İnsanda Saptanan Çiftlik Hayvanları ile İlişkili Staphylococcus aureus ST398’in Virülans ve Direnç Genlerinin In Silico Analizi

Year 2021, Volume: 18 Issue: 2, 186 - 192, 27.08.2021

Mehmet Demirci Akin Yığın Fadile Yıldız Zeyrek

https://doi.org/10.35440/hutfd.929003

Abstract

Amaç: S. aureus ST398 kökenleri çiftlik hayvanları ile ilişkili tanımlanan ilk klonal kökenlerdir ve bu kökenlerin, tüm dünyada hızla yayılması nedeniyle bu klon özel bir yer edinmiştir. Bizde bu nedenle çalışmamızda, insan enfeksiyonlarında saptanan ve açık veritabanlarında gen dizilimleri bulunan LA-MRSA ST398 ve LA-MSSA ST398 kökenleri, hayvanlardan izole edilen LA-MRSA ST398 ve insan enfeksiyonları ile ilişkili standart MSSA ve MRSA kökenleri ile virülans ve antimikrobiyal direnç gen belirteçleri açısından in silico olarak karşılaştırmayı amaçladık.
Materyal ve metod: Çalışmamızda incelenen kökenler, insanlarda saptanan ve tüm genom analizleri yapılarak açık veritabanlarına yüklenen gen dizilimleri bulunan 2 LA-MRSA ST398 ve 2 LA-MSSA ST398'dir. Bu kökenleri karşılaştırmak amacıyla, hayvandan izole edilmiş LA-MRSA ST398 ve insan enfeksiyonlarıyla ilişkili MSSA ve MRSA kökenleri incelendi. CSI filogeni, CARD ve VFanalyzer online yazılımları sırasıyla evrimsel benzerlik, antimikrobiyal direnç genleri ve virülans faktörlerini karşılaştırmak için kullanıldı.
Bulgular: İnsan kaynaklı LA-MRSA ST398 ve LA-MSSA kökenlerinin filogeni benzerliği sırasıyla %98.1 ve %94.6 tespit edildi. LA-SA-ST398 kökenlerinin tümünde, makrolid-linkozamid-streptogramin ve eritromisin direnç genleri ön planda saptanırken, LA-MRSA ST398 kökenlerinde buna tetM gibi tetrasiklin eklenmiş olarak bulundu. ST398 kökenlerinde bağlanma ve enzim işlevi ile ilişkili bazı virülans faktörlerinin aktif olmadığı tespit edildi
Sonuç: Sonuç olarak çalışmamızda incelenen insan kaynaklı çiftlik hayvanları ile ilişkili MRSA ve MSSA ST398 kökenlerinde bağışıklıktan kaçış ile ilişkili virülans faktörlerine aktive ettiği, bazı toksin virülans faktörlerini ise kullanmadığı saptandı. Bu kökenlerin geliştirdikleri hastalıkların patogenezlerini anlayabilmek için eldeki verilerin yeni gelişen moleküler tekniklerle incelenmesinin epidemiyolojik olarak avantaj kazandıracağı kanaatindeyiz.

Keywords

Staphylococcus aureus, ST398, in silico analiz, virülans genleri, direnç genleri

In Silico Analysis of Virulence and Resistance Genes of Livestock-Associated Staphylococcus aureus ST398 Detected in Humans

Abstract

Background: Staphylococcus aureus ST398 strains are the first clonal strains identified in relation to livestock and this clone has gained a special place due to the rapid spread of these strains all over the world. Therefore, in our study, we aimed to compare in silico the LA-MRSA ST398 and LA-MSSA ST398 strains detected in human infections and with gene sequences in open databases, LA-MRSA ST398 isolated from animals and standard MSSA and MRSA strains associated with human infections in terms of virulence and antimicrobial resistance gene markers.
Materials and Methods: The strains examined in this study were 2 LA-MRSA ST398 and 2 LA-MSSA ST398, which have gene sequences detected in humans and uploaded into open databases by whole genome analysis. To compare these strains, MSSA and MRSA strains associated with human infections and LA-MRSA ST398 isolated from the animal were used. CSI phylogeny, CARD and VFanalyzer online software were used to compare evolutionary similarity, antimicrobial resistance genes and virulence factors, respectively.
Results: Evolutionary similarity of human-derived ST398 LA-MRSA and LA-MSSA strains were detected in 98.1% and 94.6%, respectively. Especially macrolide-lincosamide-streptogramin and erythromycin resistance genes were found in all LA-SA-ST398 strains, while tetracycline such as tetM was added to it in LA-MRSA ST398 strains. Some virulence factors associated with binding and enzyme function were found to be inactive in ST398 strains.
Conclusion: As a conclusion, it was determined that human derived LA-MRSA and LA-MSSA ST398 strains activated the virulence factors related with immun evasion, and did not use toxins as a virulence factor. In order to understand the pathogenesis of the diseases developed by these strains, we believe that analyzing the available data with newly developed molecular techniques will provide an epidemiological advantage.

Keywords

Staphylococcus aureus, ST398, in silico analysis, virulence genes, resistance genes

References

• Heaton CJ, Gerbig GR, Sensius LD, Patel V, Smith TC. Staphylococcus aureus Epidemiology in Wildlife: A Systematic Review. Antibiotics (Basel). 2020;9(2):89. doi:10.3390/antibiotics9020089
• Gurung RR, Maharjan P, Chhetri GG. Antibiotic resistance pattern of Staphylococcus aureus with reference to MRSA isolates from pediatric patients. Future Sci OA. 2020;6(4):FSO464. doi:10.2144/fsoa-2019-0122
• Gittens-St Hilaire MV, Chase E, Alleyne D. Prevalence, molecular characteristics and antimicrobial susceptibility patterns of MRSA in hospitalized and nonhospitalized patients in Barbados. New Microbes New Infect. 2020;35:100659. doi:10.1016/j.nmni.2020.100659
• Huang YC, Chen CJ. Detection and phylogeny of Staphylococcus aureus sequence type 398 in Taiwan. J Biomed Sci. 2020;27(1):15. doi:10.1186/s12929-019-0608-8
• Bouiller K, Bertrand X, Hocquet D, Chirouze C. Human Infection of Methicillin-Susceptible Staphylococcus aureus CC398: A Review. Microorganisms. 2020;8(11):1737. doi:10.3390/microorganisms8111737
• Lu H, Zhao L, Si Y, Jian Y, Wang Y, Li T, et al. The Surge of Hypervirulent ST398 MRSA Lineage With Higher Biofilm-Forming Ability Is a Critical Threat to Clinics. Front Microbiol. 2021;12:636788. doi:10.3389/fmicb.2021.636788
• Ballhausen B, Jung P, Kriegeskorte A, Makgotlho PE, Ruffing U, von Müller L, et al. LA-MRSA CC398 differ from classical community acquired-MRSA and hospital acquired-MRSA lineages: functional analysis of infection and colonization processes. Int J Med Microbiol. 2014;304(7):777-86. doi: 10.1016/j.ijmm.2014.06.006.
• Schijffelen MJ, Boel CH, van Strijp JA, Fluit AC. Whole genome analysis of a livestock-associated methicillin-resistant Staphylococcus aureus ST398 isolate from a case of human endocarditis. BMC Genomics. 2010;11:376. doi:10.1186/1471-2164-11-376
• Golding GR, Bryden L, Levett PN, McDonald RR, Wong A, Graham MR, et al. whole-genome sequence of livestock-associated st398 methicillin-resistant staphylococcus aureus Isolated from Humans in Canada. J Bacteriol. 2012;194(23):6627-6628. doi:10.1128/JB.01680-12
• Uhlemann AC, Porcella SF, Trivedi S, Sullivan SB, Hafer C, Kennedy AD, et al. Identification of a highly transmissible animal-independent Staphylococcus aureus ST398 clone with distinct genomic and cell adhesion properties. mBio. 2012;3(2):e00027-12. Published 2012 Feb 28. doi:10.1128/mBio.00027-12
• Kashif A, McClure JA, Lakhundi S, Pham M, Chen S, Conly JM, et al. Staphylococcus aureus ST398 Virulence Is Associated With Factors Carried on Prophage ϕSa3. Front Microbiol. 2019;10:2219. doi:10.3389/fmicb.2019.02219
• Hau SJ, Bayles DO, Alt DP, Frana TS, Nicholson TL. Complete Genome Sequence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Isolated from Swine in the United States. Genome Announc. 2017;5(32):e00790-17. doi:10.1128/genomeA.00790-17
• Holden MT, Feil EJ, Lindsay JA, Peacock SJ, Day NP, Enright MC, et al. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9786-91. doi: 10.1073/pnas.0402521101.
• Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O. Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS One 2014;9(8):e104984. doi: 10.1371/journal.pone.0104984.
• Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2020;48(D1):D517-D525. doi:10.1093/nar/gkz935
• Liu B, Zheng D, Jin Q, Chen L, Yang J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res. 2019;47(D1):D687-D692. doi:10.1093/nar/gky1080
• Chueahiran S, Yindee J, Boonkham P, Suanpairintr N, Chanchaithong P. Methicillin-Resistant Staphylococcus aureus Clonal Complex 398 as a Major MRSA Lineage in Dogs and Cats in Thailand. Antibiotics (Basel). 2021;10(3):243. doi:10.3390/antibiotics10030243
• Pirolo M, Visaggio D, Gioffrè A, Artuso I, Gherardi M, Pavia G, et al. Unidirectional animal-to-human transmission of methicillin-resistant Staphylococcus aureus ST398 in pig farming; evidence from a surveillance study in southern Italy. Antimicrob Resist Infect Control. 2019;8:187. doi:10.1186/s13756-019-0650-z
• Zarfel G, Krziwanek K, Johler S, Hoenigl M, Leitner E, Kittinger C, et al. Virulence and antimicrobial resistance genes in human MRSA ST398 isolates in Austria. Epidemiol Infect. 2013;141(4):888-892. doi:10.1017/S0950268812001343
• Argudín MA, Tenhagen BA, Fetsch A, Sachsenröder J, Käsbohrer A, Schroeter A, et al. Virulence and resistance determinants of German Staphylococcus aureus ST398 isolates from nonhuman sources. Appl Environ Microbiol. 2011;77(9):3052-3060. doi:10.1128/AEM.02260-10