Database Authors
Summary The Staphylococcaceae are a family of Bacillota comprised of nine formal genera which are Gram-positive, chemoorganotrophic, non-motile and facultative anaerobes [Schleifer09, Madhaiyan20]. Of the genera within this family, the type genus Staphylococcus is arguably the most well-known due to the recognized pathogenic capacity of the species Staphylococcus aureus observed in the last three decades, with terms such as MRSA (methicillin-resistant S. aureus) and CA-MRSA (community-acquired methicillin resistant S. aureus) becoming colloquial terms by the mid-2000s [Easton09, Tong15, Bouchoucha19]. Commonly found as a commensal microbe living within the nasopharyngeal areas and on the skin of up to 30% of humans and also found on other mammals, colonization by S. aureus is most often harmless and asymptomatic [Wertheim05, Tong15, Ford20].

However, S. aureus is also a leading cause of food poisoning, bacteremia, endocarditis, skin and soft tissue infections (SSTIs), and osteoarticular (osteomyelitis), pleuropulmonary (pneumonia) and device-related infections worldwide [Ong13, Reizner14, Holland14, Tong15]. The pan-genome of S. aureus encodes a vast array of toxins and other virulence factors which aid evasion from the host immune system and facilitate persistent infections; an analysis of 64 phylogenetically, ecologically and phenotypically heterogeneous strains of S. aureus conducted in 2016 also identified that 38% of the pan genome-encoded virulence factors, such as cytotoxins and polysaccharide capsule biosynthesis genes, were also present in the core-genome [Zecconi13, Tong15, Bosi16, Cheung21].

In addition to the presence of multiple virulence factors, the drug resistance of MRSA and CA-MRSA strains of S. aureus is a significant contributing factor to its status as a leading pathogen [Guo20, Cheung21]. Whilst the widespread presence of beta-lactam resistance in these strains of S. aureus is problematic, complete resistance to the drug of last resort often used for serious and life-threatening S. aureus infections, the glycopeptide vancomycin, has been observed since 2002 and is increasing [vanHal12, Cong20].

This PGDB is based on the genome of the model strain Staphylococcus aureus aureus NCTC 8325, a strain isolated from a patient with sepsis in 1960 and utilized as the propagating strain for phage 47 of the international phage-typing system [Herbert10]. S. aureus NCTC 8325 was initially chosen for research due to its antibiotic susceptibility, and today the strain and its many derivatives, such as the phage-cured S. aureus NCTC 8325-4, are the most commonly used strains for experimental studies in the species [Iandolo02, Herbert10].

This Pathway/Genome Database (PGDB) was generated on 28-Nov-2017 by the PathoLogic [Karp10, Karp11, Caspi14] component of Pathway Tools software version 22.0 and MetaCyc version 21.5. The PGDB integrates the biochemical reaction network and metabolic pathways of the organism with its genome.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
chromosome3,2052,834343282,821,356RefSeq:NC_007795
Ortholog data available?Yes
Database Contents
Genes3,205
Pathways235
Enzymatic Reactions1,253
Transport Reactions91
Polypeptides2,836
Protein Complexes103
Enzymes694
Transporters236
Compounds981
Transcription Units1,775
tRNAs62
Growth Media2
Protein Features3,441
GO Terms32,798
Gene Essentiality Datasets2
Database Version29.0
Image of Staphylococcus aureus cells
A Scanning electron micrograph of Staphylococcus aureus cells, provided by the National Institute of Allergy and Infectious Diseases (NIAID). Used under creative commons license.
Synonyms Staphylococcus aureus subsp. aureus str. NCTC 8325
Staphylococcus aureus subsp. aureus strain NCTC 8325
Staphylococcus aureus subsp. aureus NCTC 8325
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Bacillales
Staphylococcaceae
Staphylococcus
Staphylococcus aureus
Staphylococcus aureus aureus NCTC 8325
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA57795
NCBI-Taxonomy93061
Relationship to Oxygenfacultative
Trophic Levelheterotroph
Temperature Rangemesophile
Pathogenicityhuman
NCBI Genome Typereference
Copyright SRI International 2018. All Rights Reserved.


References

Bosi16: Bosi E, Monk JM, Aziz RK, Fondi M, Nizet V, Palsson BO (2016). "Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity." Proc Natl Acad Sci U S A 113(26);E3801-9. PMID: 27286824

Bouchoucha19: Bouchoucha SL, Whatman E, Johnstone MJ (2019). "Media representation of the antimicrobial resistance (AMR) crisis: An Australian perspective." Infect Dis Health 24(1);23-31. PMID: 30541696

Caspi14: Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (2014). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases." Nucleic Acids Res 42(Database issue);D459-71. PMID: 24225315

Cheung21: Cheung GYC, Bae JS, Otto M (2021). "Pathogenicity and virulence of Staphylococcus aureus." Virulence 12(1);547-569. PMID: 33522395

Cong20: Cong Y, Yang S, Rao X (2020). "Vancomycin resistant Staphylococcus aureus infections: A review of case updating and clinical features." J Adv Res 21;169-176. PMID: 32071785

Easton09: Easton PM, Marwick CA, Williams FL, Stringer K, McCowan C, Davey P, Nathwani D (2009). "A survey on public knowledge and perceptions of methicillin-resistant Staphylococcus aureus." J Antimicrob Chemother 63(1);209-14. PMID: 18984646

Ford20: Ford CA, Hurford IM, Cassat JE (2020). "Antivirulence Strategies for the Treatment of Staphylococcus aureus Infections: A Mini Review." Front Microbiol 11;632706. PMID: 33519793

Guo20: Guo Y, Song G, Sun M, Wang J, Wang Y (2020). "Prevalence and Therapies of Antibiotic-Resistance in Staphylococcus aureus." Front Cell Infect Microbiol 10;107. PMID: 32257966

Herbert10: Herbert S, Ziebandt AK, Ohlsen K, Schafer T, Hecker M, Albrecht D, Novick R, Gotz F (2010). "Repair of global regulators in Staphylococcus aureus 8325 and comparative analysis with other clinical isolates." Infect Immun 78(6);2877-89. PMID: 20212089

Holland14: Holland TL, Arnold C, Fowler VG (2014). "Clinical management of Staphylococcus aureus bacteremia: a review." JAMA 312(13);1330-41. PMID: 25268440

Iandolo02: Iandolo JJ, Worrell V, Groicher KH, Qian Y, Tian R, Kenton S, Dorman A, Ji H, Lin S, Loh P, Qi S, Zhu H, Roe BA (2002). "Comparative analysis of the genomes of the temperate bacteriophages phi 11, phi 12 and phi 13 of Staphylococcus aureus 8325." Gene 289(1-2);109-18. PMID: 12036589

Karp10: Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R (2010). "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology." Brief Bioinform 11(1);40-79. PMID: 19955237

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Madhaiyan20: Madhaiyan M, Wirth JS, Saravanan VS (2020). "Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae." Int J Syst Evol Microbiol 70(11);5926-5936. PMID: 33052802

Ong13: Ong SJ, Huang YC, Tan HY, Ma DH, Lin HC, Yeh LK, Chen PY, Chen HC, Chuang CC, Chang CJ, Hsiao CH (2013). "Staphylococcus aureus keratitis: a review of hospital cases." PLoS One 8(11);e80119. PMID: 24244625

Reizner14: Reizner W, Hunter JG, O'Malley NT, Southgate RD, Schwarz EM, Kates SL (2014). "A systematic review of animal models for Staphylococcus aureus osteomyelitis." Eur Cell Mater 27;196-212. PMID: 24668594

Schleifer09: Schleifer, KH, Bell, A (2009). "Family VIII. Staphylococcaceae fam. nov." Bergey's Manual of Systematic Bacteriology: Volume 3: The Firmicutes.

Tong15: Tong SY, Davis JS, Eichenberger E, Holland TL, Fowler VG (2015). "Staphylococcus aureus infections: epidemiology, pathophysiology, clinical manifestations, and management." Clin Microbiol Rev 28(3);603-61. PMID: 26016486

vanHal12: van Hal SJ, Lodise TP, Paterson DL (2012). "The clinical significance of vancomycin minimum inhibitory concentration in Staphylococcus aureus infections: a systematic review and meta-analysis." Clin Infect Dis 54(6);755-71. PMID: 22302374

Wertheim05: Wertheim HF, Melles DC, Vos MC, van Leeuwen W, van Belkum A, Verbrugh HA, Nouwen JL (2005). "The role of nasal carriage in Staphylococcus aureus infections." Lancet Infect Dis 5(12);751-62. PMID: 16310147

Zecconi13: Zecconi A, Scali F (2013). "Staphylococcus aureus virulence factors in evasion from innate immune defenses in human and animal diseases." Immunol Lett 150(1-2);12-22. PMID: 23376548


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