{ "abstract": "Background: The rapid global spread of hypervirulence in Enterobacteriaceae, particularly in carbapenem-resistant Klebsiella pneumoniae, poses a significant public health threat. However, the key genetic vehicles and mechanisms driving horizontal transfer of hypervirulence-associated genes (iucA, iroB, rmpA, rmpA2, and peg-344) remain poorly defined, limiting effective surveillance. Methods: We performed a large-scale genomic survey of 2,869 virulence-associated plasmid sequences and 2,337 complete Enterobacteriaceae chromosomes. Using comparative genomics and evolutionary analyses, we systematically identified and characterized Hypervirulence-associated Pseudo-Compound Transposons (Hva-PCTs), defined as structured mobile elements in which hypervirulence-associated genes are flanked by insertion sequences. Results: Our results demonstrate that hypervirulence-associated genes are transmitted primarily as discrete IS-bounded units, which we term Hva-PCTs. We identified 29 distinct plasmid-borne Hva-PCTs (pHva-PCTs) and 30 chromosomal Hva-PCTs (cHva-PCTs). These modules show clear species-specific patterns: iucA/iroB-associated Hva-PCTs mainly originate in Escherichia coli and spread through IncFIB-containing multi-replicon plasmids (commonly combined with IncFIC(FII) and/or IncFII, while rmpA/rmpA2/peg-344-containing modules originate in K. pneumoniae and are disseminated via IncHI1B/repB plasmids. Three Hva-PCTs were detected on both plasmids and chromosomes (xHva-PCTs). In one clinical K. pneumoniae isolate (LS356), the identical composite module was present on both replicons. Simpler sub-modules, such as ISKqu3-rmpA2-iucA_1-IS102 and IS102-rmpA-peg-344-iroB_1-IS1A, frequently co-occur on the same plasmid; when positioned in tandem, they reconstitute the full composite structure. This assembly pattern is further supported by a partial duplication event in plasmid pP901. CD-HIT clustering (80% nucleotide identity and 90% coverage) showed that 13 of 22 major clusters contained both plasmid and chromosomal copies, with intra-cluster identities >80% across multiple sequence types and host species. Conclusion: Hypervirulence-associated genes in Enterobacteriaceae are disseminated mainly as IS-flanked Hva-PCTs rather than solely through intact virulence plasmids. These modules exhibit strong but not absolute host specificity. The presence of identical Hva-PCTs on plasmids and chromosomes suggests inter-replicon mobility, while their stepwise assembly from simpler sub-modules highlights modular accretion as a key evolutionary process. Tracking Hva-PCTs as distinct mobile units may complement existing plasmid- and gene-centric surveillance approaches for hypervirulent and convergent strains. Experimental validation of their transposition activity and phenotypic effects is still required. Author summary: Bacteria swap genes like tools, and some of those genes make them more dangerous. Hypervirulent Klebsiella pneumoniae can cause severe infections even in healthy people, and the hypervirulence-associated genes responsible are spreading fast—but how they move has been unclear. We scanned nearly 20,000 Enterobacteriaceae genomes and tracked five hypervirulence-associated genes across plasmids, chromosomes, and species. Rather than traveling as part of intact virulence-associated plasmids, these genes move in compact cassettes flanked by insertion sequences—structures we named Hva-PCTs. Different species carry different types: E. coli prefers simple iron-scavenging modules on IncFIB-based multi-replicon plasmids, while K. pneumoniae carries more complex modules combining iron genes with capsule regulators on IncHI1B/repB-based multi-replicon plasmids. Some cassettes appear in identical form on both plasmids and chromosomes, sometimes in the same strain, suggesting they can jump between replicon types. Simpler cassettes also recombine into more complex ones. Because these cassettes, not entire plasmids, are the real moving parts, tracking them could sharpen surveillance of emerging hypervirulent and drug-resistant strains. Experimental tests are still needed to confirm their mobility and effects.", "abstract_shown": true, "affiliations": [ "Department of Geriatric, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua Medicine, Tsinghua University, Beijing, China", "Department of Laboratory Medicine, Beijing Xiaotangshan Hospital, Beijing, China", "Department of Infectious Disease, Peking University Third Hospital, Beijing, China", "Medical Research Center, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China" ], "article_type": "Research Article", "arxiv": null, "author_total": 7, "authors": [ { "affs": [ 0 ], "name": "Shuaihua Fan" }, { "affs": [ 1 ], "name": "Lijun Wang" }, { "affs": [ 2 ], "name": "Chao Liu" }, { "affs": [ 3 ], "name": "Haoran Li" }, { "name": "Huaiqing Qi" }, { "name": "Pengcheng Du" }, { "name": "Jun Guo" } ], "bibtex": "https://research.draconitic.com/paper/02n4b5dtg4pjw.bib", "cited_by": 0, "doi": "10.1371/journal.ppat.1014513", "fulltext_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014513", "id": "02n4b5dtg4pjw", "issns": [ "1553-7374" ], "landing_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014513", "language": null, "licence": "CC-BY-4.0", "licence_label": "CC BY 4.0", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1313|Antibiotic Resistance in Bacteria" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/DNA/Forms of DNA/Plasmids" ], [ "plos", "/Biology and life sciences/Computational biology/Comparative genomics" ], [ "plos", "/Biology and life sciences/Evolutionary biology/Evolutionary genetics" ], [ "plos", "/Biology and life sciences/Evolutionary biology/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/Biology and life sciences/Genetics/DNA/Forms of DNA/Plasmids" ], [ "plos", "/Biology and life sciences/Genetics/Genetic elements/Mobile genetic elements/Plasmids" ], [ "plos", "/Biology and life sciences/Genetics/Genetic loci" ], [ "plos", "/Biology and life sciences/Genetics/Genomics" ], [ "plos", "/Biology and life sciences/Genetics/Genomics/Comparative genomics" ], [ "plos", "/Biology and life sciences/Genetics/Genomics/Mobile genetic elements/Plasmids" ], [ "plos", "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Bacterial pathogens/Escherichia coli" ], [ "plos", "/Biology and life sciences/Organisms/Bacteria/Enterobacteriaceae" ], [ "plos", "/Biology and life sciences/Organisms/Bacteria/Enterobacteriaceae/Escherichia/Escherichia coli" ], [ "plos", "/Biology and life sciences/Organisms/Bacteria/Gut bacteria/Escherichia/Escherichia coli" ], [ "plos", "/Biology and life sciences/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Bacterial pathogens/Escherichia coli" ], [ "plos", "/Research and analysis methods/Animal studies/Experimental organism systems/Model organisms/Escherichia coli" ], [ "plos", "/Research and analysis methods/Animal studies/Experimental organism systems/Prokaryotic models/Escherichia coli" ], [ "plos", "/Research and analysis methods/Model organisms/Escherichia coli" ] ], "openalex": "W7204943354", "pdf_url": "https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1014513&type=printable", "pmcid": null, "pmid": null, "published": "2026-09-01", "publisher": "Public Library of Science", "ris": "https://research.draconitic.com/paper/02n4b5dtg4pjw.ris", "sources": [ { "first_seen": "2026-10-30T12:18:02Z", "native_id": "10.1371/journal.ppat.1014513", "source": "plos", "url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014513" } ], "subjects": [ { "field": "biology", "origin": "plos:genetics", "subfield": "genetics-genomics" } ], "title": "Hypervirulence-associated pseudo-compound transposons as fundamental mobile units driving cross-species virulence dissemination in Enterobacteriaceae", "title_text": "Hypervirulence-associated pseudo-compound transposons as fundamental mobile units driving cross-species virulence dissemination in Enterobacteriaceae", "type": "peer-reviewed", "updated_at": "2026-10-30T12:18:02Z", "url": "https://research.draconitic.com/paper/02n4b5dtg4pjw", "venue": "PLOS Pathogens", "versions": [] }