In Silico MLST, SCCmec and SPA Typing OF Human MRSA Strains and Determination of Antimicrobial Resistance Genes

Abstract

Objectives: The incidence of MRSA still remains an important public health problem. This study aimed to perform in silico analysis of MLST, SCCmec, spa type, evolutionary similarity, and whole-genome sequencing (WGS) based antimicrobial susceptibility testing by using genomic data of MRSA strains isolated from human infections in different countries. Methods: WGS data of 30 MRSA strains were obtained as etiological agents were download from NCBI. Phylogeny analysis with large data was performed via CSI Phylogeny online software. SCCmec, MLST, and spa typing were performed using the software at the Center for Genomic Epidemiology. ResFinder 4.0 was used to perform WGS based antimicrobial susceptibility testing. Results: After in silico analysis of 30 MRSA strains, 14 different spa types, 11 different sequence types, and 9 different SCCmec types were detected. T037, ST239, and SCCmec_type_III(3A) were the most detected spa, MLST, and SCCmec types. WGS based antimicrobial susceptibility testing results were analyzed, 28, 27, and 26 out of 30 MRSA strains carrying aminoglycoside tetracycline and fluoroquinolone resistance genes respectively. Conclusion: Our in silico analysis results, we found that similar typing profiles could be observed in the strains in different geographical locations, and certain types of spa, MLST, and SCCmec can coexist.

Keywords

• MRSA
• MLST
• SCCmec
• in slico analysis
• WGS based antimicrobial test

References

1. 1. Kulkarni A. P., Nagvekar V. C., Veeraraghavan B., Warier A. R., Ahdal J., Jain R.: Current Perspectives on Treatment of Gram-Positive Infections in India: What Is the Way Forward?. Interdiscip Perspect Infect Dis. 2019, 7601847 (2019). https://doi.org/10.1155/2019/7601847
2. 2. Sarkhoo E., Udo E. E., Boswihi S. S., Monecke S., Mueller E., Ehricht R. The Dissemination and Molecular Characterization of Clonal Complex 361 (CC361) Methicillin-Resistant Staphylococcus aureus (MRSA) in Kuwait Hospitals. Front Microbiol. 12, 658772 (2021)10.3389/fmicb.2021.658772
3. 3. Shang L., Li J., Song C., et al. Hybrid Antimicrobial Peptide Targeting Staphylococcus aureus and Displaying Anti-infective Activity in a Murine Model. Front Microbiol. 11, 1767. (2020) https://doi.org/10.3389/fmicb.2020.01767
4. 4. Monecke S, Coombs G, Shore AC, et al. A field guide to pandemic, epidemic and sporadic clones of methicillin-resistant Staphylococcus aureus. PLoS One. 2011;6(4):e17936. https://doi.org/10.1371/journal.pone.0017936
5. 5. Mohammed KAS, Abdulkareem ZH, Alzaalan AR, Yaqoob AK. Spa typing of Staphylococcus aureus Isolated from Clinical Specimens from Outpatients in Iraq. Pol J Microbiol. 2021;70(1):79-85. https://doi.org/10.33073/pjm-2021-007
6. 6. Liu Y, Ji Y. Multilocus Sequence Typing of Staphylococcus aureus. Methods Mol Biol. 2020;2069:95-102. doi: 10.1007/978-1-4939-9849-4_7
7. 7. Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O. Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS One. 2014 Aug 11;9(8):e104984. https://doi.org/10.1371/journal.pone.0104984
8. 8. International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements (IWG-SCC). Classification of staphylococcal cassette chromosome mec (SCCmec): guidelines for reporting novel SCCmec elements. Antimicrob Agents Chemother. 2009 Dec;53(12):4961-7. https://doi.org/10.1128/AAC.00579-09

9. 9. Bartels MD, Petersen A, Worning P, et al. Comparing whole-genome sequencing with Sanger sequencing for spa typing of methicillin-resistant Staphylococcus aureus. J Clin Microbiol. 2014;52(12):4305-4308. https://doi.org/10.1128/JCM.01979-14
10. 10. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012 Apr;50(4):1355-61. https://doi.org/10.1128/JCM.06094-11
11. 11. Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother. 2020 Dec 1;75(12):3491-3500. 10.1093/jac/dkaa345
12. 12. Ali MS, Isa NM, Abedelrhman FM, Alyas TB, Mohammed SE, Ahmed AE, Ahmed ZSA, Lau NS, Garbi MI, Amirul AA, Seed AO, Omer RA, Mohamed SB. Genomic analysis of methicillin-resistant Staphylococcus aureus strain SO-1977 from Sudan. BMC Microbiol. 2019 Jun 11;19(1):126. 10.1186/s12866-019-1470-2
13. 13. Zhou W, Li X, Osmundson T, Shi L, Ren J, Yan H. WGS analysis of ST9-MRSA-XII isolates from live pigs in China provides insights into transmission among porcine, human and bovine hosts. J Antimicrob Chemother. 2018 Oct 1;73(10):2652-2661. https://doi.org/10.1093/jac/dky245
14. 14. Asadollahi P, Farahani NN, Mirzaii M, Khoramrooz SS, van Belkum A, Asadollahi K, Dadashi M, Darban-Sarokhalil D. Distribution of the Most Prevalent Spa Types among Clinical Isolates of Methicillin-Resistant and -Susceptible Staphylococcus aureus around the World: A Review. Front Microbiol. 2018 Feb 12;9:163. https://doi.org/10.3389/fmicb.2018.00163
15. 15. Neela V, Ghasemzadeh Moghaddam H, van Belkum A, Horst-Kreft D, Mariana NS, Ghaznavi Rad E. First report on methicillin-resistant Staphylococcus aureus of Spa type T037, Sequence Type 239, SCCmec type III/IIIA in Malaysia. Eur J Clin Microbiol Infect Dis. 2010 Jan;29(1):115-7. DOI: 10.1007/s10096-009-0813-6
16. 16. Stańkowska M, Garbacz K, Piechowicz L, Bronk M. Dissemination Of t437-SCCmecIV And Coagulase-Negative t037-SCCmecIII Types Among Borderline Oxacillin-Resistant Staphylococcus aureus Isolated From Skin Infections And Diabetic Foot Ulcers. Infect Drug Resist. 2019;12:3197-3203. DOI: 10.2147/IDR.S219557
17. 17. Dai Y, Liu J, Guo W, et al. Decreasing methicillin-resistant Staphylococcus aureus (MRSA) infections is attributable to the disappearance of predominant MRSA ST239 clones, Shanghai, 2008-2017. Emerg Microbes Infect. 2019;8(1):471-478. https://doi.org/10.1080/22221751.2019.1595161
18. 18. Gostev VV, Sidorenko SV. [Staphylococcal cassette chromosome mec, evolution and genetic lines of methicillin resistant Staphylococcus aureus]. Antibiot Khimioter. 2012;57(9-10):38-46.
19. 19. Mohammadi S, Sekawi Z, Monjezi A, Maleki MH, Soroush S, Sadeghifard N, Pakzad I, Azizi-Jalilian F, Emaneini M, Asadollahi K, Pourahmad F, Zarrilli R, Taherikalani M. Emergence of SCCmec type III with variable antimicrobial resistance profiles and spa types among methicillin-resistant Staphylococcus aureus isolated from healthcare- and community-acquired infections in the west of Iran. Int J Infect Dis. 2014;25:152-8. DOI: 10.1016/j.ijid.2014.02.018
20. 20. Ebrahim-Saraie HS, Motamedifar M, Sarvari J, Hoseini Alfatemi SM. Emergence of SCCmec Type I Obtained From Clinical Samples in Shiraz Teaching Hospitals, South-West of Iran. Jundishapur J Microbiol. 2015;8(6):e16998. doi: 10.5812/jjm.16998v2.