The genus Macrococcus is a close relative of the genus Staphylococcus. Whilst staphylococci are widespread as human pathogens, macrococci have not yet been reported from human clinical specimens. Here we investigated Gram-positive and catalase-positive cocci recovered from human clinical material and identified as Macrococcus sp. by a polyphasic taxonomic approach and by comparative genomics. Relevant phenotypic, genotypic and chemotaxonomic methods divided the analyzed strains into two separate clusters within the genus Macrococcus. Comparative genomics of four representative strains revealed enormous genome structural plasticity among the studied isolates. We hypothesize that high genomic variability is due to the presence of a com operon, which plays a key role in the natural transformation of bacilli and streptococci. The possible uptake of exogenous DNA by macrococci can contribute to a different mechanism of evolution from staphylococci, where phage-mediated horizontal gene transfer predominates. The described macrococcal genomes harbor novel plasmids, genomic islands and islets, as well as prophages. Capsule gene clusters, intracellular protease, and a fibronectin-binding protein enabling opportunistic pathogenesis were found in all four strains. Furthermore, the presence of a CRISPR-Cas system with 90 spacers in one of the sequenced genomes corresponds with the need to limit the burden of foreign DNA. The highly dynamic genomes could serve as a platform for the exchange of virulence and resistance factors, as was described for the methicillin resistance gene, which was found on the novel composite SCCmec-like element containing a unique mec gene complex that is considered to be one of the missing links in SCC evolution. The phenotypic, genotypic, chemotaxonomic and genomic results demonstrated that the analyzed strains represent one novel subspecies and three novel species of the genus Macrococcus, for which the names Macrococcus caseolyticus subsp. hominis subsp. nov. (type strain CCM 7927T = DSM 103682T), Macrococcus goetzii sp. nov. (type strain CCM 4927T = DSM 103683T), Macrococcus epidermidis sp. nov. (type strain CCM 7099T = DSM 103681T), and Macrococcus bohemicus sp. nov. (type strain CCM 7100T = DSM 103680T) are proposed. Moreover, a formal description of Macrococcus caseolyticus subsp. caseolyticus subsp. nov. and an emended description of the genus Macrococcus are provided.

Central European Institute of Technology Masaryk University Brno Czechia

Czech Collection of Microorganisms Department of Experimental Biology Faculty of Science Masaryk University Brno Czechia

Division of Genetics and Molecular Biology Department of Experimental Biology Faculty of Science Masaryk University Brno Czechia

Leibniz Institute Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures Braunschweig Germany

National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czechia

Reference Laboratory for Staphylococci National Institute of Public Health Prague Czechia

Zobrazit více v PubMed

Arndt D., Grant J. R., Marcu A., Sajed T., Pon A., Liang Y., et al. (2016). PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44, W16–W21. 10.1093/nar/gkw387 PubMed DOI PMC

Arthur M., Depardieu F., Gerbaud G., Galimand M., Leclercq R., Courvalin P. (1997). The VanS sensor negatively controls VanR-mediated transcriptional activation of glycopeptide resistance genes of Tn1546 and related elements in the absence of induction. J. Bacteriol. 179, 97–106. 10.1128/jb.179.1.97-106.1997 PubMed DOI PMC

Aziz R. K., Bartels D., Best A. A., Dejongh M., Disz T., Edwards R. A., et al. (2008). The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. 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 PubMed DOI PMC

Baida G. E., Kuzmin N. P. (1996). Mechanism of action of hemolysin III from PubMed DOI

Bay D. C., Turner R. J. (2012). Small multidrug resistance protein EmrE reduces host pH and osmotic tolerance to metabolic quaternary cation osmoprotectants. J. Bacteriol. 194, 5941–5948. 10.1128/JB.00666-12 PubMed DOI PMC

Becker K., Heilmann C., Peters G. (2014). Coagulase-negative staphylococci. Clin. Microbiol. Rev. 27, 870–926. 10.1128/CMR.00109-13 PubMed DOI PMC

Becker K., Van Alen S., Idelevich E. A., Schleimer N., Seggewiss J., Mellmann A., et al. (2018). Plasmid-encoded transferable PubMed DOI PMC

Ben Zakour N. L., Bannoehr J., Van Den Broek A. H., Thoday K. L., Fitzgerald J. R. (2011). Complete genome sequence of the canine pathogen PubMed DOI PMC

Cashion P., Holder-Franklin M. A., McCully J., Franklin M. (1977). A rapid method for the base ratio determination of bacterial DNA. Anal. Biochem. 81, 461–466. 10.1016/0003-2697(77)90720-5 PubMed DOI

Castillo D., Espejo R., Middelboe M. (2014). Genomic structure of bacteriophage 6H and its distribution as prophage in PubMed DOI

Chanchaithong P., Prapasarakul N., Perreten V., Schwendener S. (2016). Characterization of a novel composite staphylococcal cassette chromosome PubMed DOI PMC

Chen L., Zheng D., Liu B., Yang J., Jin Q. (2016). VFDB 2016: hierarchical and refined dataset for big data analysis−10 years on. Nucleic Acids Res. 44, D694–D697. 10.1093/nar/gkv1239 PubMed DOI PMC

Christie J., McNab R., Jenkinson H. F. (2002). Expression of fibronectin-binding protein FbpA modulates adhesion in PubMed DOI

Christo-Foroux E., Vallaeys T., Loux V., Dassa E., Deutscher J., Wandersman C., et al. (2017). Manual and expert annotation of the nearly complete genome sequence of PubMed DOI

Chung Y. S., Dubnau D. (1995). ComC is required for the processing and translocation of ComGC, a pilin-like competence protein of PubMed DOI

Cicconi-Hogan K. M., Belomestnykh N., Gamroth M., Ruegg P. L., Tikofsky L., Schukken Y. H. (2014). Prevalence of methicillin resistance in coagulase-negative staphylococci and PubMed DOI

CLSI (2015). Performance Standards for Antimicrobial Disk Susceptibility Tests; Approved Standard - 12th Edn. CLSI document M02-A12. Wayne, PA: Clinical and Laboratory Standards Institute.

Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. (1977). Distribution of menaquinones in actinomycetes and corynebacteria. J. Gen. Microbiol. 100, 221–230. 10.1099/00221287-100-2-221 PubMed DOI

Costa S. S., Mourato C., Viveiros M., Melo-Cristino J., Amaral L., Couto I. (2013). Description of plasmid pSM52, harbouring the gene for the Smr efflux pump, and its involvement in resistance to biocides in a meticillin-resistant PubMed DOI

Cotting K., Strauss C., Rodriguez-Campos S., Rostaher A., Fischer N. M., Roosje P. J., et al. (2017). PubMed DOI

De Ley J., Cattoir H., Reynaerts A. (1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur. J. Biochem. 12, 133–142. 10.1111/j.1432-1033.1970.tb00830.x PubMed DOI

De Vos P., Trüper H. G. (2000). Judicial Commission of the International Committee on Systematic Bacteriology; IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Int. J. Syst. Evol. Microbiol. 50, 2239–2244. 10.1099/00207713-50-6-2239 DOI

Demple B., Halbrook J., Linn S. (1983). PubMed PMC

Dhillon B. K., Laird M. R., Shay J. A., Winsor G. L., Lo R., Nizam F., et al. (2015). IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res. 43, W104–W108. 10.1093/nar/gkv401 PubMed DOI PMC

Dominguez-Moñino I., Jurado V., Gonzalez-Pimentel J. L., Miller A. Z., Hermosin B., Saiz-Jimenez C. (2018). PubMed DOI

EUCAST (2017). Breakpoint Tables for Interpretation of MICs and Zone Diameters. The European Committee on Antimicrobial Susceptibility Testing. Available online at: http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_7.1_Breakpoint_Tables.pdf

Fagerlund A., Granum P. E., Havarstein L. S. (2014). PubMed DOI

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

Gevers D., Huys G., Swings J. (2001). Applicability of rep-PCR fingerprinting for identification of PubMed DOI

Gobeli Brawand S., Cotting K., Gomez-Sanz E., Collaud A., Thomann A., Brodard I., et al. (2017). PubMed DOI

Gobeli Brawand S., Rychener L., Schwendener S., Pantucek R., Perreten V. (2018). Complete genome sequence of the type strain of PubMed DOI PMC

Gómez-Sanz E., Schwendener S., Thomann A., Gobeli Brawand S., Perreten V. (2015). First staphylococcal cassette chromosome PubMed DOI PMC

Götz F., Bannerman T., Schleifer K.-H. (2006). The genera

Grohmann E., Muth G., Espinosa M. (2003). Conjugative plasmid transfer in gram-positive bacteria. Microbiol. Mol. Biol. Rev. 67, 277–301. 10.1128/MMBR.67.2.277-301.2003 PubMed DOI PMC

Groth I., Schumann P., Weiss N., Martin K., Rainey F. A. (1996). PubMed DOI

Hansen C. M., Meixell B. W., Van Hemert C., Hare R. F., Hueffer K. (2015). Microbial infections are associated with embryo mortality in Arctic-nesting geese. Appl. Environ. Microbiol. 81, 5583–5592. 10.1128/AEM.00706-15 PubMed DOI PMC

Heir E., Sundheim G., Holck A. L. (1998). The PubMed DOI

Huss V. A., Festl H., Schleifer K. H. (1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst. Appl. Microbiol. 4, 184–192. 10.1016/S0723-2020(83)80048-4 PubMed DOI

Indráková A., Mašlanová I., Kováčová V., Doškar J., Pantuček R. (2016). The evolutionary pathway of the staphylococcal cassette chromosome element. Biologia 71, 1195–1203. 10.1515/biolog-2016-0156 DOI

Joh D., Wann E. R., Kreikemeyer B., Speziale P., Hook M. (1999). Role of fibronectin-binding MSCRAMMs in bacterial adherence and entry into mammalian cells. Matrix Biol. 18, 211–223. 10.1016/S0945-053X(99)00025-6 PubMed DOI

Jones P., Binns D., Chang H. Y., Fraser M., Li W., McAnulla C., et al. (2014). InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240. 10.1093/bioinformatics/btu031 PubMed DOI PMC

Kahánková J., Pantuček R., Goerke C., Ruzičková V., Holochová P., Doškar J. (2010). Multilocus PCR typing strategy for differentiation of PubMed DOI

Kim H. K., Thammavongsa V., Schneewind O., Missiakas D. (2012). Recurrent infections and immune evasion strategies of PubMed DOI PMC

Kloos W. E., Ballard D. N., George C. G., Webster J. A., Hubner R. J., Ludwig W., et al. (1998). Delimiting the genus PubMed DOI

Kumar S., Stecher G., Tamura K. (2016). MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874. 10.1093/molbev/msw054 PubMed DOI PMC

Laanto E., Bamford J. K., Ravantti J. J., Sundberg L. R. (2015). The use of phage FCL-2 as an alternative to chemotherapy against columnaris disease in aquaculture. Front. Microbiol. 6:829. 10.3389/fmicb.2015.00829 PubMed DOI PMC

Lagesen K., Hallin P., Rodland E. A., Staerfeldt H. H., Rognes T., Ussery D. W. (2007). RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. 10.1093/nar/gkm160 PubMed DOI PMC

Lei Y., Oshima T., Ogasawara N., Ishikawa S. (2013). Functional analysis of the protein Veg, which stimulates biofilm formation in PubMed DOI PMC

Li D., Wang Y., Schwarz S., Cai J., Fan R., Li J., et al. (2016). Co-location of the oxazolidinone resistance genes PubMed DOI

Madonna A. J., Basile F., Ferrer I., Meetani M. A., Rees J. C., Voorhees K. J. (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. 10.1002/1097-0231(20001215)14:23<2220::AID-RCM155>3.0.CO;2-4 PubMed DOI

Mannerová S., Pantuček R., Doškar J., Švec P., Snauwaert C., Vancanneyt M., et al. (2003). PubMed DOI

Meier-Kolthoff J. P., Auch A. F., Klenk H. P., Goker M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. 10.1186/1471-2105-14-60 PubMed DOI PMC

Micheel V., Hogan B., Koller T., Warnke P., Crusius S., Hinz R., et al. (2015). Screening agars for MRSA: evaluation of a stepwise diagnostic approach with two different selective agars for the screening for methicillin-resistant PubMed DOI PMC

Mukherjee A., Chettri B., Langpoklakpam J. S., Singh A. K., Chattopadhyay D. (2016). Draft genome sequence of hydrocarbon-degrading PubMed DOI PMC

Müller A., Rychli K., Muhterem-Uyar M., Zaiser A., Stessl B., Guinane C. M., et al. (2013). Tn6188 - a novel transposon in PubMed DOI PMC

Muschiol S., Balaban M., Normark S., Henriques-Normark B. (2015). Uptake of extracellular DNA: competence induced pili in natural transformation of PubMed DOI PMC

Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., et al. (2013). Assembling genomes and mini-metagenomes from highly chimeric reads,” in Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, Vol. 7821, eds Deng M., Jiang R., Sun F., Zhang X. (Berlin, Heidelberg: Springer; ), 7158–7170.

Okonechnikov K., Golosova O., Fursov M., Ugene Team. (2012). Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28, 1166–1167. 10.1093/bioinformatics/bts091 PubMed DOI

O'Riordan K., Lee J. C. (2004). PubMed DOI PMC

Pantuček R., Götz F., Doškar J., Rosypal S. (1996). Genomic variability of PubMed DOI

Pantuček R., Sedláček I., Indráková A., Vrbovská V., Mašlanová I., Kovarovic V., et al. (2017). PubMed DOI PMC

Pantuček R., Sedláček I., Petráš P., Koukalová D., Švec P., Štětina V., Vancanneyt M., et al. (2005). PubMed DOI

Pantuček R., Švec P., Dajcs J. J., Machová I., Cernohlávková J., Šedo O., et al. (2013). PubMed DOI

Parker C. T., Tindall B. J., Garrity G. M. (2015). International code of nomenclature of prokaryotes. Int. J. Syst. Evol. Microbiol. 10.1099/ijsem.0.000778. [Epub ahead of print]. PubMed DOI

Parte A. C. (2014). LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res. 42, D613–D616. 10.1093/nar/gkt1111 PubMed DOI PMC

Paterson G. K., Harrison E. M., Holmes M. A. (2014). The emergence of PubMed DOI PMC

Penadés J. R., Christie G. E. (2015). The Phage-Inducible chromosomal islands: a family of highly evolved molecular parasites. Annu. Rev. Virol. 2, 181–201. 10.1146/annurev-virology-031413-085446 PubMed DOI

Prakash O., Muduli S., Kumar R., Kumari C., Nimonkar Y., Shouche Y. S., et al. (2017). Description of PubMed DOI

Pritchard L., Glover R. H., Humphris S., Elphinstone J. G., Toth I. K. (2016). Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal. Methods 8, 12–24. 10.1039/C5AY02550H DOI

Richter M., Rosselló-Móra R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U.S.A. 106, 19126–19131. 10.1073/pnas.0906412106 PubMed DOI PMC

Rissman A. I., Mau B., Biehl B. S., Darling A. E., Glasner J. D., Perna N. T. (2009). Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics 25, 2071–2073. 10.1093/bioinformatics/btp356 PubMed DOI PMC

Rohde H., Frankenberger S., Zahringer U., Mack D. (2010). Structure, function and contribution of polysaccharide intercellular adhesin (PIA) to PubMed DOI

Rubin D., Zhang W., Karch H., Kuczius T. (2017). Distinct expression of immunoglobulin-binding proteins in Shiga Toxin-producing PubMed DOI PMC

Rubin J. E., Chirino-Trejo M. (2010). Inducibly cefoxitin-resistant Macrococcus-like organism falsely identified as methicillin-resistant PubMed DOI PMC

Sandt C. H., Hopper J. E., Hill C. W. (2002). Activation of prophage eib genes for immunoglobulin-binding proteins by genes from the IbrAB genetic island of PubMed DOI PMC

Sasser M. (1990). Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: Microbial ID Inc.

Sau S., Lee C. Y. (1996). Cloning of type 8 capsule genes and analysis of gene clusters for the production of different capsular polysaccharides in PubMed DOI PMC

Sau S., Bhasin N., Wann E. R., Lee J. C., Foster T. J., Lee C. Y. (1997). The PubMed DOI

Schleifer K. H., Bell J. A. (2009). Genus I.

Schleifer K. H., Kilpper-Balz R., Fischer U., Faller A., Endl J. (1982). Identification of “ DOI

Schleifer K.-H. (2015).

Schreiter E. R., Drennan C. L. (2007). Ribbon-helix-helix transcription factors: variations on a theme. Nat. Rev. Microbiol. 5, 710–720. 10.1038/nrmicro1717 PubMed DOI

Schumann P. (2011). Peptidoglycan structure. Methods Microbiol. 38, 101–129. 10.1016/B978-0-12-387730-7.00005-X DOI

Schwendener S., Cotting K., Perreten V. (2017). Novel methicillin resistance gene PubMed DOI PMC

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. 10.1093/nar/gkj014 PubMed DOI PMC

Švec P., Cernohlávková J., Busse H. J., Vojtková H., Pantuček R., Cnockaert M., Mašlanová I., et al. (2015). Classification of strain CCM 4446 PubMed DOI

Švec P., Pantuček R., Petráš P., Sedláček I., Nováková D. (2010). Identification of PubMed DOI

Švec P., Petráš P., Pantuček R., Doškar J., Sedláček I. (2016). High intraspecies heterogeneity within PubMed DOI

Takeuchi F., Watanabe S., Baba T., Yuzawa H., Ito T., Morimoto Y., et al. (2005). Whole-genome sequencing of PubMed DOI PMC

Thammavongsa V., Kern J. W., Missiakas D. M., Schneewind O. (2009). PubMed DOI PMC

Thammavongsa V., Schneewind O., Missiakas D. M. (2011). Enzymatic properties of PubMed DOI PMC

Tsubakishita S., Kuwahara-Arai K., Baba T., Hiramatsu K. (2010). Staphylococcal cassette chromosome PubMed DOI PMC

Vasudevan P., McElligott J., Attkisson C., Betteken M., Popham D. L. (2009). Homologues of the PubMed DOI PMC

Verstappen K. M., Huijbregts L., Spaninks M., Wagenaar J. A., Fluit A. C., Duim B. (2017). Development of a real-time PCR for detection of PubMed DOI PMC

Wang Y., Coleman-Derr D., Chen G., Gu Y. Q. (2015). OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res. 43, W78–W84. 10.1093/nar/gkv487 PubMed DOI PMC

Watts A., Ke D., Wang Q., Pillay A., Nicholson-Weller A., Lee J. C. (2005). PubMed DOI PMC

Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A., Kandler O., Truper H. G., et al. (1987). Report of the Ad-Hoc-Committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37, 463–464. 10.1099/00207713-37-4-463 DOI

Wick R. R., Schultz M. B., Zobel J., Holt K. E. (2015). Bandage: interactive visualization of PubMed DOI PMC

Yoon S. H., Ha S. M., Kwon S., Lim J., Kim Y., Seo H., et al. (2017). Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617. 10.1099/ijsem.0.001755 PubMed DOI PMC

Zechner E. L., Moncalian G., De La Cruz F. (2017). Relaxases and plasmid transfer in Gram-negative bacteria. Curr. Top. Microbiol. Immunol. 413, 93–113. 10.1007/978-3-319-75241-9_4 PubMed DOI

Zeman M., Mašlanová I., Indráková A., Šiborová M., Mikulášek K., Bendíčková K., et al. (2017). PubMed DOI PMC

Zhang Q., Ye Y. (2017). Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. BMC Bioinformatics 18:92. 10.1186/s12859-017-1512-4 PubMed DOI PMC

Genomic and taxonomic characterization of strain CCM 2573: Uncovering unique genetic features and description of Macrococcus caseolyticus subsp. lactis subsp. nov

Evidence of in vitro mecB-mediated β-lactam antibiotic resistance transfer to Staphylococcus aureus from Macrococcus psychrotolerans sp. nov., a psychrophilic bacterium from food-producing animals and human clinical specimens

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

Staphylococcus ratti sp. nov. Isolated from a Lab Rat