and it was distributed online through the American Academy of Neurology, American Epilepsy Society, American Clinical Neurophysiology Society, and International League Against Epilepsy, and through social media. Two hundred eighty-three responses were included: 119 from EEG/epilepsy-trained neurologists, 83 from non-EEG/epilepsy-trained neurologists, 75 from trainees, and 6 from advanced care providers. Most participants (78%) agreed that "an objective certification test of ability to interpret EEGs is needed for all those who interpret EEGs in clinical practice." Most participants (71%) believed that outpatient/routine EEGs may be read only by neurologists with EEG/epilepsy training; this opinion was more prevalent among EEG/epilepsy-trained (83%) versus non-EEG/epilepsy-trained neurologists (55%). Our neurology community should discuss the need to develop and implement a certification test of ability for all neurologists who wish to interpret EEGs in clinical practice. In addition, it is imperative to improve in-residency EEG education to ensure that neurology graduates achieve EEG competence before entering the workforce.

Plasmids are extrachromosomal mobile genetic elements that often carry genes responsible for antimicrobial resistance. Plasmid epidemiology aims to track the evolution and spread of plasmids, but the field currently faces significant barriers that make practical implementation using whole genome sequence data difficult. Hybrid-assembled genomes remain the most reliable way to identify and track complete plasmids; however, most genomic surveillance data exists in the form of short-read sequencing, which lacks the resolution required to accurately resolve plasmids. Despite recent advances, long-read-only assemblies have not yet reached the consistency seen in hybrid assemblies. The ideal approach to plasmid epidemiology using whole genome sequence data would consider the limitations of sequencing technologies and the constraints of existing genomic surveillance infrastructure, in addition to the unique evolutionary biology of plasmids. Here, we present ACCIO (Assembly-based Circular Contig Identification for Outbreaks), a tool which creates a reference plasmid database and uses it to infer which plasmids, and genetically related plasmid groupings, are present in an input assembly (Illumina, Nanopore, or hybrid assembly). We validated ACCIO using an internal dataset of 303 plasmid-harboring bacterial clinical and surveillance isolates collected from a single acute tertiary care center. When highly related database plasmids were grouped together, ACCIO achieved 100% sensitivity and 92.1% positive predictive value (PPV) for detection of plasmid groups using hybrid assemblies, and comparably strong performance for Illumina (93.0% sensitivity, 86.6% PPV) and Nanopore (79.3% sensitivity, 91.4% PPV) assemblies. Evaluation on three external datasets yielded consistently high performance. Finally, when benchmarked against MOB-suite, a tool for reconstruction and typing of plasmids, ACCIO demonstrated superior performance across nearly all assembly types and plasmid grouping levels. By integrating database construction, clustering, and plasmid calling into a single workflow compatible with all major sequencing platforms, ACCIO is intended to help advance plasmid epidemiology beyond its current technological and infrastructural barriers.