R. Olaniyi, C. Pozzi, L. Grimaldi, and F. Bagnoli, Staphylococcus aureus-Associated Skin and Soft Tissue Infections: Anatomical Localization, Epidemiology, Therapy and Potential Prophylaxis, Curr. Top. Microbiol. Immunol, vol.409, pp.199-227, 2017.

L. Thomer, O. Schneewind, and D. Missiakas, Pathogenesis of Staphylococcus aureus Bloodstream Infections, Annu. Rev. Pathol, vol.11, pp.343-364, 2016.

V. Peton and Y. Le-loir, Staphylococcus aureus in veterinary medicine, Infect. Genet. Evol. J. Mol. Epidemiol. Evol. Genet. Infect. Dis, vol.21, pp.602-615, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01209522

E. Hata, Bacteriological characteristics of Staphylococcus aureus isolates from humans and bulk milk, J. Dairy Sci, vol.91, pp.564-569, 2008.

G. Magro, Virulence Genes of S. aureus from Dairy Cow Mastitis and Contagiousness Risk, Toxins, vol.9, 2017.

M. E. Mulcahy and R. M. Mcloughlin, Host-Bacterial Crosstalk Determines Staphylococcus aureus Nasal Colonization, Trends Microbiol, vol.24, pp.872-886, 2016.

Y. Ofir-birin, M. Heidenreich, and N. Regev-rudzki, Pathogen-derived extracellular vesicles coordinate social behaviour and host manipulation, Semin. Cell Dev. Biol, vol.67, pp.83-90, 2017.

M. E. Kuipers, C. H. Hokke, H. H. Smits, and E. N. Nolte-'t-hoen, Pathogen-Derived Extracellular Vesicle-Associated Molecules That Affect the Host Immune System: An Overview, Front. Microbiol, vol.9, p.2182, 2018.

S. Gill, R. Catchpole, and P. Forterre, Extracellular membrane vesicles in the three domains of life and beyond, FEMS Microbiol. Rev, vol.43, pp.273-303, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02178889

M. Gurung, Staphylococcus aureus Produces Membrane-Derived Vesicles That Induce Host Cell Death, PLoS ONE, vol.6, p.27958, 2011.

B. Thay, S. N. Wai, and J. Oscarsson, Staphylococcus aureus ?-Toxin-Dependent Induction of Host Cell Death by Membrane-Derived Vesicles, PLoS ONE, vol.8, p.54661, 2013.

H. Jeon, Variation among Staphylococcus aureus membrane vesicle proteomes affects cytotoxicity of host cells, Microb. Pathog, vol.93, pp.185-193, 2016.

S. Hong, Extracellular vesicles derived from Staphylococcus aureus induce atopic dermatitis-like skin inflammation: S. aureus EV in atopic dermatitis, Allergy, vol.66, pp.351-359, 2011.

M. Kim, Staphylococcus aureus-derived extracellular vesicles induce neutrophilic pulmonary inflammation via both Th1 and Th17 cell responses, Allergy, vol.67, pp.1271-1281, 2012.

S. J. Choi, Active Immunization with Extracellular Vesicles Derived from Staphylococcus aureus Effectively Protects against Staphylococcal Lung Infections, Mainly via Th1 Cell-Mediated Immunity, PLOS ONE, vol.10, p.136021, 2015.

S. H. Jun, Staphylococcus aureus -derived membrane vesicles exacerbate skin inflammation in atopic dermatitis, Clin. Exp. Allergy, vol.47, pp.85-96, 2017.

J. Yuan, Safe Staphylococcal Platform for the Development of Multivalent Nanoscale Vesicles against Viral Infections, Nano Lett, vol.18, pp.725-733, 2018.

N. R. Tartaglia, Staphylococcus aureus Extracellular Vesicles Elicit an Immunostimulatory Response in vivo on the, Murine Mammary Gland. Front. Cell. Infect. Microbiol, vol.8, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01889276

X. He, F. Yuan, F. Lu, Y. Yin, and J. Cao, Vancomycin-induced biofilm formation by methicillin-resistant Staphylococcus aureus is associated with the secretion of membrane vesicles, Microb. Pathog, vol.110, pp.225-231, 2017.

J. Lee, Staphylococcus aureus Extracellular Vesicles Carry Biologically Active ?-Lactamase, Antimicrob. Agents Chemother, vol.57, pp.2589-2595, 2013.

F. Askarian, Staphylococcus aureus Membrane-Derived Vesicles Promote Bacterial Virulence and Confer Protective Immunity in Murine Infection Models, Front. Microbiol, vol.9, p.262, 2018.

X. Wang, C. D. Thompson, C. Weidenmaier, and J. C. Lee, Release of Staphylococcus aureus extracellular vesicles and their application as a vaccine platform, Nat. Commun, vol.9, p.1379, 2018.

K. Schlatterer, The Mechanism behind Bacterial Lipoprotein Release: Phenol-Soluble Modulins Mediate Toll-Like Receptor 2 Activation via Extracellular Vesicle Release from Staphylococcus aureus, vol.9, pp.1851-1869, 2018.

E. Lee, Gram-positive bacteria produce membrane vesicles: Proteomics-based characterization of Staphylococcus aureusderived membrane vesicles, PROTEOMICS, vol.9, pp.5425-5436, 2009.

C. Théry, Proteomic Analysis of Dendritic Cell-Derived Exosomes: A Secreted Subcellular Compartment Distinct from Apoptotic Vesicles, J. Immunol, vol.166, pp.7309-7318, 2001.

S. I. Buschow, MHC class II-associated proteins in B-cell exosomes and potential functional implications for exosome biogenesis, Immunol. Cell Biol, vol.88, pp.851-856, 2010.

L. Maréchal and C. , Molecular Basis of Virulence in Staphylococcus aureus Mastitis, PLoS ONE, vol.6, p.27354, 2011.

G. Raposo and W. Stoorvogel, Extracellular vesicles: Exosomes, microvesicles, and friends, J. Cell Biol, vol.200, pp.373-383, 2013.

R. Szatanek, The Methods of Choice for Extracellular Vesicles (EVs) Characterization, Int. J. Mol. Sci, vol.18, p.1153, 2017.

D. Kim, EVpedia: a community web portal for extracellular vesicles research, Bioinforma. Oxf. Engl, vol.31, pp.933-939, 2015.

G. P. Dubey and S. Ben-yehuda, Intercellular Nanotubes Mediate Bacterial Communication, Cell, vol.144, pp.590-600, 2011.

A. B. García, J. M. Viñuela-prieto, L. Lopez-gonzález, and F. J. Candel, Correlation between resistance mechanisms in Staphylococcus aureus and cell wall and septum thickening, Infect. Drug Resist, vol.10, pp.353-356, 2017.

K. Wooldridge, Iron uptake mechanisms of pathogenic bacteria, FEMS Microbiol. Rev, vol.12, pp.325-348, 1993.

R. Prados-rosales, Role for Mycobacterium tuberculosis membrane vesicles in iron acquisition, J. Bacteriol, vol.196, pp.1250-1256, 2014.

M. T. Nguyen and F. Götz, Lipoproteins of Gram-Positive Bacteria: Key Players in the Immune Response and Virulence. Microbiol, Mol. Biol. Rev, vol.80, pp.891-903, 2016.

S. V. Shahmirzadi, M. Nguyen, and F. Götz, Evaluation of Staphylococcus aureus Lipoproteins: Role in Nutritional Acquisition and Pathogenicity. Front. Microbiol, vol.7, 2016.

V. Schaar, T. Nordström, M. Mörgelin, and K. Riesbeck, Moraxella catarrhalis outer membrane vesicles carry ?-lactamase and promote survival of Streptococcus pneumoniae and Haemophilus influenzae by inactivating amoxicillin, Antimicrob. Agents Chemother, vol.55, pp.3845-3853, 2011.

R. Stentz, Cephalosporinases associated with outer membrane vesicles released by Bacteroides spp. protect gut pathogens and commensals against ?-lactam antibiotics, J. Antimicrob. Chemother, vol.70, pp.701-709, 2015.

O. Y. Kim, Bacterial outer membrane vesicles suppress tumor by interferon-?-mediated antitumor response, Nat. Commun, vol.8, p.626, 2017.

B. Modun and P. Williams, The staphylococcal transferrin-binding protein is a cell wall glyceraldehyde-3-phosphate dehydrogenase, Infect. Immun, vol.67, pp.1086-1092, 1999.

J. Antikainen, V. Kuparinen, K. Lähteenmäki, and T. K. Korhonen, Enolases from Gram-positive bacterial pathogens and commensal lactobacilli share functional similarity in virulence-associated traits, FEMS Immunol. Med. Microbiol, vol.51, pp.526-534, 2007.

M. Widjaja, Elongation factor Tu is a multifunctional and processed moonlighting protein, Sci. Rep, vol.7, p.11227, 2017.

C. Jeffery, Intracellular proteins moonlighting as bacterial adhesion factors, AIMS Microbiol, vol.4, pp.362-376, 2018.

P. Ebner and F. Götz, Bacterial Excretion of Cytoplasmic Proteins (ECP): Occurrence, Mechanism, and Function, Trends Microbiol, vol.27, pp.176-187, 2019.

N. L. Ben-zakour, Genome-Wide Analysis of Ruminant Staphylococcus aureus Reveals Diversification of the Core Genome, J. Bacteriol, vol.190, pp.6302-6317, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01454058

P. D. Alves, Molecular characterisation of Staphylococcus aureus strains isolated from small and large ruminants reveals a host rather than tissue specificity, Vet. Microbiol, vol.137, pp.190-195, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00409359

, Scientific RepoRtS |, vol.10, p.8467, 2020.

D. Viana, Adaptation of Staphylococcus aureus to ruminant and equine hosts involves SaPI-carried variants of von Willebrand factor-binding protein, Mol. Microbiol, vol.77, pp.1583-1594, 2010.

I. Imanishi, Exfoliative toxin E, a new Staphylococcus aureus virulence factor with host-specific activity, Sci. Rep, vol.9, p.16336, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02306146

P. M. Sharp and W. Li, The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Res, vol.15, pp.1281-1295, 1987.

M. Dos-reis, Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome, Nucleic Acids Res, vol.31, pp.6976-6985, 2003.

Y. Ishihama, Protein abundance profiling of the Escherichia coli cytosol, BMC Genomics, vol.9, p.102, 2008.

D. Zühlke, Costs of life -Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis, Sci. Rep, vol.6, p.28172, 2016.

S. Mclaughlin and D. Murray, Plasma membrane phosphoinositide organization by protein electrostatics, Nature, vol.438, pp.605-611, 2005.

T. Yeung, Membrane Phosphatidylserine Regulates Surface Charge and Protein Localization, Science, vol.319, pp.210-213, 2008.

P. Xu, R. D. Baldridge, R. J. Chi, C. G. Burd, and T. R. Graham, Phosphatidylserine flipping enhances membrane curvature and negative charge required for vesicular transport, J. Cell Biol, vol.202, pp.875-886, 2013.

L. Brown, J. M. Wolf, R. Prados-rosales, and A. Casadevall, Through the wall: extracellular vesicles in Gram-positive bacteria, mycobacteria and fungi, Nat. Rev. Microbiol, vol.13, pp.620-630, 2015.

M. F. Haurat, W. Elhenawy, and M. F. Feldman, Prokaryotic membrane vesicles: new insights on biogenesis and biological roles, Biol. Chem, vol.396, pp.95-109, 2015.

C. Schwechheimer and M. J. Kuehn, Outer-membrane vesicles from Gram-negative bacteria: biogenesis and functions, Nat. Rev. Microbiol, vol.13, pp.605-619, 2015.

L. Marechal and C. , Genome Sequences of Two Staphylococcus aureus Ovine Strains That Induce Severe (Strain O11) and Mild (Strain O46) Mastitis, J. Bacteriol, vol.193, pp.2353-2354, 2011.

L. Maréchal and C. , Surface proteins of Propionibacterium freudenreichii are involved in its anti-inflammatory properties, J. Proteomics, vol.113, pp.447-461, 2015.

L. L. Herron, Genome sequence survey identifies unique sequences and key virulence genes with unusual rates of amino Acid substitution in bovine Staphylococcus aureus, Infect. Immun, vol.70, pp.3978-3981, 2002.

G. Wilson, Genome scale analysis of the role of superantigens in Staphylococcus aureus disease pathogenesis, 2011.

D. Bouchard, Genome Sequence of Staphylococcus aureus Newbould 305, a Strain Associated with Mild Bovine Mastitis, J. Bacteriol, vol.194, pp.6292-6293, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01209374

V. Peton, Fine-tuned characterization of Staphylococcus aureus Newbould 305, a strain associated with mild and chronic mastitis in bovines, Vet. Res, vol.45, p.106, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01290602

, Four pediatric deaths from community-acquired methicillin-resistant Staphylococcus aureus -Minnesota and North Dakota, 1997-1999, Centers for Disease Control and Prevention (CDC), vol.48, pp.707-710, 1999.

T. Baba, Genome and virulence determinants of high virulence community-acquired MRSA, Lancet Lond. Engl, vol.359, pp.1819-1827, 2002.

F. Baron, Rapid and cost-effective method for micro-organism enumeration based on miniaturization of the conventional plate-counting technique, Le Lait, vol.86, pp.251-257, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00895582

O. Langella, A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification, J. Proteome Res, vol.16, pp.494-503, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01484169

B. Valot, O. Langella, E. Nano, and M. Zivy, MassChroQ: a versatile tool for mass spectrometry quantification, Proteomics, vol.11, pp.3572-3577, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01481216

M. Blein-nicolas, A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast, Mol. Cell. Proteomics, vol.14, pp.2056-2071, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02636704

A. R. Wattam, Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center, Nucleic Acids Res, vol.45, pp.535-542, 2017.

C. Yu, Y. Chen, C. Lu, and J. Hwang, Prediction of protein subcellular localization, Proteins, vol.64, pp.643-651, 2006.

P. G. Bagos, K. D. Tsirigos, T. D. Liakopoulos, and S. J. Hamodrakas, Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model, J. Proteome Res, vol.7, pp.5082-5093, 2008.

N. Y. Yu, PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes, Bioinformatics, vol.26, pp.1608-1615, 2010.

J. J. Almagro-armenteros, SignalP 5.0 improves signal peptide predictions using deep neural networks, Nat. Biotechnol, vol.37, pp.420-423, 2019.

R. L. Tatusov, M. Y. Galperin, D. A. Natale, and E. V. Koonin, The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Res, vol.28, pp.33-36, 2000.

F. Coste, G. Kerbellec, J. Gama, R. Camacho, P. B. Brazdil et al., A Similar Fragments Merging Approach to Learn Automata on Proteins, Machine Learning: ECML 2005, vol.3720, pp.522-529, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00000179

E. De-castro, ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins, Nucleic Acids Res, vol.34, pp.362-365, 2006.

M. Kumar, V. Thakur, and G. P. Raghava, COPid: composition based protein identification, In Silico Biol, vol.8, pp.121-128, 2008.

P. Stothard, The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences, BioTechniques, vol.28, p.1104, 1102.

D. Vallenet, MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis, Nucleic Acids Res. gkz926, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02403170

M. Mani, MoonProt: a database for proteins that are known to moonlight, Nucleic Acids Res, vol.43, pp.277-282, 2015.

H. Heberle, G. V. Meirelles, F. R. Da-silva, G. P. Telles, and R. Minghim, InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams, BMC Bioinformatics, vol.16, p.169, 2015.

L. S. Rocha, Rosa da Luz were supported by the International Cooperation Program CAPES/COFECUB Foundation at the Federal University of Minas Gerais funded by CAPES -the Brazilian Federal Agency for the Support and Evaluation of Graduate Education of the Brazilian Ministry of Education, PLOS ONE, vol.14, p.8467, 2018.