Staphylococcus Edaphicus

''Staphylococcus'' is a genus of Gram-positive bacteria in the family Staphylococcaceae from the order Bacillales. Under the microscope, they appear spherical ( cocci), and form in grape-like clusters. ''Staphylococcus'' species are facultative anaerobic organisms (capable of growth both aerobically and anaerobically).

The name was coined in 1880 by Scottish surgeon and bacteriologist Alexander Ogston (1844–1929), following the pattern established five years earlier with the naming of '' Streptococcus''. It combines the prefix "staphylo-" (from grc, σταφυλή, staphylē, bunch of grapes), and suffixed by the Modern (from ).

Staphylococcus was one of the leading infections in hospitals and many strains of this bacterium have become antibiotic resistant. Despite strong attempts to get rid of them, staph bacteria stay present in hospitals, where they can infect people who are most at risk of infection.

Staphylococcus includes at least 43 species. Of these, nine have two subspecies, one has three subspecies, and one has four subspecies. Many species cannot cause disease and reside normally on the skin and mucous membranes of humans and other animals. ''Staphylococcus'' species have been found to be nectar-inhabiting microbes. They are also a small component of the soil microbiome.

Taxonomy

The taxonomy is based on 16s rRNA sequences, and most of the staphylococcal species fall into 11 clusters:

# ''S. aureus'' group – ''S. argenteus'', ''S. aureus'', ''S. schweitzeri'', ''S. simiae''
# ''S. auricularis'' group – ''S. auricularis''
# ''S. carnosus'' group – ''S. carnosus'', ''S. condimenti'', ''S. debuckii'', ''S. massiliensis'', ''S. piscifermentans'', ''S. simulans''
# ''S. epidermidis'' group – ''S. capitis'', ''S. caprae'', ''S. epidermidis'', ''S. saccharolyticus''
# ''S. haemolyticus'' group – ''S. borealis'', ''S. devriesei'', ''S. haemolyticus'', ''S. hominis''
# ''S. hyicus-intermedius'' group – ''S. agnetis'', ''S. chromogenes'', ''S. cornubiensis'', ''S. felis'', ''S. delphini'', ''S. hyicus'', ''S. intermedius'', ''S. lutrae'', ''S. microti'', ''S. muscae'', ''S. pseudintermedius'', ''S. rostri'', ''S. schleiferi''
# ''S. lugdunensis'' group – ''S. lugdunensis''
# ''S. saprophyticus'' group – ''S. arlettae'', ''S. caeli'', ''S. cohnii'', ''S. equorum'', ''S. gallinarum'', ''S. kloosii'', ''S. leei'', ''S. nepalensis'', ''S. saprophyticus'', ''S. succinus'', ''S. xylosus''
# ''S. sciuri'' group – ''S. fleurettii'', ''S. lentus'', ''S. sciuri'', ''S. stepanovicii'', ''S. vitulinus''
# ''S. simulans'' group – ''S. simulans''
# ''S. warneri'' group – ''S. pasteuri'', ''S. warneri''

A twelfth group – that of ''S. caseolyticus'' – has now been removed to a new genus, ''Macrococcus'', the species of which are currently the closest known relatives of ''Staphylococcus''.

Two species were described in 2015 – ''Staphylococcus argenteus'' and ''Staphylococcus schweitzeri'' – both of which were previously considered variants of ''S. aureus''.

A new coagulase negative species – ''Staphylococcus edaphicus'' – has been isolated from Antarctica. This species is probably a member of the ''S. saprophyticus'' group.

Groups

Based on an analysis of orthologous gene content three groups (A, B and C) have been proposed.Coates-Brown R, Moran JC, Pongchaikul P, Darby AC and MJ Horsburgh MJ (2018) "Comparative genomics of ''Staphylococcus'' reveals determinants of speciation and diversification of antimicrobial defense". ''Front Microbiol''

Group A includes ''S. aureus'', ''S. borealis'', ''S. capitis'', ''S. epidermidis'', ''S. haemolyticus'', ''S. hominis'', ''S. lugdunensis'', ''S. pettenkoferi'', ''S. simiae'' and ''S. warneri''.

Group B includes ''S. arlettae'', ''S. cohnii'', ''S. equorum'', ''S. saprophyticus'' and ''S. xylosus''.

Group C includes ''S. delphini'', ''S. intermedius'' and ''S. pseudintermedius''.

Notes

The ''S. saprophyticus'' and ''S. sciuri'' groups are generally novobiocin-resistant, as is ''S. hominis'' subsp. ''novobiosepticus''.

Members of the ''S. sciuri'' group are oxidase-positive due to their possession of the enzyme cytochrome c oxidase. This group is the only clade within the staphylococci to possess this gene.

The ''S. sciuri'' group appears to be the closest relations to the genus ''Macrococcus''.

''S. pulvereri'' has been shown to be a junior synonym of ''S. vitulinus''.

Within these clades, the ''S. haemolyticus'' and ''S. simulans'' groups appear to be related, as do the ''S. aureus'' and ''S. epidermidis'' groups.

''S. lugdunensis'' appears to be related to the ''S. haemolyticus'' group.

''S. petrasii'' may be related to ''S. haemolyticus'', but this needs to be confirmed.

The taxonomic position of ''S. lyticans'', ''S. pettenkoferi'', ''S. petrasii'', and ''S. pseudolugdunensis'' has yet to be clarified. The published descriptions of these species do not appear to have been validly published.

Biochemical identification

Assignment of a strain to the genus ''Staphylococcus'' requires it to be a Gram-positive coccus that forms clusters, has an appropriate cell wall structure (including peptidoglycan type and teichoic acid presence) and G + C content of DNA in a range of 30–40 mol%.

''Staphylococcus'' species can be differentiated from other aerobic and facultative anaerobic, Gram-positive cocci by several simple tests. ''Staphylococcus'' species are facultative anaerobes (capable of growth both aerobically and anaerobically). All species grow in the presence of bile salts.

All species of ''Staphylococcus aureus'' were once thought to be coagulase-positive, but this has since been disproven.

Growth can also occur in a 6.5% NaCl solution. On Baird-Parker medium, ''Staphylococcus'' species grow fermentatively, except for ''S. saprophyticus'', which grows oxidatively. ''Staphylococcus'' species are resistant to bacitracin (0.04 U disc: resistance = < 10 mm zone of inhibition) and susceptible to furazolidone (100 μg disc: resistance = < 15 mm zone of inhibition). Further biochemical testing is needed to identify to the species level.

Coagulase production

One of the most important phenotypical features used in the classification of staphylococci is their ability to produce coagulase, an enzyme that causes blood clot formation.

Seven species are currently recognised as being coagulase-positive: ''S. aureus'', ''S. delphini'', ''S. hyicus'', ''S. intermedius'', ''S. lutrae'', ''S. pseudintermedius'', and ''S. schleiferi'' subsp. ''coagulans''. These species belong to two separate groups – the ''S. aureus'' (''S. aureus'' alone) group and the ''S. hyicus-intermedius'' group (the remaining five).

An eighth species has also been described – ''Staphylococcus leei'' – from patients with gastritis.

'' S. aureus'' is coagulase-positive, meaning it produces coagulase. However, while the majority of ''S. aureus'' strains are coagulase-positive, some may be atypical in that they do not produce coagulase. ''S. aureus'' is catalase-positive (meaning that it can produce the enzyme catalase) and able to convert hydrogen peroxide (H₂O₂) to water and oxygen, which makes the catalase test useful to distinguish staphylococci from enterococci and streptococci.

'' S. pseudintermedius'' inhabits and sometimes infects the skin of domestic dogs and cats. This organism, too, can carry the genetic material that imparts multiple bacterial resistance. It is rarely implicated in infections in humans, as a zoonosis.

''S. epidermidis'', a coagulase-negative species, is a commensal of the skin, but can cause severe infections in immunosuppressed patients and those with central venous catheters.
''S. saprophyticus'', another coagulase-negative species that is part of the normal vaginal flora, is predominantly implicated in genitourinary tract infections in sexually active young women.
In recent years, several other ''Staphylococcus'' species have been implicated in human infections, notably '' S. lugdunensis'', '' S. schleiferi'', and '' S. caprae''.

Common abbreviations for coagulase-negative staphylococci are CoNS, CNS, or CNST. The American Society for Microbiology abbreviates coagulase-negative staphylococci as "CoNS".

Genomics and molecular biology

The first ''S. aureus'' genomes to be sequenced were those of N315 and Mu50, in 2001. Many more complete ''S. aureus'' genomes have been submitted to the public databases, making it one of the most extensively sequenced bacteria. The use of genomic data is now widespread and provides a valuable resource for researchers working with ''S. aureus''. Whole genome technologies, such as sequencing projects and microarrays, have shown an enormous variety of ''S. aureus'' strains. Each contains different combinations of surface proteins and different toxins. Relating this information to pathogenic behaviour is one of the major areas of staphylococcal research. The development of molecular typing methods has enabled the tracking of different strains of ''S. aureus''. This may lead to better control of outbreak strains. A greater understanding of how the staphylococci evolve, especially due to the acquisition of mobile genetic elements encoding resistance and virulence genes is helping to identify new outbreak strains and may even prevent their emergence.

The widespread incidence of antibiotic resistance across various strains of ''S. aureus'', or across different species of ''Staphylococcus'' has been attributed to horizontal gene transfer of genes encoding antibiotic/metal resistance and virulence. A recent study demonstrated the extent of horizontal gene transfer among ''Staphylococcus'' to be much greater than previously expected, and encompasses genes with functions beyond antibiotic resistance and virulence, and beyond genes residing within the mobile genetic elements.

Various strains of ''Staphylococcus'' are available from biological research centres, such as the National Collection of Type Cultures.

Host range

Members of the genus ''Staphylococcus'' frequently colonize the skin and upper respiratory tracts of mammals and birds and also in marine sponge. Marine sponge associated ''Staphylococcus'' species are highly salt tolerant. Some species specificity has been observed in host range, such that the ''Staphylococcus'' species observed on some animals appear more rarely on more distantly related host species.
Some of the observed host specificity includes:
* ''S. arlattae'' – chickens, goats, marine sponge
* ''S. aureus'' – humans
* ''S. auricularis'' – deer, dogs, humans
* ''S. borealis'' – humans, cattle
* ''S. capitis'' – humans
* ''S. caprae'' – goats, humans
* ''S. cohnii'' – chickens, humans
* ''S. delphini'' – dolphins
* ''S. devriesei'' – cattle
* ''S. epidermidis'' – humans, marine sponge
* ''S. equorum'' – horses
* ''S. felis'' – cats
* ''S. fleurettii'' – goats
* ''S. gallinarum'' – chickens, goats, pheasants
* ''S. haemolyticus'' – humans, ''Cercocebus'', ''Erythrocebus'', '' Lemur'', '' Macca'', '' Microcebus'', '' Pan''
* ''S. hyicus'' – pigs
* ''S. leei'' – humans
* ''S. lentus'' – goats, rabbits, sheep
* ''S. lugdunensis'' – humans, goats
* ''S. lutrae'' – otters
* ''S. microti'' – voles ('' Microtus arvalis'')
* ''S. nepalensis'' – goats
* ''S. pasteuri'' – humans, goats
* ''S. pettenkoferi'' – humans
* ''S. pseudintermedius'' – dogs
* ''S. rostri'' – pigs
* ''S. schleiferi'' – humans
* ''S. sciuri'' – humans, dogs, goats
* ''S. simiae'' – South American squirrel monkeys ('' Saimiri sciureus'')
* ''S. simulans'' – humans
* ''S. warneri'' – humans, Cercopithecoidea, Pongidae
* ''S. xylosus'' – humans

Populations at risk for ''Staphylococcus aureus'' infection

It is said that anyone can develop a staph infection, although certain groups of people are at greater risk, including people with chronic conditions such as diabetes, cancer, vascular disease, eczema, lung disease, and people who inject drugs. In healthcare facilities, the risk of more serious staph infection is higher because many patients have weakened immune systems or have undergone procedures. In healthcare, the risk of more serious staph infection is higher for patients in intensive care units (ICUs), patients who have undergone certain types of surgeries and patients with medical devices inserted in their bodies.

Clinical

''Staphylococcus'' can cause a wide variety of diseases in humans and animals through either toxin production or penetration. Staphylococcal toxins are a common cause of food poisoning, for they can be produced by bacteria growing in improperly stored food items. The most common sialadenitis is caused by staphylococci, as bacterial infections. Staphylococci break down leucine into isovaleric acid, the main odor of foot odor.Stevens D, Cornmell R, Taylor D, Grimshaw SG, Riazanskaia S, Arnold DS, Fernstad SJ, Smith AM, Heaney LM, Reynolds JC, Thomas CL, Harker M. Spatial variations in the microbial community structure and diversity of the human foot is associated with the production of odorous volatiles. FEMS Microbiol Ecol. 2015 Jan;91(1):1-11. doi: 10.1093/femsec/fiu018. Epub 2014 Dec 8. PMID: 25764539.

See also

* Methicillin-resistant ''S. aureus'' (MRSA)
* Vancomycin-resistant ''S. aureus'' (VRSA)

References

External links

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''Staphylococcus''
genomes and related information at PATRIC, a Bioinformatics Resource Center funded by NIAID

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Bacteria genera
Gram-positive bacteria
Pathogenic bacteria
Staphylococcaceae