{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T12:56:25Z","timestamp":1791982585363,"version":"4.4.0"},"reference-count":74,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"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:p>\n                    Members of the genus\n                    <jats:italic>Legionella<\/jats:italic>\n                    are Gram-negative aquatic bacteria widely distributed in natural and engineered aquatic environments, yet the genomic diversity of environmental representatives remains incompletely resolved. During routine surveillance of two independent engineered water systems in Spain, two strains were recovered that could not be assigned to any described species using conventional molecular markers. To determine their taxonomic position, we applied a polyphasic approach integrating 16S rRNA and\n                    <jats:italic>mip<\/jats:italic>\n                    gene sequencing, whole-genome sequencing, phylogenomic reconstruction based on conserved core proteins, genome-based relatedness indices, and phenotypic and chemotaxonomic characterization. Phylogenetic analyses based on 16S rRNA and\n                    <jats:italic>mip<\/jats:italic>\n                    gene sequences placed both isolates within the genus\n                    <jats:italic>Legionella<\/jats:italic>\n                    while clearly separating them from recognized taxa. Genome-scale analyses confirmed deep divergence, with average nucleotide identity values of 85.01 % for\n                    <jats:italic>Legionella pelazae<\/jats:italic>\n                    sp. nov. and 70.37 % for\n                    <jats:italic>Legionella navarrensis<\/jats:italic>\n                    sp. nov. relative to their closest described species. The strains exhibited distinct genome architectures, including G+C contents of 35.52 and 48.72 mol%, and showed reproducible physiological and membrane lipid differences consistent with ecological differentiation. No acquired antimicrobial resistance determinants were detected. Taken together, these results reveal substantial intrageneric diversification among environmental\n                    <jats:italic>Legionella<\/jats:italic>\n                    populations inhabiting engineered water systems. On the basis of combined genomic, phylogenetic and phenotypic evidence, the strains represent two novel species within the genus, for which the names\n                    <jats:italic>Legionella pelazae<\/jats:italic>\n                    sp. nov. (CNM-1927-20\n                    <jats:sup>T<\/jats:sup>\n                    = CECT 31282=CCUG 78397\n                    <jats:sup>T<\/jats:sup>\n                    ) and\n                    <jats:italic>Legionella navarrensis<\/jats:italic>\n                    sp. nov. (CNM-4043-24\n                    <jats:sup>T<\/jats:sup>\n                    = CECT 31283 = CCUG 78398\n                    <jats:sup>T<\/jats:sup>\n                    ) are proposed.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1828313","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T15:35:00Z","timestamp":1788968100000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Legionella pelazae sp. nov. and Legionella navarrensis sp. nov., two novel Legionella species, reveal deep genomic diversification within engineered water systems"],"prefix":"10.3389","volume":"17","author":[{"given":"Juana Mar\u00eda","family":"Gonz\u00e1lez-Rubio","sequence":"first","affiliation":[{"name":"Legionella Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III","place":["Majadahonda, Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V\u00edctor Manuel","family":"L\u00f3pez Molina","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Scientific Core Facilities, Instituto de Salud Carlos III","place":["Majadahonda, Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Cianca Pe\u00f1a","sequence":"additional","affiliation":[{"name":"Microbiology Unit, Public Health Laboratory, Institute of Public Health and Occupational Health of Navarra (ISPLN)","place":["Navarra, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Almudena","family":"Cascajero","sequence":"additional","affiliation":[{"name":"Legionella Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III","place":["Majadahonda, Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Monz\u00f3n","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Scientific Core Facilities, Instituto de Salud Carlos III","place":["Majadahonda, Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabel","family":"Cuesta","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Scientific Core Facilities, Instituto de Salud Carlos III","place":["Majadahonda, Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernando","family":"Gonz\u00e1lez-Camacho","sequence":"additional","affiliation":[{"name":"Legionella Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III","place":["Majadahonda, Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"D690","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":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B2","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1139\/gen-2015-0175","article-title":"bcgTree: automatized phylogenetic tree building from bacterial core genomes","volume":"59","author":"Ankenbrand","year":"2016","journal-title":"Genome"},{"key":"B3","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1007\/BF01569569","article-title":"Legionella quinlivanii sp. nov. isolated from water","volume":"18","author":"Benson","year":"1989","journal-title":"Current Microbiol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat. Methods"},{"key":"B5","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinform."},{"key":"B6","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":"B7","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1038\/ng1447","article-title":"Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity","volume":"36","author":"Cazalet","year":"2004","journal-title":"Nat. Genet."},{"key":"B9","doi-asserted-by":"publisher","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: a reference database for bacterial virulence factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"B10","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"B11","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1099\/ijs.0.054171-0","article-title":"Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea","volume":"64","author":"Chun","year":"2014","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1186\/s12859-018-2336-6","article-title":"Rapid and precise alignment of raw reads against redundant databases with KMA","volume":"19","author":"Clausen","year":"2018","journal-title":"BMC Bioinformat."},{"key":"B13","volume-title":"Cowan and Steel's Manual for the Identification of Medical Bacteria","author":"Cowan","year":"1993"},{"key":"B14","doi-asserted-by":"publisher","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput. Biol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"B16","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"B17","doi-asserted-by":"publisher","first-page":"2026","DOI":"10.3390\/microorganisms8122026","article-title":"Living with legionella and other waterborne pathogens","volume":"8","author":"Falkinham","year":"2020","journal-title":"Microorganisms"},{"key":"B18","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":"B19","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1128\/CMR.15.3.506-526.2002","article-title":"Legionella and Legionnaires' disease: 25 years of investigation","volume":"15","author":"Fields","year":"2002","journal-title":"Clin. Microbiol. Rev."},{"key":"B20","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1111\/j.1469-0691.2007.01808.x","article-title":"Identification of Legionella spp. by 19 European reference laboratories: results of the European Working Group for Legionella Infections External Quality Assessment Scheme using DNA sequencing of the macrophage infectivity potentiator gene and dedicated online tools","volume":"13","author":"Fry","year":"2007","journal-title":"Clin. Microbiol. Infect."},{"key":"B21","volume-title":"Methods for General and Molecular Bacteriology","author":"Gerhardt","year":"1994"},{"key":"B22","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1038\/s41435-019-0074-z","article-title":"Intracellular parasitism, the driving force of evolution of Legionella pneumophila and the genus Legionella","volume":"20","author":"Gomez-Valero","year":"2019","journal-title":"Genes Immun."},{"key":"B23","doi-asserted-by":"publisher","first-page":"2265","DOI":"10.1073\/pnas.1808016116","article-title":"More than 18,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells","volume":"116","author":"Gomez-Valero","year":"2019","journal-title":"Proc. Natl. Acad. Sci. U S A."},{"key":"B24","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1186\/1471-2164-12-536","article-title":"Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes","volume":"12","author":"Gomez-Valero","year":"2011","journal-title":"BMC Genom."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"B26","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1093\/femsre\/fuaf022","article-title":"Foresight 2035: a perspective on the next decade of research on the management of Legionella spp. in engineered aquatic environments","volume":"49","author":"Hammes","year":"2025","journal-title":"FEMS Microbiol. Rev."},{"key":"B27","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1128\/JCM.02452-13","article-title":"Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples","volume":"52","author":"Hasman","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B29","doi-asserted-by":"publisher","first-page":"e000131","DOI":"10.1099\/mgen.0.000131","article-title":"ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads","volume":"3","author":"Hunt","year":"2017","journal-title":"Microb. Genom."},{"key":"B30","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1109\/MCSE.2007.55","article-title":"Matplotlib: a 2D graphics environment","volume":"9","author":"Hunter","year":"2007","journal-title":"Comput. Sci. Eng."},{"key":"B31","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformat."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1721","DOI":"10.1101\/gr.210641.116","article-title":"Centrifuge: rapid and sensitive classification of metagenomic sequences","volume":"26","author":"Kim","year":"2016","journal-title":"Genome Res."},{"key":"B33","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1099\/ijs.0.059774-0","article-title":"Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes","volume":"64","author":"Kim","year":"2014","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"2567","DOI":"10.1073\/pnas.0409727102","article-title":"Genomic insights that advance the species definition for prokaryotes","volume":"102","author":"Konstantinidis","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U S A."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: molecular evolutionary genetics analysis across computing platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"B36","doi-asserted-by":"publisher","first-page":"1529","DOI":"10.1128\/JCM.02981-13","article-title":"Benchmarking of methods for genomic taxonomy","volume":"52","author":"Larsen","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1093\/molbev\/msn067","article-title":"An improved general amino acid replacement matrix","volume":"25","author":"Le","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"1949","DOI":"10.1099\/00207713-51-6-1949","article-title":"Legionella gresilensis sp. nov. and Legionella beliardensis sp. nov., isolated from water in France","volume":"51","author":"Lo Presti","year":"2001","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"104","DOI":"10.7717\/peerj-cs.104","article-title":"Bracken: estimating species abundance in metagenomics data","volume":"3","author":"Lu","year":"2017","journal-title":"PeerJ. Comput. Sci."},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.25080\/Majora-92bf1922-00a","article-title":"\u201cData Structures for Statistical Computing in Python,\u201d","author":"McKinner","year":"2010","journal-title":"Proceedings of the 9th Python in Science Conference"},{"key":"B41","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/1471-2105-14-60","article-title":"Genome sequence-based species delimitation with confidence intervals and improved distance functions","volume":"14","author":"Meier-Kolthoff","year":"2013","journal-title":"BMC Bioinformat."},{"key":"B42","doi-asserted-by":"publisher","first-page":"D801","DOI":"10.1093\/nar\/gkab902","article-title":"TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes","volume":"50","author":"Meier-Kolthoff","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"B43","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":"B44","doi-asserted-by":"publisher","first-page":"11257","DOI":"10.1038\/ncomms11257","article-title":"Fast and sensitive taxonomic classification for metagenomics with Kaiju","volume":"7","author":"Menzel","year":"2016","journal-title":"Nat. Commun."},{"key":"B45","volume-title":"Sherlock Microbial Identification System Operating Manual, version 6.1","year":"2008"},{"key":"B46","doi-asserted-by":"publisher","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":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"B47","unstructured":"Monzon\n              S.\n            \n            \n              Sola\n              J. P.\n            \n            \n              Julia\n              M.\n            \n          \n          PlasmidID, 1.6.5 version\n          \n          2021"},{"key":"B48","doi-asserted-by":"publisher","first-page":"4059","DOI":"10.1038\/s41467-021-24128-2","article-title":"Re-evaluating the evidence for a universal genetic boundary among microbial species","volume":"12","author":"Murray","year":"2021","journal-title":"Nat. Commun."},{"key":"B49","doi-asserted-by":"publisher","first-page":"328","DOI":"10.3389\/fcimb.2018.00328","article-title":"Editorial: biology and pathogenesis of legionella","volume":"8","author":"Newton","year":"2018","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.3389\/fenvs.2020.611611","article-title":"Water stagnation and flow obstruction reduces the quality of potable water and increases the risk of legionelloses","volume":"8","author":"Nisar","year":"2020","journal-title":"Front. Environ. Sci."},{"key":"B51","doi-asserted-by":"publisher","first-page":"3","DOI":"10.3389\/fcimb.2018.00003","article-title":"The life cycle of L. pneumophila: cellular differentiation is linked to virulence and metabolism","volume":"8","author":"Oliva","year":"2018","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1099\/ijs.0.02268-0","article-title":"Legionella busanensis sp. nov., isolated from cooling tower water in Korea","volume":"53","author":"Park","year":"2003","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B53","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":"B54","doi-asserted-by":"publisher","first-page":"e0082724","DOI":"10.1128\/mbio.00827-24","article-title":"Amoebae as training grounds for microbial pathogens","volume":"15","author":"Price","year":"2024","journal-title":"mBio."},{"key":"B55","unstructured":"Python Language Reference version 3.9"},{"key":"B56","doi-asserted-by":"publisher","first-page":"1560","DOI":"10.1128\/JCM.36.6.1560-1567.1998","article-title":"Sequence-based classification scheme for the genus Legionella targeting the mip gene","volume":"36","author":"Ratcliff","year":"1998","journal-title":"J. Clin. Microbiol."},{"key":"B57","doi-asserted-by":"publisher","first-page":"307","DOI":"10.4161\/viru.24290","article-title":"Cellular microbiology and molecular ecology of Legionella-amoeba interaction","volume":"4","author":"Richards","year":"2013","journal-title":"Virulence"},{"key":"B58","doi-asserted-by":"publisher","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U S A."},{"key":"B59","doi-asserted-by":"publisher","first-page":"4060","DOI":"10.1038\/s41467-021-24129-1","article-title":"Reply to: \u201cRe-evaluating the evidence for a universal genetic boundary among microbial species\u201d","volume":"12","author":"Rodriguez","year":"2021","journal-title":"Nat. Commun."},{"key":"B60","volume-title":"Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids.","author":"Sasser","year":"1990"},{"key":"B61","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B62","doi-asserted-by":"publisher","first-page":"107071","DOI":"10.1016\/j.mimet.2024.107071","article-title":"Broth microdilution protocol for determining antimicrobial susceptibility of Legionella pneumophila to clinically relevant antimicrobials","volume":"228","author":"Sewell","year":"2025","journal-title":"J. Microbiol. Methods"},{"key":"B63","doi-asserted-by":"publisher","first-page":"166","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":"B64","doi-asserted-by":"publisher","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","article-title":"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models","volume":"22","author":"Stamatakis","year":"2006","journal-title":"Bioinformatics"},{"key":"B65","doi-asserted-by":"publisher","first-page":"3221","DOI":"10.1101\/2023.10.20.563221","article-title":"nf-core\/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling","volume":"2023","author":"Stamouli","year":"2023","journal-title":"bioRxiv"},{"key":"B66","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1080\/10635150701472164","article-title":"Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments","volume":"56","author":"Talavera","year":"2007","journal-title":"Syst. Biol."},{"key":"B67","first-page":"512","article-title":"Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees","volume":"10","author":"Tamura","year":"1993","journal-title":"Mol. Biol. Evol."},{"key":"B68","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: molecular evolutionary genetics analysis version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"B69","unstructured":"Vm\n              D.\n            \n            \n              Peltzer\n              A.\n            \n            \n              Straub\n              D.\n            \n            \n              Bot\n              N.-C.\n            \n            \n              Wuennemann\n              F.\n            \n            \n              Garcia\n              M. U.\n            \n          \n          nf-core\/bacass: v2.4.0\n          \n          2024"},{"key":"B70","doi-asserted-by":"publisher","first-page":"e1005595","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"B71","doi-asserted-by":"publisher","first-page":"2120","DOI":"10.1128\/jcm.25.11.2120-2122.1987","article-title":"Legionella birminghamensis sp. nov. isolated from a cardiac transplant recipient","volume":"25","author":"Wilkinson","year":"1987","journal-title":"J. Clin. Microbiol."},{"key":"B72","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"B73","doi-asserted-by":"publisher","first-page":"1415157","DOI":"10.3389\/fpubh.2024.1415157","article-title":"A review of Legionella transmission risk in built environments: sources, regulations, sampling, and detection","volume":"12","author":"Yao","year":"2024","journal-title":"Front. Public Health"},{"key":"B74","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1007\/s10482-017-0844-4","article-title":"A large-scale evaluation of algorithms to calculate average nucleotide identity","volume":"110","author":"Yoon","year":"2017","journal-title":"Antonie Van Leeuwenhoek"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1828313\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T15:35:04Z","timestamp":1788968104000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1828313\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,9]]},"references-count":74,"alternative-id":["10.3389\/fmicb.2026.1828313"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1828313","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,9]]},"article-number":"1828313"}}