Editing Staphylococcus aureus (section)

== Classical diagnosis ==
[[File:Staph sputum.JPG|thumb|250px|Typical gram-positive cocci, in clusters, from a sputum sample, Gram stain]]

Depending upon the type of infection present, an appropriate specimen is obtained accordingly and sent to the laboratory for definitive identification by using biochemical or enzyme-based tests. A [[Gram stain]] is first performed to guide the way, which should show typical [[Gram-positive]] bacteria, cocci, in clusters. Second, the isolate is cultured on [[mannitol salt agar]], which is a selective medium with 7.5% [[sodium chloride|NaCl]] that allows ''S. aureus'' to grow, producing yellow-colored colonies as a result of [[mannitol]] fermentation and subsequent drop in the medium's [[pH]].<ref>{{cite journal| vauthors = Shields P, Tsang AY |date=2006-10-09|title=Mannitol Salt Agar Plates Protocols|url=https://www.asmscience.org/content/education/protocol/protocol.3034|access-date=2020-12-31|website=www.asmscience.org|language=en}}</ref><ref>{{cite web|date=2020-01-14|title=Mannitol Salt Agar (MSA) {{!}} Culture Media|url=https://microbenotes.com/mannitol-salt-agar-msa/|access-date=2020-12-31|website=Microbe Notes|language=en-US}}</ref>

Furthermore, for differentiation on the species level, [[catalase]] (positive for all ''Staphylococcus'' species), [[coagulase]] ([[fibrin]] clot formation, positive for ''S. aureus''), [[DNAse]] (zone of clearance on DNase agar), [[lipase]] (a yellow color and rancid odor smell), and [[phosphatase]] (a pink color) tests are all done. For staphylococcal food poisoning, phage typing can be performed to determine whether the staphylococci recovered from the food were the source of infection.<ref>{{cite journal | vauthors = Saint-Martin M, Charest G, Desranleau JM | title = Bacteriophage typing in investigations of staphylococcal food-poisoning outbreaks | journal = Canadian Journal of Public Health | volume = 42 | issue = 9 | pages = 351–8 | date = September 1951 | pmid = 14879282 | url = https://www.jstor.org/stable/41980177 | jstor = 41980177 }}</ref>

=== Rapid diagnosis and typing ===

[[Medical laboratory|Diagnostic microbiology laboratories and reference laboratories]] are key for identifying outbreaks and new strains of ''S. aureus''. Recent genetic advances have enabled reliable and rapid techniques for the identification and characterization of clinical isolates of ''S. aureus'' in real time. These tools support infection control strategies to limit bacterial spread and ensure the appropriate use of antibiotics. [[Quantitative PCR]] is increasingly being used to identify outbreaks of infection.<ref name= FrancoisP >{{cite book |chapter-url=http://www.horizonpress.com/staph|vauthors=Francois P, Schrenzel J|year=2008|chapter=Rapid Diagnosis and Typing of ''Staphylococcus aureus''|title=Staphylococcus: Molecular Genetics|publisher=Caister Academic Press |isbn=978-1-904455-29-5}}</ref><ref name=Mackay>{{cite book | editor = Mackay IM | title = Real-Time PCR in Microbiology: From Diagnosis to Characterization | publisher = Caister Academic Press | year = 2007 | isbn = 978-1-904455-18-9}}</ref>

When observing the evolvement of ''S. aureus'' and its ability to adapt to each modified antibiotic, two basic methods known as "band-based" or "sequence-based" are employed.<ref name="Deurenberg_2008">{{cite journal | vauthors = Deurenberg RH, Stobberingh EE | title = The evolution of ''Staphylococcus aureus'' | journal = Infection, Genetics and Evolution | volume = 8 | issue = 6 | pages = 747–763 | date = December 2008 | pmid = 18718557 | doi = 10.1016/j.meegid.2008.07.007 | bibcode = 2008InfGE...8..747D }}</ref> Keeping these two methods in mind, other methods such as [[multilocus sequence typing]] (MLST), [[pulsed-field gel electrophoresis]] (PFGE), [[bacteriophage typing]], spa locus typing, and SCCmec typing are often conducted more than others.<ref>{{cite journal | vauthors = Aires de Sousa M, Conceição T, Simas C, de Lencastre H | title = Comparison of genetic backgrounds of methicillin-resistant and -susceptible ''Staphylococcus aureus'' isolates from Portuguese hospitals and the community | journal = Journal of Clinical Microbiology | volume = 43 | issue = 10 | pages = 5150–7 | date = October 2005 | pmid = 16207977 | pmc = 1248511 | doi = 10.1128/JCM.43.10.5150-5157.2005 }}</ref> With these methods, it can be determined where strains of MRSA originated and also where they are currently.<ref name="Kim, J 2009">{{cite journal | vauthors = Kim J | year = 2009 | title = Understanding the Evolution of Methicillin-Resistant ''Staphylococcus aureus'' | journal = Clinical Microbiology Newsletter | volume = 31 | issue = 3| pages = 17–23 | doi = 10.1016/j.clinmicnews.2009.01.002 }}</ref>

With MLST, this technique of typing uses fragments of several housekeeping genes known as ''aroE, glpF, gmk, pta, tip,'' and ''yqiL''. These sequences are then assigned a number which give to a string of several numbers that serve as the allelic profile. Although this is a common method, a limitation about this method is the maintenance of the microarray which detects newly allelic profiles, making it a costly and time-consuming experiment.<ref name="Deurenberg_2008"/>

With PFGE, a method which is still very much used dating back to its first success in 1980s, remains capable of helping differentiate MRSA isolates.<ref name="Kim, J 2009"/> To accomplish this, the technique uses multiple gel electrophoresis, along with a voltage gradient to display clear resolutions of molecules. The ''S. aureus'' fragments then transition down the gel, producing specific band patterns that are later compared with other isolates in hopes of identifying related strains. Limitations of the method include practical difficulties with uniform band patterns and PFGE sensitivity as a whole.{{citation needed|date=August 2022}}

Spa locus typing is also considered a popular technique that uses a single locus zone in a polymorphic region of ''S. aureus'' to distinguish any form of mutations.<ref name="Kim, J 2009"/> Although this technique is often inexpensive and less time-consuming, the chance of losing discriminatory power making it hard to differentiate between MLST clonal complexes exemplifies a crucial limitation.{{citation needed|date=August 2022}}