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Research article

Food Microbiology and Biotechnology

Comparative Genomic Analysis of Staphylococcus aureus FORC_001 and S. aureus MRSA252 Reveals the Characteristics of Antibiotic Resistance and Virulence Factors for Human Infection

Sooyeon Lim 1, Dong-Hoon Lee 2, Woori Kwak 3, Hakdong Shin 1, Hye-Jin Ku 2, Jong-eun Lee 4, Gun Eui Lee 4, Heebal Kim 1, Sang-Ho Choi 1, Sangryeol Ryu 1 and Ju-Hoon Lee 2*

1Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea, 2Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea, 3C&K Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea, 4DNA Link, Inc. 12F, Asan Institute for Life Sciences 1, Seoul 138-736, Republic of Korea

Received: October 6, 2014; Accepted: October 22, 2014

J. Microbiol. Biotechnol. 2015; 25(1): 98-108

Published January 28, 2015 https://doi.org/10.4014/jmb.1410.10005

Copyright © The Korean Society for Microbiology and Biotechnology.

Abstract

Staphylococcus aureus is an important foodborne pathogen that causes diverse diseases ranging from minor infections to life-threatening conditions in humans and animals. To further understand its pathogenesis, the genome of the strain S. aureus FORC_001 was isolated from a contaminated food. Its genome consists of 2,886,017 bp double-stranded DNA with a GC content of 32.8%. It is predicted to contain 2,728 open reading frames, 57 tRNAs, and 6 rRNA operons, including 1 additional 5S rRNA gene. Comparative phylogenetic tree analysis of 40 complete S. aureus genome sequences using average nucleotide identity (ANI) revealed that strain FORC_001 belonged to Group I. The closest phylogenetic match was S. aureus MRSA252, according to a whole-genome ANI (99.87%), suggesting that they might share a common ancestor. Comparative genome analysis of FORC_001 and MRSA252 revealed two non-homologous regions: Regions I and II. The presence of various antibiotic resistance genes, including the SCCmec cluster in Region I of MRSA252, suggests that this strain might have acquired the SCCmec cluster to adapt to specific environments containing methicillin. Region II of both genomes contains prophage regions but their DNA sequence identity is very low, suggesting that the prophages might differ. This is the first report of the complete genome sequence of S. aureus isolated from a real foodborne outbreak in South Korea. This report would be helpful to extend our understanding about the genome, general characteristics, and virulence factors of S. aureus for further studies of pathogenesis, rapid detection, and epidemiological investigation in foodborne outbreak.

Keywords

Staphylococcus aureus, genome, foodborne pathogen, antibiotic resistance, virulence factor

References

  1. Albuquerque W, Macrae A, Sousa O, Vieira G, Vieira R. 2007. Multiple drug resistant Staphylococcus aureus strains isolated from a fish market and from fish handlers. Braz. J. Microbiol. 38: 131-134.
    CrossRef
  2. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
    Pubmed PMC CrossRef
  3. Balaban N, Rasooly A. 2000. Staphylococcal enterotoxins. Int. J. Food Microbiol. 61: 1-10.
    CrossRef
  4. Barber M, Rozwadowska-Dowzenko M. 1948. Infection by penicillin-resistant staphylococci. Lancet 252: 641-644.
    CrossRef
  5. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. 2005. ACT: the Artemis Comparison Tool. Bioinformatics 21: 3422-3423.
    Pubmed CrossRef
  6. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10: 563-569.
    Pubmed CrossRef
  7. Cooper JE, Feil EJ. 2006. The phylogeny of Staphylococcus aureus - which genes make the best intra-species markers? Microbiology 152: 1297-1305.
    Pubmed CrossRef
  8. Delcher AL, Salzberg SL, Phillippy AM. 2003. Using MUMmer to identify similar regions in large sequence sets. Curr. Protoc. Bioinformatics DOI: 10.1002/0471250953.
    CrossRef
  9. Demuth PJ, Gerding DN, Crossley K. 1979. Staphylococcus aureus bacteriuria. Arch. Intern. Med. 139: 78.
    Pubmed CrossRef
  10. Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, et al. 2010. Accessing the SEED genome databases via web services API: tools for programmers. BMC Genomics 11: 319.
    CrossRef
  11. Ferry T, Perpoint T, Vandenesch F, Etienne J. 2005. Virulence determinants in Staphylococcus aureus and their involvement in clinical syndromes. Curr. Infect. Dis. Rep. 7:420-428.
    Pubmed CrossRef
  12. Fetsch A, Contzen M, Hartelt K, Kleiser A, Maassen S, Rau J, et al. 2014. Staphylococcus aureus food-poisoning outbreak associated with the consumption of ice-cream. Int. J. Food Microbiol. 187: 1-6.
    Pubmed CrossRef
  13. Götz F, Bannerman T, Schleifer K-H. 2006. The genera Staphylococcus and Macrococcus, pp. 5-75. The Prokaryotes. Springer.
  14. Gao J, Stewart GC. 2004. Regulatory elements of the Staphylococcus aureus protein A (Spa) promoter. J. Bacteriol. 186: 3738-3748.
    Pubmed PMC CrossRef
  15. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57: 81-91.
    Pubmed CrossRef
  16. Hall TA. 1999. Presented at the Nucleic Acids Symposium Series.
  17. Hartman BJ, Tomasz A. 1984. Low-affinity penicillin-binding protein associated with beta-lactam resistance in Staphylococcus aureus. J. Bacteriol. 158: 513-516.
    Pubmed PMC
  18. Hummerjohann J, Naskova J, Baumgartner A, Graber HU. 2014. Enterotoxin-producing Staphylococcus aureus genotype B as a major contaminant in Swiss raw milk cheese. J. Dairy Sci. 97: 1305-1312.
    Pubmed CrossRef
  19. Konstantinidis KT, Tiedje JM. 2007. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr. Opin. Microbiol. 10: 504-509.
    Pubmed CrossRef
  20. Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, et al. 2001. Whole genome sequencing of methicillin-resistant Staphylococcus aureus. Lancet 357: 1225-1240.
    CrossRef
  21. Lee JH, Karamychev VN, Kozyavkin SA, Mills D, Pavlov AR, Pavlova NV, et al. 2008. Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics 9: 247.
    Pubmed PMC CrossRef
  22. Loffler B, Hussain M, Grundmeier M, Bruck M, Holzinger D, Varga G, et al. 2010. Staphylococcus aureus pantonvalentine leukocidin is a very potent cytotoxic factor for human neutrophils. PLoS Pathog. 6: e1000715.
    Pubmed PMC CrossRef
  23. Moreillon P, Entenza JM, Francioli P, McDevitt D, Foster TJ, Francois P, Vaudaux P. 1995. Role of Staphylococcus aureus coagulase and clumping factor in pathogenesis of experimental endocarditis. Infect. Immun. 63: 4738-4743.
    Pubmed PMC
  24. Musser JM, Kapur V. 1992. Clonal analysis of methicillinresistant Staphylococcus aureus strains from intercontinental sources: association of the mec gene with divergent phylogenetic lineages implies dissemination by horizontal transfer and recombination. J. Clin. Microbiol. 30: 2058-2063.
    Pubmed PMC
  25. Oguttu JW, McCrindle CME, Makita K, Grace D. 2014. Investigation of the food value chain of ready-to-eat chicken and the associated risk for staphylococcal food poisoning in Tshwane Metropole, South Africa. Food Control 45: 87-94.
    CrossRef
  26. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
    Pubmed CrossRef
  27. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
    Pubmed
  28. Schelin J, Wallin-Carlquist N, Cohn MT, Lindqvist R, Barker GC, Radstrom P. 2011. The formation of Staphylococcus aureus enterotoxin in food environments and advances in risk assessment. Virulence 2: 580-592.
    Pubmed PMC CrossRef
  29. Schlievert PM, Strandberg KL, Lin YC, Peterson ML, Leung DY. 2010. Secreted virulence factor comparison between methicillin-resistant and methicillin-sensitive Staphylococcus aureus, and its relevance to atopic dermatitis. J. Allergy Clin. Immun. 125: 39-49.
    Pubmed PMC CrossRef
  30. Suzuki Y, Omoe K, Hu DL, Sato'o Y, Ono HK, Monma C, et al. 2014. Molecular epidemiological characterization of Staphylococcus aureus isolates originating from food poisoning outbreaks that occurred in Tokyo, Japan. Microbiol Immunol. DOI: 10.1111/1348-0421.
  31. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30: 2725-2729.
    Pubmed PMC CrossRef
  32. Tranter HS. 1990. Foodborne staphylococcal illness. Lancet. 336: 1044-1046.
    CrossRef
  33. Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, et al. 2006. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 7: 142.
    Pubmed PMC CrossRef
  34. Wu S, Zhu Z, Fu L, Niu B, Li W. 2011. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12: 444.
    Pubmed PMC CrossRef

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Article

Research article

J. Microbiol. Biotechnol. 2015; 25(1): 98-108

Published online January 28, 2015 https://doi.org/10.4014/jmb.1410.10005

Copyright © The Korean Society for Microbiology and Biotechnology.

Comparative Genomic Analysis of Staphylococcus aureus FORC_001 and S. aureus MRSA252 Reveals the Characteristics of Antibiotic Resistance and Virulence Factors for Human Infection

Sooyeon Lim 1, Dong-Hoon Lee 2, Woori Kwak 3, Hakdong Shin 1, Hye-Jin Ku 2, Jong-eun Lee 4, Gun Eui Lee 4, Heebal Kim 1, Sang-Ho Choi 1, Sangryeol Ryu 1 and Ju-Hoon Lee 2*

1Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea, 2Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea, 3C&K Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea, 4DNA Link, Inc. 12F, Asan Institute for Life Sciences 1, Seoul 138-736, Republic of Korea

Received: October 6, 2014; Accepted: October 22, 2014

Abstract

Staphylococcus aureus is an important foodborne pathogen that causes diverse diseases ranging
from minor infections to life-threatening conditions in humans and animals. To further
understand its pathogenesis, the genome of the strain S. aureus FORC_001 was isolated from a
contaminated food. Its genome consists of 2,886,017 bp double-stranded DNA with a GC
content of 32.8%. It is predicted to contain 2,728 open reading frames, 57 tRNAs, and 6 rRNA
operons, including 1 additional 5S rRNA gene. Comparative phylogenetic tree analysis of 40
complete S. aureus genome sequences using average nucleotide identity (ANI) revealed that
strain FORC_001 belonged to Group I. The closest phylogenetic match was S. aureus
MRSA252, according to a whole-genome ANI (99.87%), suggesting that they might share a
common ancestor. Comparative genome analysis of FORC_001 and MRSA252 revealed two
non-homologous regions: Regions I and II. The presence of various antibiotic resistance genes,
including the SCCmec cluster in Region I of MRSA252, suggests that this strain might have
acquired the SCCmec cluster to adapt to specific environments containing methicillin. Region
II of both genomes contains prophage regions but their DNA sequence identity is very low,
suggesting that the prophages might differ. This is the first report of the complete genome
sequence of S. aureus isolated from a real foodborne outbreak in South Korea. This report
would be helpful to extend our understanding about the genome, general characteristics, and
virulence factors of S. aureus for further studies of pathogenesis, rapid detection, and
epidemiological investigation in foodborne outbreak.

Keywords: Staphylococcus aureus, genome, foodborne pathogen, antibiotic resistance, virulence factor

References

  1. Albuquerque W, Macrae A, Sousa O, Vieira G, Vieira R. 2007. Multiple drug resistant Staphylococcus aureus strains isolated from a fish market and from fish handlers. Braz. J. Microbiol. 38: 131-134.
    CrossRef
  2. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
    Pubmed KoreaMed CrossRef
  3. Balaban N, Rasooly A. 2000. Staphylococcal enterotoxins. Int. J. Food Microbiol. 61: 1-10.
    CrossRef
  4. Barber M, Rozwadowska-Dowzenko M. 1948. Infection by penicillin-resistant staphylococci. Lancet 252: 641-644.
    CrossRef
  5. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. 2005. ACT: the Artemis Comparison Tool. Bioinformatics 21: 3422-3423.
    Pubmed CrossRef
  6. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10: 563-569.
    Pubmed CrossRef
  7. Cooper JE, Feil EJ. 2006. The phylogeny of Staphylococcus aureus - which genes make the best intra-species markers? Microbiology 152: 1297-1305.
    Pubmed CrossRef
  8. Delcher AL, Salzberg SL, Phillippy AM. 2003. Using MUMmer to identify similar regions in large sequence sets. Curr. Protoc. Bioinformatics DOI: 10.1002/0471250953.
    CrossRef
  9. Demuth PJ, Gerding DN, Crossley K. 1979. Staphylococcus aureus bacteriuria. Arch. Intern. Med. 139: 78.
    Pubmed CrossRef
  10. Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, et al. 2010. Accessing the SEED genome databases via web services API: tools for programmers. BMC Genomics 11: 319.
    CrossRef
  11. Ferry T, Perpoint T, Vandenesch F, Etienne J. 2005. Virulence determinants in Staphylococcus aureus and their involvement in clinical syndromes. Curr. Infect. Dis. Rep. 7:420-428.
    Pubmed CrossRef
  12. Fetsch A, Contzen M, Hartelt K, Kleiser A, Maassen S, Rau J, et al. 2014. Staphylococcus aureus food-poisoning outbreak associated with the consumption of ice-cream. Int. J. Food Microbiol. 187: 1-6.
    Pubmed CrossRef
  13. Götz F, Bannerman T, Schleifer K-H. 2006. The genera Staphylococcus and Macrococcus, pp. 5-75. The Prokaryotes. Springer.
  14. Gao J, Stewart GC. 2004. Regulatory elements of the Staphylococcus aureus protein A (Spa) promoter. J. Bacteriol. 186: 3738-3748.
    Pubmed KoreaMed CrossRef
  15. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57: 81-91.
    Pubmed CrossRef
  16. Hall TA. 1999. Presented at the Nucleic Acids Symposium Series.
  17. Hartman BJ, Tomasz A. 1984. Low-affinity penicillin-binding protein associated with beta-lactam resistance in Staphylococcus aureus. J. Bacteriol. 158: 513-516.
    Pubmed KoreaMed
  18. Hummerjohann J, Naskova J, Baumgartner A, Graber HU. 2014. Enterotoxin-producing Staphylococcus aureus genotype B as a major contaminant in Swiss raw milk cheese. J. Dairy Sci. 97: 1305-1312.
    Pubmed CrossRef
  19. Konstantinidis KT, Tiedje JM. 2007. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr. Opin. Microbiol. 10: 504-509.
    Pubmed CrossRef
  20. Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, et al. 2001. Whole genome sequencing of methicillin-resistant Staphylococcus aureus. Lancet 357: 1225-1240.
    CrossRef
  21. Lee JH, Karamychev VN, Kozyavkin SA, Mills D, Pavlov AR, Pavlova NV, et al. 2008. Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics 9: 247.
    Pubmed KoreaMed CrossRef
  22. Loffler B, Hussain M, Grundmeier M, Bruck M, Holzinger D, Varga G, et al. 2010. Staphylococcus aureus pantonvalentine leukocidin is a very potent cytotoxic factor for human neutrophils. PLoS Pathog. 6: e1000715.
    Pubmed KoreaMed CrossRef
  23. Moreillon P, Entenza JM, Francioli P, McDevitt D, Foster TJ, Francois P, Vaudaux P. 1995. Role of Staphylococcus aureus coagulase and clumping factor in pathogenesis of experimental endocarditis. Infect. Immun. 63: 4738-4743.
    Pubmed KoreaMed
  24. Musser JM, Kapur V. 1992. Clonal analysis of methicillinresistant Staphylococcus aureus strains from intercontinental sources: association of the mec gene with divergent phylogenetic lineages implies dissemination by horizontal transfer and recombination. J. Clin. Microbiol. 30: 2058-2063.
    Pubmed KoreaMed
  25. Oguttu JW, McCrindle CME, Makita K, Grace D. 2014. Investigation of the food value chain of ready-to-eat chicken and the associated risk for staphylococcal food poisoning in Tshwane Metropole, South Africa. Food Control 45: 87-94.
    CrossRef
  26. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
    Pubmed CrossRef
  27. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
    Pubmed
  28. Schelin J, Wallin-Carlquist N, Cohn MT, Lindqvist R, Barker GC, Radstrom P. 2011. The formation of Staphylococcus aureus enterotoxin in food environments and advances in risk assessment. Virulence 2: 580-592.
    Pubmed KoreaMed CrossRef
  29. Schlievert PM, Strandberg KL, Lin YC, Peterson ML, Leung DY. 2010. Secreted virulence factor comparison between methicillin-resistant and methicillin-sensitive Staphylococcus aureus, and its relevance to atopic dermatitis. J. Allergy Clin. Immun. 125: 39-49.
    Pubmed KoreaMed CrossRef
  30. Suzuki Y, Omoe K, Hu DL, Sato'o Y, Ono HK, Monma C, et al. 2014. Molecular epidemiological characterization of Staphylococcus aureus isolates originating from food poisoning outbreaks that occurred in Tokyo, Japan. Microbiol Immunol. DOI: 10.1111/1348-0421.
  31. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30: 2725-2729.
    Pubmed KoreaMed CrossRef
  32. Tranter HS. 1990. Foodborne staphylococcal illness. Lancet. 336: 1044-1046.
    CrossRef
  33. Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, et al. 2006. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 7: 142.
    Pubmed KoreaMed CrossRef
  34. Wu S, Zhu Z, Fu L, Niu B, Li W. 2011. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12: 444.
    Pubmed KoreaMed CrossRef