Strain CCM 2573 is a Gram-positive bacterium that has been intensively studied in the past due to its distinct chemotaxonomic properties, but its reliable taxonomic classification has not been satisfactorily clarified. Whole-genome sequencing and comparative genomic analyses performed in this study revealed that the strain belongs to the Macrococcus caseolyticus phylogenetic clade. Genome-to-genome comparisons confirmed the closest relationship to the type strains of M. caseolyticus subsp. hominis CCM 7927T and M. caseolyticus subsp. caseolyticus DSM 20597T. However, the strain harbored unique genomic elements distinguishing it from its nearest phylogenetic neighbors. Its accessory genome contains dozens of insertion sequences, a 92-kbp composite transposon with unique palindromic repeat loci associated with a CRISPR-Cas adaptive immune system, a pseudo-staphylococcal chromosome cassette, and several additional genomic islets. Unlike other macrococci, strain CCM 2573 exhibits a specific peptidoglycan composition (L-Lys-Gly₂-Ser₂-Gly) and shows a higher phylogenetic divergence of aminoacyltransferases (FemABX) involved in interpeptide bridge synthesis. In addition, it reveals distinct biochemical characteristics from both subspecies of M. caseolyticus, particularly in its ability to produce acid from galactose, cellobiose, melezitose, and turanose, as well as in its susceptibility to novobiocin. The MALDI-TOF mass spectra enable differentiation of the strain from other type strains of the genus Macrococcus. The results of polyphasic taxonomy obtained in this study showed that strain CCM 2573 belongs to the species M. caseolyticus, but it is distinct from both validly named M. caseolyticus subspecies. We propose to assign the analyzed strain as a new subspecies, Macrococcus caseolyticus subsp. lactis subsp. nov. The type strain is CCM 2573T (= DSM 20227T).

Central European Institute of Technology Masaryk University Brno 625 00 Czech Republic

Department of Experimental Biology Czech Collection of Microorganisms Faculty of Science Masaryk University Brno 625 00 Czech Republic

Department of Experimental Biology Section of Genetics and Molecular Biology Faculty of Science Masaryk University Brno 611 37 Czech Republic

Institute of Microbiology Czech Academy of Sciences BIOCEV Vestec 252 50 Czech Republic

Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures 38124 Braunschweig Germany

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Archibald AR, Stafford GH (1972) A polymer of N-acetylglucosamine 1-phosphate in the wall of Staphylococcus lactis 2102. Biochem J 130:681–690. https://doi.org/10.1042/bj1300681 PubMed DOI PMC

Archibald AR, Baddiley J, Button D, Heptinstall S, Stafford GH (1968) Occurrence of polymers containing N-acetylglucosamine l-phosphate in bacterial walls. Nature 219:855–856. https://doi.org/10.1038/219855a0 PubMed DOI

Archibald AR, Coapes HE, Stafford GH (1969) The action of dilute alkali on bacterial cell walls. Biochem J 113:899–900. https://doi.org/10.1042/bj1130899 PubMed DOI PMC

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75 PubMed DOI PMC

Baba T, Kuwahara-Arai K, Uchiyama I, Takeuchi F, Ito T, Hiramatsu K (2009) Complete genome sequence of Macrococcus caseolyticus strain JCSCS5402, reflecting the ancestral genome of the human-pathogenic staphylococci. J Bacteriol 191:1180–1190. https://doi.org/10.1128/JB.01058-08 PubMed DOI

Baird-Parker AC (1963) A classification of micrococci and staphylococci based on physiological and biochemical tests. J Gen Microbiol 30:409–427. https://doi.org/10.1099/00221287-30-3-409 PubMed DOI

Baird-Parker AC (1965) The classification of staphylococci and micrococci from world-wide sources. J Gen Microbiol 38:363–387. https://doi.org/10.1099/00221287-38-3-363 PubMed DOI

Belhout C, Wang F, Rossano A, Collaud A, Fernandez JE, Marchionatti E, Keller JE, Overesch G, Kaessmeyer S, Schwendener S, Perreten V (2025) Macrococcus animalis sp. nov. and Macrococcus equi sp. nov., isolated from different animals’ origins. Int J Syst Evol Microbiol 75:006861. https://doi.org/10.1099/ijsem.0.006861 DOI

Bello S, Mudassir SH, Rudra B, Gupta RS (2023) Phylogenomic and molecular markers based studies on Staphylococcaceae and Gemella species. Proposals for an emended family Staphylococcaceae and three new families (Abyssicoccaceae fam. nov., Salinicoccaceae fam. nov. and Gemellaceae fam. nov.) harboring four new genera, Lacicoccus gen. nov., Macrococcoides gen. nov., Gemelliphila gen. nov., and Phocicoccus gen. nov. Antonie Van Leeuwenhoek 116:937–973. https://doi.org/10.1007/s10482-023-01857-6

Bertelli C, Laird MR, Williams KP, Simon Fraser University Research, Computing G, Lau BY, Hoad G, Winsor GL, Brinkman FSL (2017) IslandViewer 4: expanded prediction of genomic Islands for larger-scale datasets. Nucleic Acids Res 45:W30–W35. https://doi.org/10.1093/nar/gkx343 PubMed DOI PMC

Brooks D, Baddiley J (1969) The mechanism of biosynthesis and direction of chain extension of a poly-(N-acetylglucosamine 1-phosphate) from the walls of Staphylococcus lactis N.C.T.C. 2102. Biochem J 113:635–642. https://doi.org/10.1042/bj1130635 PubMed DOI PMC

Carroll LM, Pierneef R, Mafuna T, Magwedere K, Matle I (2023) Genus-wide genomic characterization of Macrococcus: insights into evolution, population structure, and functional potential. Front Microbiol 14:1181376. https://doi.org/10.3389/fmicb.2023.1181376 PubMed DOI PMC

Chalita M, Kim YO, Park S, Oh HS, Cho JH, Moon J, Baek N, Moon C, Lee K, Yang J, Nam GG, Jung Y, Na SI, Bailey MJ, Chun J (2024) EzBioCloud: a genome-driven database and platform for microbiome identification and discovery. Int J Syst Evol Microbiol 74:006421. https://doi.org/10.1099/ijsem.0.006421 PubMed DOI PMC

Chanchaithong P, Perreten V, Schwendener S (2019) Macrococcus canis contains recombinogenic methicillin resistance elements and the mecB plasmid found in Staphylococcus aureus. J Antimicrob Chemother 74:2531–2536. https://doi.org/10.1093/jac/dkz260 PubMed DOI

Chaurasia P, Pratap S, von Ossowski I, Palva A, Krishnan V (2016) New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit. Sci Rep 6:28664. https://doi.org/10.1038/srep28664 PubMed DOI PMC

Chung YS, Dubnau D (1998) All seven comG open reading frames are required for DNA binding during transformation of competent Bacillus subtilis. J Bacteriol 180:41–45. https://doi.org/10.1128/JB.180.1.41-45.1998 PubMed DOI PMC

Cobbe N, Heck MM (2004) The evolution of SMC proteins: phylogenetic analysis and structural implications. Mol Biol Evol 21:332–347. https://doi.org/10.1093/molbev/msh023 PubMed DOI

Cotting K, Strauss C, Rodriguez-Campos S, Rostaher A, Fischer NM, Roosje PJ, Favrot C, Perreten V (2017) Macrococcus canis and M. caseolyticus in dogs: occurrence, genetic diversity and antibiotic resistance. Vet Dermatol 28:559–563. https://doi.org/10.1111/vde.12474 PubMed DOI

Cury J, Touchon M, Rocha EPC (2017) Integrative and conjugative elements and their hosts: composition, distribution and organization. Nucleic Acids Res 45:8943–8956. https://doi.org/10.1093/nar/gkx607 PubMed DOI PMC

Cury J, Oliveira PH, de la Cruz F, Rocha EPC (2018) Host range and genetic plasticity explain the coexistence of integrative and extrachromosomal mobile genetic elements. Mol Biol Evol 35:2230–2239. https://doi.org/10.1093/molbev/msy123 PubMed DOI PMC

Dalia TN, Machouri M, Lacrouts C, Fauconnet Y, Guerois R, Andreani J, Radicella JP, Dalia AB (2025) DprA recruits comm to facilitate recombination during natural transformation in Gram-negative bacteria. Proc Natl Acad Sci U S A 122:e2421764122. https://doi.org/10.1073/pnas.2421764122 PubMed DOI PMC

Freiwald A, Sauer S (2009) Phylogenetic classification and identification of bacteria by mass spectrometry. Nat Protoc 4:732–742. https://doi.org/10.1038/nprot.2009.37 PubMed DOI

Gobeli Brawand S, Cotting K, Gómez-Sanz E, Collaud A, Thomann A, Brodard I, Rodriguez-Campos S, Strauss C, Perreten V (2017) Macrococcus canis sp. nov., a skin bacterium associated with infections in dogs. Int J Syst Evol Microbiol 67:621–626. https://doi.org/10.1099/ijsem.0.001673 PubMed DOI

Gómez-Sanz E, Schwendener S, Thomann A, Gobeli Brawand S, Perreten V (2015) First Staphylococcal Cassette Chromosome mec containing a mecB-carrying gene complex independent of transposon Tn6045 in a Macrococcus canis isolate from a canine infection. Antimicrob Agents Chemother 59:4577–4583. https://doi.org/10.1128/AAC.05064-14 PubMed DOI PMC

Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57. https://doi.org/10.1093/nar/gkm360 PubMed DOI PMC

Hancock IC, Baddiley J (1985) Biosynthesis of the bacterial envelope polymers teichoic acid and teichuronic acid. The Enzymes of Biological Membranes, Vol 2 Biosynthesis and Metabolism, Springer, New York, NY, pp 279–307

Hansen CM, Meixell BW, Van Hemert C, Hare RF, Hueffer K (2015) Microbial infections are associated with embryo mortality in arctic-nesting geese. Appl Environ Microbiol 81:5583–5592. https://doi.org/10.1128/AEM.00706-15 PubMed DOI PMC

Hegde SS, Shrader TE (2001) FemABX family members are novel nonribosomal peptidyltransferases and important pathogen-specific drug targets. J Biol Chem 276:6998–7003. https://doi.org/10.1074/jbc.M008591200 PubMed DOI

Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9:5114. https://doi.org/10.1038/s41467-018-07641-9 PubMed DOI PMC

Jost G, Schwendener S, Liassine N, Perreten V (2021) Methicillin-resistant Macrococcus canis in a human wound. Infect Genet Evol 96:105125. https://doi.org/10.1016/j.meegid.2021.105125 PubMed DOI

Keller JE, Schwendener S, Overesch G, Perreten V (2022) Macrococcus armenti sp. nov., a novel bacterium isolated from the skin and nasal cavities of healthy pigs and calves. Int J Syst Evol Microbiol 72:005245. https://doi.org/10.1099/ijsem.0.005245 DOI

Kim J, Na SI, Kim D, Chun J (2021) UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 59:609–615. https://doi.org/10.1007/s12275-021-1231-4 PubMed DOI

Kloos WE, Ballard DN, George CG, Webster JA, Hubner RJ, Ludwig W, Schleifer KH, Fiedler F, Schubert K (1998) Delimiting the genus Staphylococcus through description of Macrococcus caseolyticus gen. nov., comb. nov. and Macrococcus equipercicus sp. nov., Macrococcus bovicus sp. nov. and Macrococcus carouselicus sp. nov. Int J Syst Bacteriol 48:859–877. https://doi.org/10.1099/00207713-48-3-859 PubMed DOI

Kovařovic V, Sedláček I, Petráš P, Králová S, Mašlaňová I, Švec P, Neumann-Schaal M, Botka T, Gelbíčová T, Staňková E, Doškař J, Pantůček R (2022) Staphylococcus ratti sp. nov. isolated from a lab rat. Pathogens 11:51. https://doi.org/10.3390/pathogens11010051 PubMed DOI PMC

Kovařovic V, Finstrlová A, Sedláček I, Petráš P, Švec P, Mašlaňová I, Neumann-Schaal M, Šedo O, Botka T, Staňková E, Doškař J, Pantůček R (2023) Staphylococcus brunensis sp. nov. Isolated from human clinical specimens with a Staphylococcal Cassette Chromosome-related genomic island outside of the rlmH gene bearing the ccrDE recombinase gene complex. Microbiol Spectr 11:e01342–23. https://doi.org/10.1128/spectrum.01342-23 PubMed DOI PMC

Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096 PubMed DOI PMC

Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923 PubMed DOI PMC

Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094–3100. https://doi.org/10.1093/bioinformatics/bty191 PubMed DOI PMC

Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, Coulouris G, Chitsaz F, Derbyshire MK, Durkin AS, Gonzales NR, Gwadz M, Lanczycki CJ, Song JS, Thanki N, Wang J, Yamashita RA, Yang M, Zheng C, Marchler-Bauer A, Thibaud-Nissen F (2021) RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res 49:D1020–D1028. https://doi.org/10.1093/nar/gkaa1105 PubMed DOI

Madhaiyan M, Wirth JS, Saravanan VS (2020) Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae. Int J Syst Evol Microbiol 70:5926–5936. https://doi.org/10.1099/ijsem.0.004498 PubMed DOI

Madonna AJ, Basile F, Ferrer I, Meetani MA, Rees JC, Voorhees KJ (2000) On-probe sample pretreatment for the detection of proteins above 15 KDa from whole cell bacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 14:2220–2229. https://doi.org/10.1002/1097-0231(20001215)14:23%3C2220::AID-RCM155%3E3.0.CO;2-4 PubMed DOI

Mašlaňová I, Wertheimer Z, Sedláček I, Švec P, Indráková A, Kovařovic V, Schumann P, Spröer C, Králová S, Šedo O, Krištofová L, Vrbovská V, Füzik T, Petráš P, Zdráhal Z, Růžičková V, Doškař J, Pantůček R (2018) 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. Front Microbiol 9:1178. https://doi.org/10.3389/fmicb.2018.01178 PubMed DOI PMC

Mašlaňová I, Kovařovic V, Botka T, Švec P, Sedláček I, Šedo O, Finstrlová A, Neumann-Schaal M, Kirstein S, Schwendener S, Staňková E, Rovňáková K, Petráš P, Doškař J, Perreten V, Pantůček R (2025) Evidence of in vitro mecB-mediated beta-lactam antibiotic resistance transfer to Staphylococcus aureus from Macrococcus psychrotolerans sp. nov., a psychrophilic bacterium from food-producing animals and human clinical specimens. Appl Environ Microbiol 91:e01652–24. https://doi.org/10.1128/aem.01652-24 PubMed DOI PMC

Mazhar S, Hill C, McAuliffe O (2018) The genus Macrococcus: an insight into its biology, evolution, and relationship with Staphylococcus. Adv Appl Microbiol 105:1–50. https://doi.org/10.1016/bs.aambs.2018.05.002 PubMed DOI

Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M (2021) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 49:gkab902. https://doi.org/10.1093/nar/gkab902 DOI

Musa AO, Santona A, Desogi MA, Fiamma M, Adam A, Ibrahim DH, Hajedriss FA, Almake FA, Faki MT, Awadap MI, Taviani E, Rubino S, Paglietti B (2025) Macrococcus caseolyticus in early-onset neonatal sepsis, Kassala, Sudan. J Infect Dev Ctries 19:462–466. https://doi.org/10.3855/jidc.21090 PubMed DOI

Muschiol S, Balaban M, Normark S, Henriques-Normark B (2015) Uptake of extracellular DNA: competence induced pili in natural transformation of Streptococcus pneumoniae. BioEssays 37:426–435. https://doi.org/10.1002/bies.201400125 PubMed DOI PMC

Naas T, Blot M, Fitch WM, Arber W (1994) Insertion sequence-related genetic variation in resting Escherichia coli K-12. Genetics 136:721–730. https://doi.org/10.1093/genetics/136.3.721 PubMed DOI PMC

Olasz F, Stalder R, Arber W (1993) Formation of the tandem repeat (IS30) PubMed DOI

Pantůček R, Švec P, Dajcs JJ, Machová I, Černohlavková J, Šedo O, Gelbíčová T, Mašlaňová I, Doškař J, Zdráhal Z, Růžičková V, Sedláček I (2013) Staphylococcus petrasii sp. nov. including S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov., isolated from human clinical specimens and human ear infections. Syst Appl Microbiol 36:90–95. https://doi.org/10.1016/j.syapm.2012.11.004 PubMed DOI

Pohja MS (1960) Micrococci in fermented meat products: classification and description of 171 different strains. Acta Agralia Fennica 96:1–80

Pohja MS, Gyllenberg HG (1962) Numerical taxonomy of micrococci of fermented meat origin. J Appl Bacteriol 25:341–351. https://doi.org/10.1111/j.1365-2672.1962.tb04747.x DOI

Rohrer S, Berger-Bachi B (2003) FemABX peptidyl transferases: a link between branched-chain cell wall peptide formation and beta-lactam resistance in gram-positive Cocci. Antimicrob Agents Chemother 47:837–846. https://doi.org/10.1128/AAC.47.3.837-846.2003 PubMed DOI PMC

Russel J, Pinilla-Redondo R, Mayo-Munoz D, Shah SA, Sorensen SJ (2020) CRISPRCasTyper: automated identification, annotation, and classification of CRISPR-Cas loci. CRISPR J 3:462–469. https://doi.org/10.1089/crispr.2020.0059 PubMed DOI

Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454 PubMed DOI

Sansevere EA, Robinson DA (2017) Staphylococci on ICE: overlooked agents of horizontal gene transfer. Mob Genet Elem 7:1–10. https://doi.org/10.1080/2159256X.2017.1368433 DOI

Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty Acids, MIDI Technical Note 101. MIDI Inc., Newark, DE

Schiffer CJ, Ehrmann MA (2025) Macrococcus Capreoli sp. nov., a new fosfomycin resistant species isolated from feces and nasal swabs of deer. Syst Appl Microbiol 48:126620. https://doi.org/10.1016/j.syapm.2025.126620 PubMed DOI

Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36: 407–477. https://doi.org/10.1128/br.36.4.407-477.1972 PubMed DOI PMC

Schumann P (2011) Peptidoglycan structure. Methods Microbiol 38:101–129. https://doi.org/10.1016/b978-0-12-387730-7.00005-x DOI

Schwendener S, Perreten V (2022) 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. J Antimicrob Chemother 77:1796–1827. https://doi.org/10.1093/jac/dkac107 PubMed DOI

Schwendener S, Cotting K, Perreten V (2017) Novel methicillin resistance gene mecD in clinical Macrococcus caseolyticus strains from bovine and canine sources. Sci Rep 7:43797. https://doi.org/10.1038/srep43797 PubMed DOI PMC

Shaw C, Stitt JM, Cowan ST (1951) Staphylococci and their classification. J Gen Microbiol 5:1010–1023. https://doi.org/10.1099/00221287-5-5-1010 PubMed DOI

Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34:D32–D36. https://doi.org/10.1093/nar/gkj014 PubMed DOI

Skerman VBD, Sneath PHA, McGowan V (1980) Approved lists of bacterial names. Int J Syst Evol Microbiol 30:225–420. https://doi.org/10.1099/00207713-30-1-225 DOI

Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27:1009–1010. https://doi.org/10.1093/bioinformatics/btr039 PubMed DOI PMC

Švec P, Pantůček R, Petráš P, Sedláček I, Nováková D (2010) Identification of Staphylococcus spp. using (GTG) PubMed DOI

Takeuchi F, Watanabe S, Baba T, Yuzawa H, Ito T, Morimoto Y, Kuroda M, Cui L, Takahashi M, Ankai A, Baba S, Fukui S, Lee JC, Hiramatsu K (2005) Whole-genome sequencing of Staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of human-colonizing staphylococcal species. J Bacteriol 187:7292–7308. https://doi.org/10.1128/JB.187.21.7292-7308.2005 PubMed DOI PMC

Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526. https://doi.org/10.1093/oxfordjournals.molbev.a040023 PubMed DOI

Tesson F, Herve A, Mordret E, Touchon M, d’Humieres C, Cury J, Bernheim A (2022) Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat Commun 13:2561. https://doi.org/10.1038/s41467-022-30269-9 PubMed DOI PMC

Tsubakishita S, Kuwahara-Arai K, Baba T, Hiramatsu K (2010) Staphylococcal Cassette Chromosome mec-like element in Macrococcus caseolyticus. Antimicrob Agents Chemother 54:1469–1475. https://doi.org/10.1128/AAC.00575-09 PubMed DOI PMC

Vieira S, Huber KJ, Neumann-Schaal M, Geppert A, Luckner M, Wanner G, Overmann J (2021) Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil. Int J Syst Evol Microbiol 71:004631. https://doi.org/10.1099/ijsem.0.004631 DOI

Wang M, Goh YX, Tai C, Wang H, Deng Z, Ou HY (2022) VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens. Nucleic Acids Res 50:W768–W773. https://doi.org/10.1093/nar/gkac321 PubMed DOI PMC

Wick RR, Holt KE (2022) Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLoS Comput Biol 18:e1009802. https://doi.org/10.1371/journal.pcbi.1009802 PubMed DOI PMC

Wick RR, Judd LM, Cerdeira LT, Hawkey J, Meric G, Vezina B, Wyres KL, Holt KE (2021) Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biol 22:266. https://doi.org/10.1186/s13059-021-02483-z PubMed DOI PMC

WingettSW, Andrews S (2018) FastQ screen: a tool for multi-genome mapping and quality control. F1000Research 7:1338. https://doi.org/10.12688/f1000research.15931.2

Wishart DS, Han S, Saha S, Oler E, Peters H, Grant JR, Stothard P, Gautam V (2023) PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res 51:W443–W450. https://doi.org/10.1093/nar/gkad382 PubMed DOI PMC