{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T01:01:47Z","timestamp":1793149307810,"version":"4.5.0"},"reference-count":111,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,7,20]],"date-time":"2023-07-20T00:00:00Z","timestamp":1689811200000},"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":"Introduction<\/jats:title>Macrococcus<\/jats:italic> species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, Macrococcus<\/jats:italic> spp. can be opportunistic pathogens in both veterinary and human clinical settings. This study aimed to provide insight into the evolution, population structure, and functional potential of the Macrococcus<\/jats:italic> genus, with an emphasis on antimicrobial resistance (AMR) and virulence potential.<\/jats:p><\/jats:sec>Methods<\/jats:title>All high-quality, publicly available Macrococcus<\/jats:italic> genomes (n<\/jats:italic>\u2009=\u2009104, accessed 27 August 2022), plus six South African genomes sequenced here (two strains from bovine clinical mastitis cases and four strains from beef products), underwent taxonomic assignment (using four different approaches), AMR determinant detection (via AMRFinderPlus), and virulence factor detection (using DIAMOND and the core Virulence Factor Database).<\/jats:p><\/jats:sec>Results<\/jats:title>Overall, the 110 Macrococcus<\/jats:italic> genomes were of animal commensal, veterinary clinical, food-associated (including food spoilage), and environmental origins; five genomes (4.5%) originated from human clinical cases. Notably, none of the taxonomic assignment methods produced identical results, highlighting the potential for Macrococcus<\/jats:italic> species misidentifications. The most common predicted antimicrobial classes associated with AMR determinants identified across Macrococcus<\/jats:italic> included macrolides, beta-lactams, and aminoglycosides (n<\/jats:italic>\u2009=\u200981, 61, and 44 of 110 genomes; 73.6, 55.5, and 40.0%, respectively). Genes showing homology to Staphylococcus aureus<\/jats:italic> exoenzyme aureolysin were detected across multiple species (using 90% coverage, n<\/jats:italic>\u2009=\u200940 and 77 genomes harboring aureolysin-like genes at 60 and 40% amino acid [AA] identity, respectively). S. aureus<\/jats:italic> Panton-Valentine leucocidin toxin-associated lukF-PV<\/jats:italic> and lukS-PV<\/jats:italic> homologs were identified in eight M. canis<\/jats:italic> genomes (\u226540% AA identity, &gt;85% coverage). Using a method that delineates populations using recent gene flow (PopCOGenT), two species (M. caseolyticus<\/jats:italic> and M. armenti<\/jats:italic>) were composed of multiple within-species populations. Notably, M. armenti<\/jats:italic> was partitioned into two populations, which differed in functional potential (e.g., one harbored beta-lactamase family, type II toxin-antitoxin system, and stress response proteins, while the other possessed a Type VII secretion system; PopCOGenT p<\/jats:italic>\u2009&lt;\u20090.05).<\/jats:p><\/jats:sec>Discussion<\/jats:title>Overall, this study leverages all publicly available Macrococcus<\/jats:italic> genomes in addition to newly sequenced genomes from South Africa to identify genomic elements associated with AMR or virulence potential, which can be queried in future experiments.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2023.1181376","type":"journal-article","created":{"date-parts":[[2023,7,21]],"date-time":"2023-07-21T08:54:32Z","timestamp":1689929672000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":20,"title":["Genus-wide genomic characterization of Macrococcus: insights into evolution, population structure, and functional potential"],"prefix":"10.3389","volume":"14","author":[{"given":"Laura M.","family":"Carroll","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rian","family":"Pierneef","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thendo","family":"Mafuna","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kudakwashe","family":"Magwedere","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Itumeleng","family":"Matle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,7,20]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1600","DOI":"10.1093\/bioinformatics\/btl140","article-title":"Improved scoring of functional groups from gene expression data by decorrelating GO graph structure","volume":"22","author":"Alexa","year":"2006","journal-title":"Bioinformatics"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1186\/s12917-022-03297-2","article-title":"A prevalence and molecular characterization of novel pathogenic strains of Macrococcus caseolyticus isolated from external wounds of donkeys in Khartoum state -Sudan","volume":"18","author":"Ali","year":"2022","journal-title":"BMC Vet. Res."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1975","DOI":"10.1128\/JCM.00081-16","article-title":"Practical value of food pathogen traceability through building a whole-genome sequencing network and database","volume":"54","author":"Allard","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1016\/j.cell.2019.06.033","article-title":"A reverse ecology approach based on a biological definition of microbial populations","volume":"178","author":"Arevalo","year":"2019","journal-title":"Cell"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"W29","DOI":"10.1093\/nar\/gkab335","article-title":"antiSMASH 6.0: improving cluster detection and comparison capabilities","volume":"49","author":"Blin","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"690","DOI":"10.3390\/pathogens11060690","article-title":"What is Anthrax?","volume":"11","author":"Bower","year":"2022","journal-title":"Pathogens"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"e0258262","DOI":"10.1371\/journal.pone.0258262","article-title":"An economic evaluation of the whole genome sequencing source tracking program in the U.S","volume":"16","author":"Brown","year":"2021","journal-title":"PLoS One"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1089\/fpd.2019.2662","article-title":"Use of whole-genome sequencing for food safety and public health in the United States","volume":"16","author":"Brown","year":"2019","journal-title":"Foodborne Pathog. Dis."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref12","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":"ref13","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":"ref14","first-page":"2021.2005.2003.442509","article-title":"Accurate de novo identification of biosynthetic gene clusters with GECCO","author":"Carroll","year":"2021","journal-title":"bioRxiv"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"e00034","DOI":"10.1128\/mBio.00034-20","article-title":"Proposal of a taxonomic nomenclature for the Bacillus cereus group which reconciles genomic definitions of bacterial species with clinical and industrial phenotypes","volume":"11","author":"Carroll","year":"2020","journal-title":"MBio"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"2531","DOI":"10.1093\/jac\/dkz260","article-title":"Macrococcus canis contains recombinogenic methicillin resistance elements and the mecB plasmid found in Staphylococcus aureus","volume":"74","author":"Chanchaithong","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database","author":"Chaumeil","year":"2019","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1111\/vde.12474","article-title":"Macrococcus canis and M. caseolyticus in dogs: occurrence, genetic diversity and antibiotic resistance","volume":"28","author":"Cotting","year":"2017","journal-title":"Vet. Dermatol."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1093\/infdis\/18.5.437","article-title":"The Bacteria of Milk Freshly Drawn From Normal Udders","volume":"18","author":"Evans","year":"1916","journal-title":"J. Infect. Dis."},{"key":"ref22","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":"ref23","doi-asserted-by":"publisher","first-page":"e00483","DOI":"10.1128\/AAC.00483-19","article-title":"Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates","volume":"63","author":"Feldgarden","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1186\/s13073-021-00934-7","article-title":"An implementation science approach to evaluating pathogen whole genome sequencing in public health","volume":"13","author":"Ferdinand","year":"2021","journal-title":"Genome Med."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"e1277","DOI":"10.1093\/cid\/ciac726","article-title":"Clinical implementation of routine whole-genome sequencing for hospital infection control of multi-drug resistant pathogens","volume":"76","author":"Forde","year":"2023","journal-title":"Clin. Infect. Dis."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"590","DOI":"10.3390\/antibiotics9090590","article-title":"Methicillin-resistant Macrococcus bohemicus encoding a divergent SCCmecB element","volume":"9","author":"Foster","year":"2020","journal-title":"Antibiotics"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"ref28","first-page":"1207.3907","article-title":"Haplotype-based variant detection from short-read sequencing","author":"Garrison","year":"2012","journal-title":"arXiv"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1099\/ijsem.0.001673","article-title":"Macrococcus canis sp. nov., a skin bacterium associated with infections in dogs","volume":"67","author":"Gobeli Brawand","year":"2017","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"4577","DOI":"10.1128\/AAC.05064-14","article-title":"First staphylococcal cassette chromosome mec containing a mecB-carrying gene complex independent of transposon Tn6045 in a Macrococcus canis isolate from a canine infection","volume":"59","author":"Gomez-Sanz","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref31","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":"ref32","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1038\/s41467-019-08853-3","article-title":"Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage","volume":"10","author":"Hendriksen","year":"2019","journal-title":"Nat. Commun."},{"key":"ref33","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":"ref34","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":"ref35","doi-asserted-by":"publisher","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":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1186\/1471-2105-11-595","article-title":"BIGSdb: scalable analysis of bacterial genome variation at the population level","volume":"11","author":"Jolley","year":"2010","journal-title":"BMC Bioinform."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"105125","DOI":"10.1016\/j.meegid.2021.105125","article-title":"Methicillin-resistant Macrococcus canis in a human wound","volume":"96","author":"Jost","year":"2021","journal-title":"Infect. Genet. Evol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref39","doi-asserted-by":"publisher","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":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"D454","DOI":"10.1093\/nar\/gkz882","article-title":"MIBiG 2.0: a repository for biosynthetic gene clusters of known function","volume":"48","author":"Kautsar","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.005245","article-title":"Macrococcus armenti sp. nov., a novel bacterium isolated from the skin and nasal cavities of healthy pigs and calves","volume":"72","author":"Keller","year":"2022","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1073\/pnas.78.1.454","article-title":"Estimation of evolutionary distances between homologous nucleotide sequences","volume":"78","author":"Kimura","year":"1981","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"D73","DOI":"10.1093\/nar\/gkv1226","article-title":"Assembly: a resource for assembled genomes at NCBI","volume":"44","author":"Kitts","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref44","first-page":"859","article-title":"Delimiting the genus Staphylococcus through description of Macrococcus caseolyticus gen. nov., comb. nov. and Macrococcus equipercicus sp. nov., and Macrococcus bovicus sp. no. and Macrococcus carouselicus sp. nov","volume-title":"Int. J. Syst. Bacteriol.","author":"Kloos","year":"1998"},{"key":"ref45","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":"ref46","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.1099\/ijsem.0.000760","article-title":"OrthoANI: an improved algorithm and software for calculating average nucleotide identity","volume":"66","author":"Lee","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"ref49","first-page":"1303.3997","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013","journal-title":"arXiv"},{"key":"ref50","author":"Li","year":"2019"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"D687","DOI":"10.1093\/nar\/gky1080","article-title":"VFDB 2019: a comparative pathogenomic platform with an interactive web interface","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"e1000715","DOI":"10.1371\/journal.ppat.1000715","article-title":"Staphylococcus aureus Panton-Valentine leukocidin is a very potent cytotoxic factor for human neutrophils","volume":"6","author":"Loffler","year":"2010","journal-title":"PLoS Pathog."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"e000191","DOI":"10.1099\/mgen.0.000191","article-title":"Genome analysis of methicillin resistance in Macrococcus caseolyticus from dairy cattle in England and Wales","volume":"4","author":"Macfadyen","year":"2018","journal-title":"Microb. Genom."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"1647","DOI":"10.1099\/ijs.0.02683-0","article-title":"Macrococcus brunensis sp. nov., Macrococcus hajekii sp. nov. and Macrococcus lamae sp. nov., from the skin of llamas","volume":"53","author":"Mannerova","year":"2003","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"1178","DOI":"10.3389\/fmicb.2018.01178","article-title":"Description and comparative genomics of Macrococcus caseolyticus subsp. hominis subsp. nov., Macrococcus goetzii sp. nov., Macrococcus epidermidis sp. nov., and Macrococcus bohemicus sp. nov., novel macrococci from human clinical material with virulence potential and suspected uptake of foreign DNA by natural transformation","volume":"9","author":"Maslanova","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"e00343","DOI":"10.1128\/MRA.00343-19","article-title":"Draft genome sequences of Macrococcus caseolyticus, Macrococcus canis, Macrococcus bohemicus, and Macrococcus goetzii","volume":"8","author":"Mazhar","year":"","journal-title":"Microbiol. Resour. Announc."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"e00343","DOI":"10.1128\/MRA.00344-19","article-title":"Draft genome sequences of the type strains of six Macrococcus species","volume":"8","author":"Mazhar","year":"","journal-title":"Microbiol. Resour. Announc."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/bs.aambs.2018.05.002","article-title":"The genus Macrococcus: an insight into its biology, evolution, and relationship with Staphylococcus","volume":"105","author":"Mazhar","year":"2018","journal-title":"Adv. Appl. Microbiol."},{"key":"ref62","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 Bioinform."},{"key":"ref63","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":"ref64","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1038\/nmeth.2575","article-title":"Accurate and universal delineation of prokaryotic species","volume":"10","author":"Mende","year":"2013","journal-title":"Nat. Methods"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.1038\/s41467-019-08844-4","article-title":"Microbial abundance, activity and population genomic profiling with mOTUs2","volume":"10","author":"Milanese","year":"2019","journal-title":"Nat. Commun."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1093\/molbev\/mst024","article-title":"Ultrafast approximation for phylogenetic bootstrap","volume":"30","author":"Minh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","article-title":"Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis","volume":"399","author":"Murray","year":"2022","journal-title":"Lancet"},{"key":"ref68","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1038\/s41589-019-0400-9","article-title":"A computational framework to explore large-scale biosynthetic diversity","volume":"16","author":"Navarro-Munoz","year":"2020","journal-title":"Nat. Chem. Biol."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"29063","DOI":"10.1073\/pnas.2013694117","article-title":"The role of \"spillover\" in antibiotic resistance","volume":"117","author":"Olesen","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"108356","DOI":"10.1016\/j.ijfoodmicro.2019.108356","article-title":"Environmental heterogeneity of Staphylococcus species from alkaline fermented foods and associated toxins and antimicrobial resistance genetic elements","volume":"311","author":"Ouoba","year":"2019","journal-title":"Int. J. Food Microbiol."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"e000056","DOI":"10.1099\/mgen.0.000083","article-title":"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments","volume":"2","author":"Page","year":"2016","journal-title":"Microb. Genom."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","article-title":"APE: Analyses of Phylogenetics and Evolution in R language","volume":"20","author":"Paradis","year":"2004","journal-title":"Bioinformatics"},{"key":"ref74","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Paradis","year":"2019","journal-title":"Bioinformatics"},{"key":"ref75","doi-asserted-by":"publisher","first-page":"D785","DOI":"10.1093\/nar\/gkab776","article-title":"GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy","volume":"50","author":"Parks","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref76","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":"ref77","doi-asserted-by":"publisher","first-page":"5607","DOI":"10.1099\/ijsem.0.004332","article-title":"List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ","volume":"70","author":"Parte","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref78","doi-asserted-by":"publisher","first-page":"166","DOI":"10.3389\/fcimb.2017.00166","article-title":"Staphylococcus aureus manipulates innate immunity through own and host-expressed proteases","volume":"7","author":"Pietrocola","year":"2017","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref79","doi-asserted-by":"publisher","first-page":"4296","DOI":"10.1128\/JCM.39.12.4296-4301.2001","article-title":"Rapid and accurate species-level identification of coagulase-negative staphylococci by using the sodA gene as a target","volume":"39","author":"Poyart","year":"2001","journal-title":"J. Clin. Microbiol."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2--approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"ref81","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"ref82","volume-title":"\"R: A language and environment for statistical computing\". 4.1.2 ed","year":"2021"},{"key":"ref83","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1007\/s00284-020-02281-z","article-title":"Technological applications of Macrococcus caseolyticus and its impact on food safety","volume":"78","author":"Ramos","year":"2021","journal-title":"Curr. Microbiol."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1093\/clinchem\/hvaa172","article-title":"Genomic prediction of antimicrobial resistance: ready or not, here it comes!","volume":"66","author":"Ransom","year":"2020","journal-title":"Clin. Chem."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1016\/j.cmi.2017.11.001","article-title":"Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology","volume":"24","author":"Rossen","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"ref86","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baaa062","article-title":"NCBI Taxonomy: a comprehensive update on curation, resources and tools","author":"Schoch","year":"2020","journal-title":"Database 2020: baaa062"},{"key":"ref87","doi-asserted-by":"publisher","first-page":"43797","DOI":"10.1038\/srep43797","article-title":"Novel methicillin resistance gene mecD in clinical Macrococcus caseolyticus strains from bovine and canine sources","volume":"7","author":"Schwendener","year":"2017","journal-title":"Sci. Rep."},{"key":"ref88","doi-asserted-by":"publisher","first-page":"1796","DOI":"10.1093\/jac\/dkac107","article-title":"The bla and mec families of beta-lactam resistance genes in the genera Macrococcus, Mammaliicoccus and Staphylococcus: an in-depth analysis with emphasis on Macrococcus","volume":"77","author":"Schwendener","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"ref89","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":"ref90","article-title":"\"samclip: filter SAM file for soft and hard clipped alignments\". 0.2 ed","author":"Seemann","year":"2019"},{"key":"ref91","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/S1473-3099(12)70238-4","article-title":"The role of the Panton-Valentine leucocidin toxin in staphylococcal disease: a systematic review and meta-analysis","volume":"13","author":"Shallcross","year":"2013","journal-title":"Lancet Infect. Dis."},{"key":"ref92","first-page":"113","article-title":"Rapid neighbour-joining","volume-title":"Algorithms in bioinformatics. 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Evol."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s13059-018-1540-z","article-title":"SKESA: strategic k-mer extension for scrupulous assemblies","volume":"19","author":"Souvorov","year":"2018","journal-title":"Genome Biol."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"ref97","doi-asserted-by":"publisher","first-page":"808","DOI":"10.3389\/fmicb.2017.00808","article-title":"The public health impact of a publically available, environmental database of microbial genomes","volume":"8","author":"Stevens","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref98","doi-asserted-by":"publisher","first-page":"2202","DOI":"10.1093\/bioinformatics\/btv112","article-title":"Unified representation of genetic variants","volume":"31","author":"Tan","year":"2015","journal-title":"Bioinformatics"},{"key":"ref99","first-page":"57","article-title":"Some probabilistic and statistical problems in the analysis of DNA sequences","volume":"17","author":"Tavar\u00e9","year":"1986","journal-title":"Lect. Math. Life Sci."},{"key":"ref100","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1016\/j.mib.2008.09.006","article-title":"Comparative genomics: the bacterial pan-genome","volume":"11","author":"Tettelin","year":"2008","journal-title":"Curr. Opin. Microbiol."},{"key":"ref101","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1038\/nrmicro3521","article-title":"Staphylococcal manipulation of host immune responses","volume":"13","author":"Thammavongsa","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"ref102","doi-asserted-by":"publisher","first-page":"D330","DOI":"10.1093\/nar\/gky1055","article-title":"The Gene Ontology Resource: 20 years and still GOing strong","volume":"47","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"93","DOI":"10.12688\/wellcomeopenres.14694.1","article-title":"RhierBAPS: an R implementation of the population clustering algorithm hierBAPS","volume":"3","author":"Tonkin-Hill","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref104","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1186\/s13059-020-02090-4","article-title":"Producing polished prokaryotic pangenomes with the Panaroo pipeline","volume":"21","author":"Tonkin-Hill","year":"2020","journal-title":"Genome Biol."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"1963","DOI":"10.4315\/0362-028X.JFP-18-069","article-title":"Molecular characterization and antibiotic resistance of foodborne pathogens in street-vended ready-to-eat meat sold in South Africa","volume":"81","author":"Tshipamba","year":"2018","journal-title":"J. Food Prot."},{"key":"ref106","doi-asserted-by":"publisher","first-page":"3167","DOI":"10.1111\/j.1742-4658.2008.06470.x","article-title":"The metalloprotease PrtV from Vibrio cholerae","volume":"275","author":"Vaitkevicius","year":"2008","journal-title":"FEBS J."},{"key":"ref107","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant graphics for data analysis","author":"Wickham","year":"2016"},{"key":"ref108","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1093\/genetics\/139.2.993","article-title":"A space-time process model for the evolution of DNA sequences","volume":"139","author":"Yang","year":"1995","journal-title":"Genetics"},{"key":"ref109","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"},{"key":"ref110","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1186\/s12866-022-02679-8","article-title":"Characteristics of population structure, antimicrobial resistance, virulence factors, and morphology of methicillin-resistant Macrococcus caseolyticus in global clades","volume":"22","author":"Zhang","year":"2022","journal-title":"BMC Microbiol."},{"key":"ref111","doi-asserted-by":"publisher","first-page":"1667","DOI":"10.1101\/gr.260828.120","article-title":"Accurate reconstruction of bacterial pan- and core genomes with PEPPAN","volume":"30","author":"Zhou","year":"2020","journal-title":"Genome Res."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1181376\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,21]],"date-time":"2023-07-21T08:54:52Z","timestamp":1689929692000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1181376\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,20]]},"references-count":111,"alternative-id":["10.3389\/fmicb.2023.1181376"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2023.1181376","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,7,20]]},"article-number":"1181376"}}