{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T18:34:12Z","timestamp":1787337252540,"version":"build-2736575974"},"update-to":[{"DOI":"10.1371\/journal.ppat.1014507","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T00:00:00Z","timestamp":1787270400000}}],"reference-count":86,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Bee Disease Insurance"},{"name":"British Beekeepers Association"},{"DOI":"10.13039\/501100000741","name":"University of Warwick","doi-asserted-by":"publisher","award":["Chancellor\u2019s Scholarship"],"award-info":[{"award-number":["Chancellor\u2019s Scholarship"]}],"id":[{"id":"10.13039\/501100000741","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    Honeybees of the species\n                    <jats:italic>Apis mellifera<\/jats:italic>\n                    are important pollinators of crops and wild plants.\n                    <jats:italic>Paenibacillus larvae<\/jats:italic>\n                    , a spore-forming bacterium, is a problematic pathogen that causes American foulbrood (AFB) in honeybee larvae worldwide. In many countries, AFB is a notifiable disease, requiring the destruction of diseased colonies, resulting in economic loss that impacts beekeeping and agriculture. Disease onset starts with larval ingestion of\n                    <jats:italic>P. larvae<\/jats:italic>\n                    spores, which germinate into growing cells that proliferate in the larval gut, leading to larval death and eventually bee colony collapse. As infection progresses,\n                    <jats:italic>P. larvae<\/jats:italic>\n                    produce spores, reinitiating the disease cycle. Thus, growth, sporulation and germination underlie AFB. In this study, using various microbiological assays, quantitative cell biology methods, transmission electron microscopy and genomics, we sought to identify genetic and phenotypic characteristics associated with the predominant ERIC I and ERIC II genotypes of\n                    <jats:italic>P. larvae<\/jats:italic>\n                    during growth, sporulation and germination. Extending previous findings, our data identify genetic differences between ERIC I and ERIC II strains and some genetic variation between strains of the same ERIC type. Furthermore, we describe significant differences in cellular morphology during growth, differences in spore envelope structure and differences in germination efficiency between ERIC I and ERIC II genotypes. Collectively, our findings improve understanding of\n                    <jats:italic>P. larvae<\/jats:italic>\n                    biology and provide a foundation for developing genotype-specific disease management strategies for AFB.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1014507","type":"journal-article","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T17:43:24Z","timestamp":1786643004000},"page":"e1014507","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative genomics and phenotypic divergence of ERIC I and ERIC II genotypes of Paenibacillus larvae, the causative agent of American Foulbrood disease"],"prefix":"10.1371","volume":"22","author":[{"given":"Md. Mubarack","family":"Hossain","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaitlyn","family":"Coleman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matej","family":"Medvecky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Moore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xavier","family":"Didelot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Chandler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4541-0145","authenticated-orcid":true,"given":"Christopher D. A.","family":"Rodrigues","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,8,13]]},"reference":[{"issue":"1870","key":"ppat.1014507.ref001","doi-asserted-by":"crossref","first-page":"20172140","DOI":"10.1098\/rspb.2017.2140","article-title":"The worldwide importance of honey bees as pollinators in natural habitats","volume":"285","author":"K-LJ Hung","year":"2018","journal-title":"Proc R Soc B Biol Sci"},{"key":"ppat.1014507.ref002","unstructured":"Breeze TD, Garratt MP, Senapathi D, Willcox BK, Potts SG. Economic benefits of pollination to global food systems\u2013evidence and knowledge gaps."},{"issue":"6229","key":"ppat.1014507.ref003","doi-asserted-by":"crossref","first-page":"1255957","DOI":"10.1126\/science.1255957","article-title":"Bee declines driven by combined stress from parasites, pesticides, and lack of flowers","volume":"347","author":"D Goulson","year":"2015","journal-title":"Science"},{"issue":"2","key":"ppat.1014507.ref004","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1007\/s11259-025-11034-x","article-title":"High prevalence of Paenibacillus larvae, the pathogenic agent of American foulbrood disease, in Palestinian honey bee colonies","volume":"50","author":"M Alqurneh","year":"2026","journal-title":"Vet Res Commun"},{"issue":"4","key":"ppat.1014507.ref005","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1006\/jipa.2001.5032","article-title":"Adult honeybee\u2019s resistance against Paenibacillus larvae larvae, the causative agent of the American foulbrood","volume":"77","author":"U Riessberger-Gall\u00e9","year":"2001","journal-title":"J Invertebr Pathol"},{"key":"ppat.1014507.ref006","doi-asserted-by":"crossref","first-page":"667096","DOI":"10.3389\/fmicb.2021.667096","article-title":"Antimicrobial resistance genes in bacteria isolated from Japanese honey, and their potential for conferring macrolide and lincosamide resistance in the American foulbrood pathogen Paenibacillus larvae","volume":"12","author":"M Okamoto","year":"2021","journal-title":"Front Microbiol"},{"issue":"1","key":"ppat.1014507.ref007","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1186\/s12866-023-02902-0","article-title":"Probiotic candidates for controlling Paenibacillus larvae, a causative agent of American foulbrood disease in honey bee","volume":"23","author":"A-T Truong","year":"2023","journal-title":"BMC Microbiol"},{"issue":"1","key":"ppat.1014507.ref008","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1080\/0005772X.1999.11099415","article-title":"American foulbrood: a review of its biology, diagnosis and control","volume":"80","author":"H Hansen","year":"1999","journal-title":"Bee World"},{"issue":"17","key":"ppat.1014507.ref009","doi-asserted-by":"crossref","first-page":"7387","DOI":"10.1007\/s00253-016-7716-0","article-title":"Biology of Paenibacillus larvae, a deadly pathogen of honey bee larvae","volume":"100","author":"J Ebeling","year":"2016","journal-title":"Appl Microbiol Biotechnol"},{"issue":"3","key":"ppat.1014507.ref010","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0090914","article-title":"How to kill the honey bee larva: genomic potential and virulence mechanisms of Paenibacillus larvae","volume":"9","author":"M Djukic","year":"2014","journal-title":"PLoS One"},{"key":"ppat.1014507.ref011","volume-title":"Bacteriophages for treating American Foulbrood and the neutralization of Paenibacillus larvae spores","author":"TS Brady","year":"2018"},{"issue":"1","key":"ppat.1014507.ref012","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.jip.2008.05.010","article-title":"Distribution of Paenibacillus larvae spores inside honey bee colonies and its relevance for diagnosis","volume":"99","author":"M Gillard","year":"2008","journal-title":"J Invertebr Pathol"},{"issue":"3","key":"ppat.1014507.ref013","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1007\/s43538-025-00399-x","article-title":"Honeybees and colony collapse disorder: understanding key drivers and economic implications","volume":"91","author":"G Singh","year":"2025","journal-title":"Proc Indian Natl Sci Acad"},{"issue":"2","key":"ppat.1014507.ref014","doi-asserted-by":"crossref","first-page":"151394","DOI":"10.1016\/j.ijmm.2020.151394","article-title":"Discovery of Paenibacillus larvae ERIC V: phenotypic and genomic comparison to genotypes ERIC I-IV reveal different inventories of virulence factors which correlate with epidemiological prevalences of American Foulbrood","volume":"310","author":"H Beims","year":"2020","journal-title":"Int J Med Microbiol"},{"issue":"1","key":"ppat.1014507.ref015","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1080\/21505594.2019.1603133","article-title":"Comprehensive proteomic analysis of exoproteins expressed by ERIC I, II, III and IV Paenibacillus larvae genotypes reveals a wide range of virulence factors","volume":"10","author":"T Erban","year":"2019","journal-title":"Virulence"},{"issue":"1","key":"ppat.1014507.ref016","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1007\/s40588-018-0083-0","article-title":"Bacterial diseases in honeybees","volume":"5","author":"E Forsgren","year":"2018","journal-title":"Curr Clin Microbiol Rep"},{"issue":"6","key":"ppat.1014507.ref017","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1051\/apido:2001103","article-title":"Resistance to American foulbrood disease by honey bee colonies Apis mellifera bred for hygienic behavior","volume":"32","author":"M Spivak","year":"2001","journal-title":"Apidologie"},{"issue":"3","key":"ppat.1014507.ref018","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1111\/j.1365-2672.2011.05214.x","article-title":"Heterologous expression of green fluorescent protein in Paenibacillus larvae, the causative agent of American Foulbrood of honey bees","volume":"112","author":"L Poppinga","year":"2012","journal-title":"J Appl Microbiol"},{"key":"ppat.1014507.ref019","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.redox.2017.03.002","article-title":"Fluorescent proteins such as eGFP lead to catalytic oxidative stress in cells","volume":"12","author":"D Ganini","year":"2017","journal-title":"Redox Biol"},{"issue":"2","key":"ppat.1014507.ref020","doi-asserted-by":"crossref","first-page":"225","DOI":"10.3390\/microorganisms9020225","article-title":"Fructose and trehalose selectively enhance in vitro sporulation of Paenibacillus larvae ERIC I and ERIC II strains","volume":"9","author":"M Laho","year":"2021","journal-title":"Microorganisms"},{"key":"ppat.1014507.ref021","doi-asserted-by":"crossref","first-page":"102633","DOI":"10.1016\/j.mib.2025.102633","article-title":"Compartmentalization during bacterial spore formation","volume":"87","author":"O Iwa\u0144ska","year":"2025","journal-title":"Curr Opin Microbiol"},{"issue":"2","key":"ppat.1014507.ref022","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.micron.2005.10.001","article-title":"Application of transmission electron microscopy to the clinical study of viral and bacterial infections: present and future","volume":"37","author":"A Curry","year":"2006","journal-title":"Micron"},{"key":"ppat.1014507.ref023","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/S0958-6946(01)00157-1","article-title":"Bacterial endospores the ultimate survivors","volume":"12","author":"A Atrih","year":"2002","journal-title":"Int Dairy J"},{"key":"ppat.1014507.ref024","doi-asserted-by":"crossref","first-page":"79","DOI":"10.2323\/jgam.2021.10.006","article-title":"Visualization and characterization of spore morphogenesis in Paenibacillus polymyxa ATCC39564","volume":"68","author":"K Abe","year":"2022","journal-title":"J Gen Appl Microbiol"},{"issue":"5","key":"ppat.1014507.ref025","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1128\/JB.01958-12","article-title":"Requirements for in vitro germination of Paenibacillus larvae spores","volume":"195","author":"I Alvarado","year":"2013","journal-title":"J Bacteriol"},{"issue":"4","key":"ppat.1014507.ref026","doi-asserted-by":"crossref","first-page":"362","DOI":"10.3390\/insects12040362","article-title":"ERIC and WGS typing of Paenibacillus larvae in Slovenia: investigation of ERIC I outbreaks","volume":"12","author":"A \u017dugelj","year":"2021","journal-title":"Insects"},{"key":"ppat.1014507.ref027","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1186\/1471-2164-12-450","article-title":"Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees","volume":"12","author":"QWT Chan","year":"2011","journal-title":"BMC Genom"},{"issue":"9","key":"ppat.1014507.ref028","doi-asserted-by":"crossref","first-page":"5042","DOI":"10.1111\/1462-2920.15442","article-title":"Development and evaluation of a core genome multilocus sequence typing scheme for Paenibacillus larvae, the deadly American foulbrood pathogen of honeybees","volume":"23","author":"EuroPLarva Consortium","year":"2021","journal-title":"Environ Microbiol"},{"key":"ppat.1014507.ref029","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.ijppaw.2022.05.004","article-title":"\u201cMigratory beekeeping and its influence on the prevalence and dispersal of pathogens to managed and wild bees\u201d","volume":"18","author":"V Mart\u00ednez-L\u00f3pez","year":"2022","journal-title":"Int J Parasitol Parasites Wildl"},{"issue":"4","key":"ppat.1014507.ref030","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1093\/glycob\/cwad011","article-title":"Regulation of trehalose metabolism in insects: from genes to the metabolite window","volume":"33","author":"MB Tellis","year":"2023","journal-title":"Glycobiology"},{"issue":"1","key":"ppat.1014507.ref031","doi-asserted-by":"crossref","first-page":"1192","DOI":"10.1080\/21505594.2020.1809326","article-title":"Trehalose and bacterial virulence","volume":"11","author":"M Vanaporn","year":"2020","journal-title":"Virulence"},{"issue":"20","key":"ppat.1014507.ref032","doi-asserted-by":"crossref","first-page":"7261","DOI":"10.1128\/AEM.01259-15","article-title":"Interactions between cooccurring lactic acid bacteria in honey bee hives","volume":"81","author":"ZP Rokop","year":"2015","journal-title":"Appl Environ Microbiol"},{"key":"ppat.1014507.ref033","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1099\/ijs.0.63928-0","article-title":"Reclassification of Paenibacillus larvae subsp. pulvifaciens and Paenibacillus larvae subsp. larvae as Paenibacillus larvae without subspecies differentiation","volume":"56","author":"E Genersch","year":"2006","journal-title":"Int J Syst Evol Microbiol"},{"issue":"2","key":"ppat.1014507.ref034","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/s41396-019-0541-6","article-title":"Novel probiotic approach to counter Paenibacillus larvae infection in honey bees","volume":"14","author":"BA Daisley","year":"2020","journal-title":"ISME J"},{"issue":"1","key":"ppat.1014507.ref035","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.cell.2006.05.038","article-title":"MipZ, a spatial regulator coordinating chromosome segregation with cell division in Caulobacter","volume":"126","author":"M Thanbichler","year":"2006","journal-title":"Cell"},{"key":"ppat.1014507.ref036","article-title":"American Foulbrood in honeybees and its causative agent, Paenibacillus larvae","author":"E Genersch","year":"2010","journal-title":"J Invertebr Pathol"},{"issue":"11","key":"ppat.1014507.ref037","doi-asserted-by":"crossref","first-page":"7551","DOI":"10.1128\/AEM.71.11.7551-7555.2005","article-title":"Strain- and genotype-specific differences in virulence of Paenibacillus larvae subsp. larvae, a bacterial pathogen causing American foulbrood disease in honeybees","volume":"71","author":"E Genersch","year":"2005","journal-title":"Appl Environ Microbiol"},{"issue":"3","key":"ppat.1014507.ref038","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1128\/MMBR.00001-06","article-title":"The selective value of bacterial shape","volume":"70","author":"KD Young","year":"2006","journal-title":"Microbiol Mol Biol Rev"},{"issue":"2","key":"ppat.1014507.ref039","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1038\/nrmicro1820","article-title":"Morphological plasticity as a bacterial survival strategy","volume":"6","author":"SS Justice","year":"2008","journal-title":"Nat Rev Microbiol"},{"issue":"8","key":"ppat.1014507.ref040","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1016\/j.tim.2017.03.006","article-title":"Shapeshifting to survive: shape determination and regulation in Caulobacter crescentus","volume":"25","author":"SA Woldemeskel","year":"2017","journal-title":"Trends Microbiol"},{"issue":"6","key":"ppat.1014507.ref041","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1016\/j.mib.2012.10.011","article-title":"Polarity and cell fate asymmetry in Caulobacter crescentus","volume":"15","author":"CG Tsokos","year":"2012","journal-title":"Curr Opin Microbiol"},{"issue":"7","key":"ppat.1014507.ref042","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1002\/bit.260350704","article-title":"Plasmid\u2010encoded protein: the principal factor in the \u201cmetabolic burden\u201d associated with recombinant bacteria","volume":"35","author":"WE Bentley","year":"1990","journal-title":"Biotechnol Bioeng"},{"key":"ppat.1014507.ref043","doi-asserted-by":"crossref","first-page":"172","DOI":"10.3389\/fmicb.2014.00172","article-title":"Recombinant protein expression in Escherichia coli: advances and challenges","volume":"5","author":"GL Rosano","year":"2014","journal-title":"Front Microbiol"},{"issue":"4","key":"ppat.1014507.ref044","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1016\/j.micres.2008.03.004","article-title":"Abnormal cell division caused by inclusion bodies in E. coli; increased resistance against external stress","volume":"163","author":"KK Lee","year":"2008","journal-title":"Microbiol Res"},{"issue":"6","key":"ppat.1014507.ref045","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1016\/j.mib.2004.10.001","article-title":"Sporulation of Bacillus subtilis","volume":"7","author":"PJ Piggot","year":"2004","journal-title":"Curr Opin Microbiol"},{"issue":"1","key":"ppat.1014507.ref046","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1111\/j.1574-6976.2008.00148.x","article-title":"Generation of multiple cell types in Bacillus subtilis","volume":"33","author":"D Lopez","year":"2009","journal-title":"FEMS Microbiol Rev"},{"issue":"5","key":"ppat.1014507.ref047","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/femsre\/fuy021","article-title":"Sporulation environment influences spore properties in Bacillus: evidence and insights on underlying molecular and physiological mechanisms","volume":"42","author":"C Bressuire-Isoard","year":"2018","journal-title":"FEMS Microbiol Rev"},{"issue":"2","key":"ppat.1014507.ref048","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nrmicro750","article-title":"Regulation of endospore formation in Bacillus subtilis","volume":"1","author":"J Errington","year":"2003","journal-title":"Nat Rev Microbiol"},{"issue":"6","key":"ppat.1014507.ref049","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.1111\/j.1365-2958.2005.04659.x","article-title":"Phosphatases modulate the bistable sporulation gene expression pattern in Bacillus subtilis","volume":"56","author":"J-W Veening","year":"2005","journal-title":"Mol Microbiol"},{"issue":"3","key":"ppat.1014507.ref050","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1128\/am.29.3.345-351.1975","article-title":"Influence of carbohydrates on growth and sporulation of Clostridium perfringens type A","volume":"29","author":"RG Labbe","year":"1975","journal-title":"Appl Microbiol"},{"key":"ppat.1014507.ref051","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1128\/9781555819323.ch8","article-title":"Spore peptidoglycan.","author":"DL Popham","year":"2016","journal-title":"The bacterial spore: from molecules to systems"},{"issue":"17","key":"ppat.1014507.ref052","doi-asserted-by":"crossref","first-page":"4603","DOI":"10.1128\/JB.180.17.4603-4612.1998","article-title":"Peptidoglycan structural dynamics during germination of Bacillus subtilis 168 endospores","volume":"180","author":"A Atrih","year":"1998","journal-title":"J Bacteriol"},{"issue":"30","key":"ppat.1014507.ref053","doi-asserted-by":"crossref","first-page":"11146","DOI":"10.1080\/10408398.2023.2233184","article-title":"Bacillus spore germination: mechanisms, identification, and antibacterial strategies","volume":"64","author":"L Fan","year":"2024","journal-title":"Crit Rev Food Sci Nutr"},{"key":"ppat.1014507.ref054","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1128\/9781555819323.ch10","article-title":"Spore resistance properties.","author":"P Setlow","year":"2016","journal-title":"The bacterial spore: from molecules to systems"},{"issue":"6","key":"ppat.1014507.ref055","doi-asserted-by":"crossref","first-page":"1612","DOI":"10.1111\/j.1462-2920.2008.01579.x","article-title":"Fluorescence in situ hybridization (FISH) analysis of the interactions between honeybee larvae and Paenibacillus larvae, the causative agent of American foulbrood of honeybees (Apis mellifera)","volume":"10","author":"D Yue","year":"2008","journal-title":"Environ Microbiol"},{"issue":"3","key":"ppat.1014507.ref056","doi-asserted-by":"crossref","first-page":"180","DOI":"10.3390\/vetsci10030180","article-title":"American foulbrood-old and always new challenge","volume":"10","author":"K Matovi\u0107","year":"2023","journal-title":"Vet Sci"},{"issue":"2","key":"ppat.1014507.ref057","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.tim.2010.10.004","article-title":"Germination of spores of Bacillales and Clostridiales species: mechanisms and proteins involved","volume":"19","author":"D Paredes-Sabja","year":"2011","journal-title":"Trends Microbiol"},{"key":"ppat.1014507.ref058","doi-asserted-by":"crossref","first-page":"2381","DOI":"10.1099\/mic.0.27125-0","article-title":"Biochemical characterization of different genotypes of Paenibacillus larvae subsp. larvae, a honey bee bacterial pathogen","volume":"150","author":"S Neuendorf","year":"2004","journal-title":"Microbiology (Reading)"},{"issue":"4","key":"ppat.1014507.ref059","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1007\/s00003-008-0379-8","article-title":"Paenibacillus larvae and American foulbrood \u2013 long since known and still surprising","volume":"3","author":"E Genersch","year":"2008","journal-title":"J Verbr Lebensm"},{"issue":"4","key":"ppat.1014507.ref060","doi-asserted-by":"crossref","first-page":"1414","DOI":"10.1111\/1462-2920.12625","article-title":"Biogeography of Paenibacillus larvae, the causative agent of American foulbrood, using a new multilocus sequence typing scheme","volume":"17","author":"BJ Morrissey","year":"2015","journal-title":"Environ Microbiol"},{"key":"ppat.1014507.ref061","doi-asserted-by":"crossref","DOI":"10.1002\/cpmc.45","article-title":"Growth and laboratory maintenance of Paenibacillus larvae","volume":"48","author":"OS Mahdi","year":"2018","journal-title":"Curr Protoc Microbiol"},{"issue":"3","key":"ppat.1014507.ref062","first-page":"147","article-title":"Evaluation of culture media for Paenibacillus larvae applied to studies of antimicrobial activity","volume":"40","author":"LB Gende","year":"2008","journal-title":"Rev Argent Microbiol"},{"key":"ppat.1014507.ref063","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1007\/978-1-0716-1099-2_2","article-title":"The Illumina sequencing protocol and the NovaSeq 6000 system.","volume-title":"Bacterial pangenomics: methods and protocols","author":"A Modi","year":"2021"},{"key":"ppat.1014507.ref064","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.12688\/f1000research.15931.1","article-title":"FastQ Screen: a tool for multi-genome mapping and quality control","volume":"7","author":"SW Wingett","year":"2018","journal-title":"F1000Research"},{"issue":"15","key":"ppat.1014507.ref065","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"5","key":"ppat.1014507.ref066","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"A Bankevich","year":"2012","journal-title":"J Comput Biol"},{"issue":"14","key":"ppat.1014507.ref067","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"T Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ppat.1014507.ref068","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"BP Alcock","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"16","key":"ppat.1014507.ref069","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gks406","article-title":"PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies","volume":"40","author":"S Akhter","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"ppat.1014507.ref070","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"A Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ppat.1014507.ref071","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1186\/1471-2164-12-402","article-title":"BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons","volume":"12","author":"N-F Alikhan","year":"2011","journal-title":"BMC Genom"},{"key":"ppat.1014507.ref072","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae1010","article-title":"UniProt: the universal protein knowledgebase in 2025","volume":"53","author":"UniProt Consortium","year":"2025","journal-title":"Nucleic Acids Res"},{"issue":"22","key":"ppat.1014507.ref073","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"AJ Page","year":"2015","journal-title":"Bioinformatics"},{"issue":"4","key":"ppat.1014507.ref074","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"K Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"5","key":"ppat.1014507.ref075","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"BQ Minh","year":"2020","journal-title":"Mol Biol Evol"},{"key":"ppat.1014507.ref076","article-title":"OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes","volume":"51","author":"J Sun","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"16","key":"ppat.1014507.ref077","doi-asserted-by":"crossref","first-page":"2473","DOI":"10.1093\/bioinformatics\/btab007","article-title":"Clinker & clustermap.js: automatic generation of gene cluster comparison figures","volume":"37","author":"CLM Gilchrist","year":"2021","journal-title":"Bioinformatics"},{"key":"ppat.1014507.ref078","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"KA Jolley","year":"2018","journal-title":"Wellcome Open Res"},{"issue":"11","key":"ppat.1014507.ref079","first-page":"000685","article-title":"Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification","volume":"7","author":"O Schwengers","year":"2021","journal-title":"Microb Genom"},{"issue":"11","key":"ppat.1014507.ref080","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"PJ Cock","year":"2009","journal-title":"Bioinformatics"},{"issue":"2","key":"ppat.1014507.ref081","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004041","article-title":"ClonalFrameML: efficient inference of recombination in whole bacterial genomes","volume":"11","author":"X Didelot","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"ppat.1014507.ref082","doi-asserted-by":"crossref","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":"I Letunic","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"ppat.1014507.ref083","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1002\/mrd.22489","article-title":"The ImageJ ecosystem: an open platform for biomedical image analysis","volume":"82","author":"J Schindelin","year":"2015","journal-title":"Mol Reprod Dev"},{"issue":"7","key":"ppat.1014507.ref084","doi-asserted-by":"crossref","first-page":"16077","DOI":"10.1038\/nmicrobiol.2016.77","article-title":"MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis","volume":"1","author":"A Ducret","year":"2016","journal-title":"Nat Microbiol"},{"issue":"12","key":"ppat.1014507.ref085","doi-asserted-by":"crossref","first-page":"4727","DOI":"10.35940\/ijitee.L3591.1081219","article-title":"Exploratory data analysis using Python","volume":"8","author":"K Sahoo","year":"2019","journal-title":"IJITEE"},{"issue":"2","key":"ppat.1014507.ref086","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1021\/ci960402j","article-title":"GraphPad prism, data analysis, and scientific graphing","volume":"37","author":"ML Swift","year":"1997","journal-title":"J Chem Inf Comput Sci"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1014507","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T00:00:00Z","timestamp":1787270400000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1014507","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T17:52:15Z","timestamp":1787334735000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1014507"}},"subtitle":[],"editor":[{"given":"William","family":"Navarre","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,13]]},"references-count":86,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1014507","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,13]]}}}