Abdullahi, I. N., Lozano, C., Latorre-Fernández, J., Zarazaga, M., Stegger, M., & Torres, C. (2025). Genomic analysis of multi-drug resistant coagulase-negative staphylococci from healthy humans and animals revealed unusual mechanisms of resistance and CRISPR-Cas system. International Microbiology, 28(5), 941–963. https://doi.org/10.1007/s10123-024-00577-9
Agapov, A., Baker, K. S., Bedekar, P., Bhatia, R. P., Blower, T. R., Brockhurst, M. A., Brown, C., Chong, C. E., Fothergill, J. L., Graham, S., Hall, J. P., Maestri, A., McQuarrie, S., Olina, A., Pagliara, S., Recker, M., Richmond, A., Shaw, S. J., Szczelkun, M. D., ... Westra, E. R. (2024). Multi-layered genome defences in bacteria. Current Opinion in Microbiology, 78, Article 102436. https://doi.org/10.1016/j.mib.2024.102436
Alves, J., Vrieling, M., Ring, N., Yebra, G., Pickering, A., Prajsnar, T. K., Renshaw, S. A., & Fitzgerald, J. R. (2024). Experimental evolution of Staphylococcus aureus in macrophages: Dissection of a conditional adaptive trait promoting intracellular survival. mBio, 15(6), Article e0034624. https://doi.org/10.1128/mbio.00346-24
Anas, M., Lone, S. A., Malik, A., & Ahmad, J. (2025). Antimicrobial resistance and public health risks associated with staphylococci isolated from raw and processed meat products. Foodborne Pathogens and Disease, 22(1), 39–50. https://doi.org/10.1089/fpd.2024.0081
Becker, K., Heilmann, C., & Peters, G. (2014). Coagulase-negative staphylococci. Clinical Microbiology Reviews, 27(4), 870–926. https://doi.org/10.1128/CMR.00109-13
Benson, H. J. (2002). Microbiological applications: Laboratory manual in general microbiology. McGraw-Hill.
Bjorland, J., Steinum, T., Kvitle, B., Waage, S., Sunde, M., & Heir, E. (2005). Widespread distribution of disinfectant resistance genes among staphylococci of bovine and caprine origin in Norway. Journal of Clinical Microbiology, 43(9), 4363–4368. https://doi.org/10.1128/JCM.43.9.4363-4368.2005
Byczkowska-Rostkowska, Z., Gajewska, J., & Chajęcka-Wierzchowska, W. (2025). Whole genome analysis and antimicrobial resistance assessment of Staphylococcus epidermidis isolated from food sources. Science of the Total Environment, 993, Article 179999. https://doi.org/10.1016/j.scitotenv.2025.179999
Chajęcka-Wierzchowska, W., Gajewska, J., Zakrzewski, A. J., Caggia, C., & Zadernowska, A. (2023). Molecular analysis of pathogenicity, adhesive matrix molecules (MSCRAMMs) and biofilm genes of coagulase-negative staphylococci isolated from ready-to-eat food. International Journal of Environmental Research and Public Health, 20(2), Article 1375. https://doi.org/10.3390/ijerph20021375
Choudhary, D., Foster, K. R., & Uphoff, S. (2024). The master regulator OxyR orchestrates bacterial oxidative stress response genes in space and time. Cell Systems, 15(11), 1033–1045.e6. https://doi.org/10.1016/j.cels.2024.10.003
Chu, D., & Wei, L. (2020). Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations. BMC Genomics, 21(1), Article 333. https://doi.org/10.1186/s12864-020-6745-3
Connor, C. H., Higgs, C. K., Horan, K., Kwong, J. C., Grayson, M. L., Howden, B. P., Seemann, T., Gorrie, C. L., & Sherry, N. L. (2025). Rapid, reference-free identification of bacterial pathogen transmission using optimized split k-mer analysis. Microbial Genomics, 11(3), Article 001347. https://doi.org/10.1099/mgen.0.001347
Dündar, T., & Köksal Çakırlar, F. (2025). Antimicrobial resistance in coagulase negative staphylococci: Genome analysis and role of horizontal gene transfer. Research in Microbiology, 176(5-6), Article 104298. https://doi.org/10.1016/j.resmic.2025.104298
Forbes, B. A., Sahm, D. F., & Weissfeld, A. S. (2016). Study guide for Bailey and Scott's diagnostic microbiology. Elsevier Health Sciences.
Furuta, Y., & Kobayashi, I. (2022). Restriction-modification systems as mobile epigenetic elements. In Bacterial integrative mobile genetic elements (pp. 85–103). CRC Press.
Girma, A. (2024). Staphylococcus aureus: Current perspectives on molecular pathogenesis and virulence. Cell Surface, 13, Article 100137. https://doi.org/10.1016/j.tcsw.2024.100137
Gómez-Casanova, N., Gutiérrez-Zufiaurre, M. N., Blázquez de Castro, A. M., & Muñoz-Bellido, J. L. (2024). Genomic insights into Staphylococcus aureus isolates exhibiting diminished daptomycin susceptibility. Pathogens, 13(3), Article 206. https://doi.org/10.3390/pathogens13030206
Hamza, M., Sivaraman, G. K., & Mothadaka, M. P. (2024). Genomic portraits of methicillin-resistant staphylococci (MRS) from food fish unveiled the genes associated with staphylococcal food poisoning (SFP), virulence and antimicrobial resistance. BMC Microbiology, 24(1), Article 334. https://doi.org/10.1186/s12866-024-03469-0
Hemmati, Z., Soltani Borchaloee, A., Bazrafshan, F., Jahan Latibari, B., Mehrpour Ghaziani, P., Hashemi Khou, M. (2024). Study on the prevalence of methicillin-resistant Staphylococcus aureus infection, antibiotic resistance pattern, biofilms genes, and antibiotic resistance genes from clinical samples. Archives of Razi Institute, 79(5), 923–928. https://doi.org/10.32592/ARI.2024.79.5.923
Hiramatsu, K., Ito, T., Tsubakishita, S., Sasaki, T., Takeuchi, F., Morimoto, Y., Katayama, Y., Matsuo, M., Kuwahara-Arai, K., Hishinuma, T., Baba, T., & et al. (2013). Genomic basis for methicillin resistance in Staphylococcus aureus. Infection & Chemotherapy, 45(2), 117–136. https://doi.org/10.3947/ic.2013.45.2.117
Huang, S., Li, J., Liu, D., Zou, Y., Hang, T., Yuan, H., Yang, Y., Li, H., Dong, M., Qian, Y., Sun, Y., Huang, C., & Bai, G. (2025). Performance testing for the sensitivity and resolution of low-pass WGS for small CNV detection. BMC Medical Genomics, 18(1), Article 203. https://doi.org/10.1186/s12920-025-02263-9
Jiang, G., Liu, K., Qing, Y., Qin, L., Zou, Z., Liu, Z. (2024). Global trends of antibiotic resistance genes in Staphylococcus aureus: A comprehensive genomic analysis. Foodborne Pathogens and Disease, 21(10), 653–661. https://doi.org/10.1089/fpd.2024.0043
Kahraman Yılmaz, D., & Berik, N. (2024). Phenotypic and genotypic antibiotic resistance of Staphylococcus warneri and Staphylococcus pasteuri isolated from stuffed mussels. Aquatic Sciences and Engineering, 39(3), 172–178. https://doi.org/10.26650/ASE20241397385
Kang, H., Gao, A., & Zhu, Y. (2025). Bacterial restriction-modification systems: Mechanisms of defense against phage infection. Biophysics Reports, 11(5), 330–343. https://doi.org/10.52601/bpr.2025.240070
Karlsson, A., Alarcón, L. A., Piñeiro-Iglesias, B., Jacobsson, G., Skovbjerg, S., Moore, E. R. B., Kopparapu, P. K., Jin, T., & Karlsson, R. (2024). Surface-shaving of Staphylococcus aureus strains and quantitative proteomic analysis reveal differences in protein abundance of the surfaceome. Microorganisms, 12(8), Article 1725. https://doi.org/10.3390/microorganisms12081725
Liu, G. Y. (2009). Molecular pathogenesis of Staphylococcus aureus infection. Pediatric Research, 65(5 Pt 2), 71R–77R. https://doi.org/10.1203/PDR.0b013e31819dc44d
Loenen, W. A., Dryden, D. T., Raleigh, E. A., & Wilson, G. G. (2014). Type I restriction enzymes and their relatives. Nucleic Acids Research, 42(1), 20–44. https://doi.org/10.1093/nar/gkt847
López Gutierrez, L., Bettin Martinez, A., & Suárez Mahecha, H. (2017). Methicillin resistant Staphylococcus aureus isolated from meat raw in Cartagena, Colombia. Revista Facultad Nacional de Agronomía Medellín, 70(1). https://doi.org/10.15446/rfna.v70n1.61768
Merda, D., Vila-Nova, M., Bonis, M., Boutigny, A. L., Brauge, T., Cavaiuolo, M., Cunty, A., Regnier, A., Sayeb, M., Vingadassalon, N., Yvon, C., Chesnais, V., & et al. (2024). Unraveling the impact of genome assembly on bacterial typing: A one health perspective. BMC Genomics, 25(1), Article 1059. https://doi.org/10.1186/s12864-024-10982-z
Moges, M., Rodland, E. K., Legesse, T., & Argaw, A. (2024). Antibiotic resistance patterns of Staphylococcus aureus and Enterobacteriaceae isolated from street foods in selected towns of Ethiopia. BMC Infectious Diseases, 24(1), Article 367. https://doi.org/10.1186/s12879-024-09266-4
Morello, J. A., Mizer, H. E., & Granato, P. A. (2006). Laboratory manual and workbook in microbiology. McGraw-Hill.
Nei, M., & Kumar, S. (2000). Molecular evolution and phylogenetics. Oxford University Press. https://doi.org/10.1093/oso/9780195135848.001.0001
Nocera, F. P., & De Martino, L. (2024). Methicillin-resistant Staphylococcus pseudintermedius: Epidemiological changes, antibiotic resistance, and alternative therapeutic strategies. Veterinary Research Communications, 48, 3505–3515. https://doi.org/10.1007/s11259-024-10508-8
Ramos, B., & Cunha, M. V. (2024). The mobilome of Staphylococcus aureus from wild ungulates reveals epidemiological links at the animal-human interface. Environmental Pollution, 356, Article 124241. https://doi.org/10.1016/j.envpol.2024.124241
Rao, Y., Ahmed, N., Pritchard, J., & O'Brien, E. P. (2023). Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer. BMC Bioinformatics, 24(1), Article 462. https://doi.org/10.1186/s12859-023-05521-8
Shaw, L. P., Rocha, E. P. C., & MacLean, R. C. (2023). Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria. Nucleic Acids Research, 51(13), 6806–6818. https://doi.org/10.1093/nar/gkad452
Smillie, C., Garcillán-Barcia, M. P., Francia, M. V., Rocha, E. P., & de la Cruz, F. (2010). Mobility of plasmids. Microbiology and Molecular Biology Reviews, 74(3), 434–452. https://doi.org/10.1128/MMBR.00020-10
Sun, C., Yan, Y., Zhang, Y., Dong, J., Chen, X., Gao, F., Zhang, H., Wang, Z., Wu, C., Ye, X., Wang, F. (2025). Genome loci with selection signatures revealed in a domesticated mandarin fish population. BMC Genomics, 26(1), Article 947. https://doi.org/10.1186/s12864-025-12145-0
Titouche, Y., Akkou, M., Djaoui, Y., Chergui, A., Mechoub, D., Bentayeb, L., Fatihi, A., Nia, Y., & Hennekinne, J. A. (2025). Investigation of biofilm formation ability and antibiotic resistance of Staphylococcus aureus isolates from food products. Foodborne Pathogens and Disease, 22(9), 619–625. https://doi.org/10.1089/fpd.2024.0121
Vasu, K., & Nagaraja, V. (2013). Diverse functions of restriction-modification systems in addition to cellular defense. Microbiology and Molecular Biology Reviews, 77(1), 53–72. https://doi.org/10.1128/MMBR.00044-12
Wang, Y. T., Lin, Y. T., Wan, T. W., Wang, D. Y., Lin, H. Y., Lin, C. Y., & Chen, Y. C. (2019). Distribution of antibiotic resistance genes among Staphylococcus species isolated from ready-to-eat foods. Journal of Food and Drug Analysis, 27(4), 841–848. https://doi.org/10.1016/j.jfda.2019.05.003
Yaseen, A. A., Khashan, B. A., & Abedalhammed, H. S. (2020). A study on survey of bacterial contamination of some cake's types in the Iraqi market. Biochemical & Cellular Archives, 20(2), 5231–5238.
Zhang, J., & Qian, W. (2025). Functional synonymous mutations and their evolutionary consequences. Nature Reviews Genetics, 26(11), 789–804. https://doi.org/10.1038/s41576-025-00850-1
Zhao, N., Zhou, Z., Cui, S., Zhang, X., Zhu, S., Wang, Y., Zenda, T., & Wenjing, L. (2025). Advanced imaging-enabled understanding of cell wall remodeling mechanisms mediating plant drought stress tolerance. Frontiers in Plant Science, 16, Article 1635078. https://doi.org/10.3389/fpls.2025.1635078
