{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T06:05:05Z","timestamp":1780380305939,"version":"3.54.1"},"reference-count":37,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T00:00:00Z","timestamp":1780358400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Bacillus licheniformis<\/jats:italic>\n                      is an opportunistic pathogen in clinical settings. However, the emergence of clinical strains carrying horizontally acquired virulence determinants, including chromosomal genomic islands harboring\n                      <jats:italic>yopX<\/jats:italic>\n                      , a putative type IV secretion system (T4SS), and plasmids bearing toxin-antitoxin systems and additional virulence factors, poses a significant challenge to diagnosis and treatment. Moreover, the genetic basis of the pathogenicity of clinical isolates has not been comprehensively studied.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      A pathogenic\n                      <jats:italic>B. licheniformis<\/jats:italic>\n                      strain (LSDY01) isolated from a skin infection was subjected to whole-genome sequencing and comparative genomic analyses. Phylogenetic reconstruction, pan-genome analysis, and detailed characterization of plasmid and chromosomal virulence determinants were performed. Antimicrobial susceptibility testing was performed according to standardized guidelines. Biofilm formation assays were also conducted. The cytotoxic effect of LSDY01 on HEK293 cells was evaluated using a CCK-8 assay.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Strain LSDY01 belonged to\n                      <jats:italic>B. licheniformis<\/jats:italic>\n                      ST20, differing by only one allele from the prevalent ST3. Its closest relatives were the Daqu-derived strains CP143961.1 and CP143962.1. A unique horizontally acquired genomic island (~157 27\u202fkb, GC 33.03%) and a putative type IV secretion system (T4SS) gene cluster were identified on the chromosome of this strain. A novel plasmid (pLSDY01), which is highly similar to environmental plasmids, harbors\n                      <jats:italic>yopX<\/jats:italic>\n                      , a toxin-antitoxin system,\n                      <jats:italic>pilT<\/jats:italic>\n                      , and a pistol ribozyme. LSDY01 was susceptible to imipenem and vancomycin but resistant to penicillin, erythromycin, and chloramphenicol. The CCK-8 assay revealed a non-significant trend toward reduced HEK293 cell viability after co-culture with LSDY01 (\n                      <jats:italic>p<\/jats:italic>\n                      = 0.0545 at 2\u202fh of CCK-8 incubation).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      Our findings suggest that horizontal gene transfer, including plasmid acquisition and potential phage integration, may have enabled\n                      <jats:italic>B. licheniformis<\/jats:italic>\n                      to evolve into a pathogen, highlighting the need to reassess the safety of traditionally non-pathogenic microbes.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1815181","type":"journal-article","created":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T05:40:47Z","timestamp":1780378847000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic characterization of a pathogenic Bacillus licheniformis strain LSDY01: deciphering its genetic diversity and virulence-associated traits"],"prefix":"10.3389","volume":"17","author":[{"given":"Lingfeng","family":"Liang","sequence":"first","affiliation":[{"name":"Department of Infectious Diseases, Lishui Hospital of Wenzhou Medical University, The First Affiliated Hospital of Lishui University, Lishui People's Hospital","place":["Lishui, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenqiu","family":"Shang","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Lishui Hospital of Wenzhou Medical University, The First Affiliated Hospital of Lishui University, Lishui People's Hospital","place":["Lishui, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aixia","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Lishui Hospital of Wenzhou Medical University, The First Affiliated Hospital of Lishui University, Lishui People's Hospital","place":["Lishui, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"De","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Lishui Hospital of Wenzhou Medical University, The First Affiliated Hospital of Lishui University, Lishui People's Hospital","place":["Lishui, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ningjun","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Lishui Hospital of Wenzhou Medical University, The First Affiliated Hospital of Lishui University, Lishui People's Hospital","place":["Lishui, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin","family":"Jing","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Lishui Hospital of Wenzhou Medical University, The First Affiliated Hospital of Lishui University, Lishui People's Hospital","place":["Lishui, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziqi","family":"Yang","sequence":"additional","affiliation":[{"name":"Guangxi Medical University Oncology School","place":["Nanning, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wugao","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Lishui Hospital of Wenzhou Medical University, The First Affiliated Hospital of Lishui University, Lishui People's Hospital","place":["Lishui, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,2]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1186\/1471-2164-12-402","article-title":"BLAST ring image generator (BRIG): simple prokaryote genome comparisons","volume":"12","author":"Alikhan","year":"2011","journal-title":"BMC Genomics"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1590\/s1517-838220090002000033","article-title":"Adherence assays and slime production of vibrio alginolyticus and Vibrio parahaemolyticus","volume":"40","author":"Ben Abdallah","year":"2009","journal-title":"Braz. J. Microbiol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"W51","DOI":"10.1093\/nar\/gkaf335","article-title":"Bakta web\u2014rapid and standardized genome annotation on scalable infrastructures","volume":"53","author":"Beyvers","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1016\/s0966-842x(02)02459-9","article-title":"Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved","volume":"10","author":"Boyd","year":"2002","journal-title":"Trends Microbiol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1128\/mmbr.68.3.560-602.2004","article-title":"Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion","volume":"68","author":"Br\u00fcssow","year":"2004","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1038\/s41579-023-00926-x","article-title":"Plasmids, a molecular cornerstone of antimicrobial resistance in the one health era","volume":"22","author":"Casta\u00f1eda-Barba","year":"2024","journal-title":"Nat. Rev. Microbiol."},{"key":"ref8","volume-title":"CLSI Guideline M45","year":"2015"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"920","DOI":"10.1017\/ice.2025.10223","article-title":"A widespread dissemination of Bacillus licheniformis in a tertiary hospital: an outbreak or pseudo-outbreak?","volume":"46","author":"Deniz","year":"2025","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"12728","DOI":"10.1038\/s41598-021-91456-0","article-title":"AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence","volume":"11","author":"Feldgarden","year":"2021","journal-title":"Sci. Rep."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"1707","DOI":"10.1111\/j.1462-5822.2006.00794.x","article-title":"Pathogenicity islands: a molecular toolbox for bacterial virulence","volume":"8","author":"Gal-Mor","year":"2006","journal-title":"Cell. Microbiol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1111\/mmi.13896","article-title":"Type IV secretion in gram-negative and gram-positive bacteria","volume":"107","author":"Grohmann","year":"2018","journal-title":"Mol. Microbiol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1007\/978-3-319-75241-9_5","article-title":"Mechanisms of conjugative transfer and type IV secretion-mediated effector transport in gram-positive bacteria","volume":"413","author":"Grohmann","year":"2017","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"1518","DOI":"10.1248\/bpb.19.1518","article-title":"A combined assay of cell viability and in vitro cytotoxicity with a highly water-soluble tetrazolium salt, neutral red and crystal violet","volume":"19","author":"Ishiyama","year":"1996","journal-title":"Biol. Pharm. Bull."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1186\/s12866-024-03312-6","article-title":"Genetic recombination-mediated evolutionary interactions between phages of potential industrial importance and prophages of their hosts within or across the domains of Escherichia, Listeria, Salmonella, Campylobacter, and Staphylococcus","volume":"24","author":"Kobakhidze","year":"2024","journal-title":"BMC Microbiol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"W229","DOI":"10.1093\/nar\/gky352","article-title":"oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements","volume":"46","author":"Li","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022: a general classification scheme for bacterial virulence factors","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"msaf192","DOI":"10.1093\/molbev\/msaf192","article-title":"Impact of natural transformation on the acquisition of novel genes in bacteria","volume":"42","author":"Mazzamurro","year":"2025","journal-title":"Mol. Biol. Evol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"5198","DOI":"10.1038\/s41467-019-13070-z","article-title":"Multiple conformations facilitate PilT function in the type IV pilus","volume":"10","author":"McCallum","year":"2019","journal-title":"Nat. Commun."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1126\/science.abb6151","article-title":"A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity","volume":"369","author":"Meeske","year":"2020","journal-title":"Science"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"2182","DOI":"10.1038\/s41467-019-10210-3","article-title":"TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy","volume":"10","author":"Meier-Kolthoff","year":"2019","journal-title":"Nat. Commun."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"7331","DOI":"10.1039\/d0cs00617c","article-title":"Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes","volume":"49","author":"Micura","year":"2020","journal-title":"Chem. Soc. Rev."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1080\/07388551.2021.1873239","article-title":"Biotechnological applications of Bacillus licheniformis","volume":"41","author":"Muras","year":"2021","journal-title":"Crit. Rev. Biotechnol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"880","DOI":"10.3390\/genes16080880","article-title":"Integrated whole-genome sequencing and in silico characterization of Salmonella Cerro and Schwarzengrund from Brazil","volume":"16","author":"Nunes","year":"2025","journal-title":"Genes (Basel)"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"6304","DOI":"10.1038\/s44318-025-00584-0","article-title":"Type IV secretion systems: from structures to mechanisms","volume":"44","author":"Paillard","year":"2025","journal-title":"EMBO J."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"661026","DOI":"10.3389\/fcimb.2021.661026","article-title":"RNA regulated toxin-antitoxin Systems in Pathogenic Bacteria","volume":"11","author":"Sarpong","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"102138","DOI":"10.1016\/j.mib.2022.01.009","article-title":"Strain wars and the evolution of opportunistic pathogens","volume":"67","author":"Sheppard","year":"2022","journal-title":"Curr. Opin. Microbiol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"1893","DOI":"10.3390\/pharmaceutics15071893","article-title":"Bacillus licheniformis: a producer of antimicrobial substances, including antimycobacterials, which are feasible for medical applications","volume":"15","author":"Shleeva","year":"2023","journal-title":"Pharmaceutics"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"e000166","DOI":"10.1099\/mgen.0.000166","article-title":"chewBBACA: a complete suite for gene-by-gene schema creation and strain identification","volume":"4","author":"Silva","year":"2018","journal-title":"Microb. Genom."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"727022","DOI":"10.3389\/fmicb.2021.727022","article-title":"Whole genome sequence-based identification of Clostridium estertheticum complex strains supports the need for taxonomic reclassification within the species Clostridium estertheticum","volume":"12","author":"Wambui","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1146\/annurev-micro-032521-022006","article-title":"Mobile genetic element flexibility as an underlying principle to bacterial evolution","volume":"77","author":"Weisberg","year":"2023","journal-title":"Ann. Rev. Microbiol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"100485","DOI":"10.1016\/j.ijmmb.2023.100485","article-title":"Bacillus licheniformis bloodstream infections associated with oral probiotic administration: two case reports","volume":"47","author":"Zou","year":"2024","journal-title":"Indian J. Med. Microbiol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"e00186","DOI":"10.1128\/msystems.00186-18","article-title":"Mobile compensatory mutations promote plasmid survival","volume":"4","author":"Zwanzig","year":"2019","journal-title":"mSystems"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1815181\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T05:40:48Z","timestamp":1780378848000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1815181\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,2]]},"references-count":37,"alternative-id":["10.3389\/fmicb.2026.1815181"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1815181","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,2]]},"article-number":"1815181"}}