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Farklı Salmonella Typhimurium kökenlerinin taşıdıkları patojenite adası ve direnç genlerinin in silico analizi

Yıl 2021, Cilt: 32 Sayı: 2, 151 - 156, 30.12.2021
https://doi.org/10.35864/evmd.960813

Öz

Salmonella Typhimurium, dünyada en sık izole edilen Salmonella serotiplerinden birisidir. Tüm genom analizi gibi yeni moleküler yöntemlerin gelişmesi ile, antibiyotik direnci ve farklı genlerin karşılaştırmalı analizleri daha kolay yapılabilmektedir. Çalışmamızda farklı S. Typhimurium kökenlerine ait genomik verilerin, taşıdıkları patojenite adaları, MLST, seqserotipleri ve direnç genleri açısından karşılaştırmalı in silico analizini gerçekleştirmeyi amaçladık. Çalışmamıza genomik verileri NCBI’da yer alan 15 farklı S. Typhimurium kökenini dahil edildi. Kökenlerin birbirleri ile evrimsel olarak yakınlıkları CSI filogeni ile antimikrobiyal direnç belirteçlerinin varlığı ise ResFinder yazılımı ile gerçekleştirildi. Salmonella kökenlerine ait patojenite adaları, MLST ve serotip tespiti için sırasıyla SPIFinder, MLST ve SeqSero yazılımları kullanıldı. Çalışmamıza dahil edilen 15 S. Typhimurium kökeninin birbirlerine %97 ve üstünde genomik benzerlik gösterdikleri tespit edildi. MLST analizlerine göre 9 köken (%60) ST19 olarak bulundu. Tüm kökenlerin SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-14 patojenite adalarını taşıdıkları gözlenirken, SGI1 patojenite adası sadece 3 kökende tespit edildi. Aminoglikozid direnci ile ilişkili aac(6')-Iaa geni tüm kökenlerde saptandı. Yeni nesil dizileme tekniklerinin gelişimi, S. Typhimurium gibi önemli enfeksiyon etkenlerine ait yeni moleküler epidemiyolojik veriler elde edilmesini sağlamaktadır. Bu verilerin karşılaştırmalı in silico analizleri ile enfeksiyonlarda kullandıkları virülans genlerinin analizleri ve moleküler patogenez mekanizmalarının aydınlatılması sağlanabilecektir.

Kaynakça

  • Anderson C.J., Kendall M.M. (2017). Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation. Front Microbiol. 2017;8:1983.
  • Bahramianfard H, Derakhshandeh A, Naziri Z, Khaltabadi Farahani R. (2021). Prevalence, virulence factor and antimicrobial resistance analysis of Salmonella Enteritidis from poultry and egg samples in Iran. BMC Vet ReS. 2021;17(1):196.
  • Banerji S, Simon S, Tille A, Fruth A, Flieger A.(2020). Genome-based Salmonella serotyping as the new gold standard. Sci Rep. 9;10(1):4333.
  • Barilleau E, Védrine M, Koczerka M, et al.(2021). Investigation of the invasion mechanism mediated by the outer membrane protein PagN of Salmonella Typhimurium. BMC Microbiol. 21(1):153.
  • 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. (2020). ResFinder 4.0 for predictions of phenotypes from genotypeS. J Antimicrob Chemother. 1;75(12):3491-3500.
  • Boyd, D.A., Peters, G.A., Ng, L.K., and Mulvey, M.R. (2000). Partial characterization of a genomic island associated with the multidrug resistance region of Salmonella enterica Typhimurium DT104. FEMS Microbiol Lett 189: 285– 291
  • Carden S, Okoro C, Dougan G, Monack D. (2015). Non-typhoidal Salmonella Typhimurium ST313 isolates that cause bacteremia in humans stimulate less inflammasome activation than ST19 isolates associated with gastroenteritiS. Pathog DiS. 73(4):ftu023.
  • Gart E.V., Suchodolski J.S., Welsh T.H. Jr, Alaniz R.C., Randel R.D., Lawhon S.D.(2016). Salmonella Typhimurium and Multidirectional Communication in the Gut. Front Microbiol. 2016;7:1827.
  • Hayward M.R., AbuOun M., La Ragione R.M., Tchórzewska M.A., Cooley W.A., Everest D.J., Petrovska L., Jansen V.A., Woodward M.J. (2014). SPI-23 of S. Derby: role in adherence and invasion of porcine tissueS. PLoS One. 19;9(9):e107857.
  • Ibrahim G.M., Morin P.M. (2018). Salmonella Serotyping Using Whole Genome Sequencing. Front Microbiol. 13;9:2993.
  • Ilyas B, Tsai CN, Coombes BK. (2017). Evolution of Salmonella-Host Cell Interactions through a Dynamic Bacterial Genome. Front Cell Infect Microbiol. 7:428.
  • Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O.(2014). Solving the problem of comparing whole bacterial genomes across different sequencing platformS. PLoS One. 11;9(8):e104984.
  • Kingsley RA, Humphries AD, Weening EH, De Zoete MR, Winter S, Papaconstantinopoulou A, Dougan G, Bäumler AJ.(2003). Molecular and phenotypic analysis of the CS54 island of Salmonella enterica serotype typhimurium: identification of intestinal colonization and persistence determinant S. Infect Immun. 71(2):629-40.
  • Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O. (2012). Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012;50(4):1355-61.
  • Lerminiaux NA, MacKenzie KD, Cameron ADS. (2020). Salmonella Pathogenicity Island 1 (SPI-1): The Evolution and Stabilization of a Core Genomic Type Three Secretion System. MicroorganismS. 8(4):576.
  • Monte DFM, Sellera FP, Lopes R, Keelara S, Landgraf M, Greene S, et al. (2020) Class 1 integron-borne cassettes harboring blaCARB-2 gene in multidrug-resistant and virulent Salmonella Typhimurium ST19 strains recovered from clinical human stool samples, United StateS. PLoS ONE 15 (10): e0240978.
  • Patchanee P, Tanamai P, Tadee P, Hitchings MD, Calland JK, Sheppard SK, Meunsene D, Pascoe B, Tadee P. (2020). Whole-genome characterisation of multidrug resistant monophasic variants of Salmonella Typhimurium from pig production in Thailand. PeerJ 8:e9700
  • Rau RB, de Lima-Morales D, Wink PL, Ribeiro AR, Barth AL. (2020). Salmonella enterica mcr-1 Positive from Food in Brazil: Detection and Characterization. Foodborne Pathog DiS. 17(3):202-208.
  • Roer L, Hendriksen RS, Leekitcharoenphon P, Lukjancenko O, Kaas RS, Hasman H, Aarestrup FM.(2016). Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems? mSystemS. 2016;1(3):e00009-16.
  • Singh N, Li X, Beshearse E, Blanton JL, DeMent J, Havelaar AH.(2021). Molecular Epidemiology of Salmonellosis in Florida, USA, 2017-2018. Front Med (Lausanne). 8:656827.
  • Unlu O, Aktas Z, Tugrul HM.(2018). Analysis of Virulence Factors and Antimicrobial Resistance in Salmonella Using Molecular Techniques and Identification of Clonal Relationships Among the StrainS. Microb Drug Resist. 2018 Dec;24(10):1475-1482.
  • Urrutia IM, Fuentes JA, Valenzuela LM, Ortega AP, Hidalgo AA, Mora GC.(2014). Salmonella Typhi shdA: pseudogene or allelic variant? Infect Genet Evol. 2014;26:146-52.
  • Velásquez JC, Hidalgo AA, Villagra N, Santiviago CA, Mora GC, Fuentes JA.(2016). SPI-9 of Salmonella enterica serovar Typhi is constituted by an operon positively regulated by RpoS and contributes to adherence to epithelial cells in culture. Microbiology (Reading). 162(8):1367-1378
  • Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. (2015).Salmonella serotype determination utilizing high-throughput genome sequencing data. J Clin Microbiol. 53(5):1685-92.
  • Yang C, Shao W, Wei L, Chen L, Zhu A, Pan Z. (2021). Subtyping Salmonella isolated from pet dogs with multilocus sequence typing (MLST) and clustered regularly interspaced short palindromic repeats (CRISPRs). AMB ExpresS. 11(1):60.

In silico analysis of pathogenicity island and resistance genes carried by different Salmonella Typhimurium strains

Yıl 2021, Cilt: 32 Sayı: 2, 151 - 156, 30.12.2021
https://doi.org/10.35864/evmd.960813

Öz

Salmonella Typhimurium is one of the most frequently isolated Salmonella serotypes in the world. With the path of the new strategy of analysis like the whole genome, comparative analyzes of weaknesses and different genes can be done more easily. In our study, S. Typhimurium has different origins, it is aimed for different purposes to analyze genomic data, calculus pathogens islands, belonging MLST, seqs types, and silico genes. Our study included 15 different S. Typhimurium strains whose local data were obtained in NCBI. Evolutionary affinities of origins with C. Pathogenicity islands of Salmonella origin, SPIFinder, MLST, and SeqSero software for MLST. It was determined that Typhimurium origins showed 97% and more genomic similarity. According to MLST analysis, origin 9 (60%) was found to be ST19. While all were observed to carry pathogenicity islands SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-14, only 3 were detected in the SGI1 pathogenicity island. The aminoglycoside-related aac(6')-Iaa gene was detected in all strains. It would seem that the course of sequencing techniques such as the next generation is to obtain a new epidemiological route for owners of S. Typhimurium. With these data comparative analyzes, virulence genes that can be applied and the analyzes that can be corrected can be elucidated.

Kaynakça

  • Anderson C.J., Kendall M.M. (2017). Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation. Front Microbiol. 2017;8:1983.
  • Bahramianfard H, Derakhshandeh A, Naziri Z, Khaltabadi Farahani R. (2021). Prevalence, virulence factor and antimicrobial resistance analysis of Salmonella Enteritidis from poultry and egg samples in Iran. BMC Vet ReS. 2021;17(1):196.
  • Banerji S, Simon S, Tille A, Fruth A, Flieger A.(2020). Genome-based Salmonella serotyping as the new gold standard. Sci Rep. 9;10(1):4333.
  • Barilleau E, Védrine M, Koczerka M, et al.(2021). Investigation of the invasion mechanism mediated by the outer membrane protein PagN of Salmonella Typhimurium. BMC Microbiol. 21(1):153.
  • 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. (2020). ResFinder 4.0 for predictions of phenotypes from genotypeS. J Antimicrob Chemother. 1;75(12):3491-3500.
  • Boyd, D.A., Peters, G.A., Ng, L.K., and Mulvey, M.R. (2000). Partial characterization of a genomic island associated with the multidrug resistance region of Salmonella enterica Typhimurium DT104. FEMS Microbiol Lett 189: 285– 291
  • Carden S, Okoro C, Dougan G, Monack D. (2015). Non-typhoidal Salmonella Typhimurium ST313 isolates that cause bacteremia in humans stimulate less inflammasome activation than ST19 isolates associated with gastroenteritiS. Pathog DiS. 73(4):ftu023.
  • Gart E.V., Suchodolski J.S., Welsh T.H. Jr, Alaniz R.C., Randel R.D., Lawhon S.D.(2016). Salmonella Typhimurium and Multidirectional Communication in the Gut. Front Microbiol. 2016;7:1827.
  • Hayward M.R., AbuOun M., La Ragione R.M., Tchórzewska M.A., Cooley W.A., Everest D.J., Petrovska L., Jansen V.A., Woodward M.J. (2014). SPI-23 of S. Derby: role in adherence and invasion of porcine tissueS. PLoS One. 19;9(9):e107857.
  • Ibrahim G.M., Morin P.M. (2018). Salmonella Serotyping Using Whole Genome Sequencing. Front Microbiol. 13;9:2993.
  • Ilyas B, Tsai CN, Coombes BK. (2017). Evolution of Salmonella-Host Cell Interactions through a Dynamic Bacterial Genome. Front Cell Infect Microbiol. 7:428.
  • Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O.(2014). Solving the problem of comparing whole bacterial genomes across different sequencing platformS. PLoS One. 11;9(8):e104984.
  • Kingsley RA, Humphries AD, Weening EH, De Zoete MR, Winter S, Papaconstantinopoulou A, Dougan G, Bäumler AJ.(2003). Molecular and phenotypic analysis of the CS54 island of Salmonella enterica serotype typhimurium: identification of intestinal colonization and persistence determinant S. Infect Immun. 71(2):629-40.
  • Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O. (2012). Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012;50(4):1355-61.
  • Lerminiaux NA, MacKenzie KD, Cameron ADS. (2020). Salmonella Pathogenicity Island 1 (SPI-1): The Evolution and Stabilization of a Core Genomic Type Three Secretion System. MicroorganismS. 8(4):576.
  • Monte DFM, Sellera FP, Lopes R, Keelara S, Landgraf M, Greene S, et al. (2020) Class 1 integron-borne cassettes harboring blaCARB-2 gene in multidrug-resistant and virulent Salmonella Typhimurium ST19 strains recovered from clinical human stool samples, United StateS. PLoS ONE 15 (10): e0240978.
  • Patchanee P, Tanamai P, Tadee P, Hitchings MD, Calland JK, Sheppard SK, Meunsene D, Pascoe B, Tadee P. (2020). Whole-genome characterisation of multidrug resistant monophasic variants of Salmonella Typhimurium from pig production in Thailand. PeerJ 8:e9700
  • Rau RB, de Lima-Morales D, Wink PL, Ribeiro AR, Barth AL. (2020). Salmonella enterica mcr-1 Positive from Food in Brazil: Detection and Characterization. Foodborne Pathog DiS. 17(3):202-208.
  • Roer L, Hendriksen RS, Leekitcharoenphon P, Lukjancenko O, Kaas RS, Hasman H, Aarestrup FM.(2016). Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems? mSystemS. 2016;1(3):e00009-16.
  • Singh N, Li X, Beshearse E, Blanton JL, DeMent J, Havelaar AH.(2021). Molecular Epidemiology of Salmonellosis in Florida, USA, 2017-2018. Front Med (Lausanne). 8:656827.
  • Unlu O, Aktas Z, Tugrul HM.(2018). Analysis of Virulence Factors and Antimicrobial Resistance in Salmonella Using Molecular Techniques and Identification of Clonal Relationships Among the StrainS. Microb Drug Resist. 2018 Dec;24(10):1475-1482.
  • Urrutia IM, Fuentes JA, Valenzuela LM, Ortega AP, Hidalgo AA, Mora GC.(2014). Salmonella Typhi shdA: pseudogene or allelic variant? Infect Genet Evol. 2014;26:146-52.
  • Velásquez JC, Hidalgo AA, Villagra N, Santiviago CA, Mora GC, Fuentes JA.(2016). SPI-9 of Salmonella enterica serovar Typhi is constituted by an operon positively regulated by RpoS and contributes to adherence to epithelial cells in culture. Microbiology (Reading). 162(8):1367-1378
  • Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. (2015).Salmonella serotype determination utilizing high-throughput genome sequencing data. J Clin Microbiol. 53(5):1685-92.
  • Yang C, Shao W, Wei L, Chen L, Zhu A, Pan Z. (2021). Subtyping Salmonella isolated from pet dogs with multilocus sequence typing (MLST) and clustered regularly interspaced short palindromic repeats (CRISPRs). AMB ExpresS. 11(1):60.
Toplam 25 adet kaynakça vardır.

Ayrıntılar

Birincil Dil Türkçe
Konular Veteriner Bilimleri
Bölüm Araştırma Makaleleri
Yazarlar

Özge Ünlü 0000-0002-5411-5925

Mehmet Demirci 0000-0001-9670-2426

Akin Yığın 0000-0001-9758-1697

Seda Ekici 0000-0002-7982-5261

Erken Görünüm Tarihi 30 Aralık 2021
Yayımlanma Tarihi 30 Aralık 2021
Gönderilme Tarihi 1 Temmuz 2021
Yayımlandığı Sayı Yıl 2021 Cilt: 32 Sayı: 2

Kaynak Göster

APA Ünlü, Ö., Demirci, M., Yığın, A., Ekici, S. (2021). Farklı Salmonella Typhimurium kökenlerinin taşıdıkları patojenite adası ve direnç genlerinin in silico analizi. Etlik Veteriner Mikrobiyoloji Dergisi, 32(2), 151-156. https://doi.org/10.35864/evmd.960813


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