Staphylococcus

Staphylococcus (from the Greek σταφυλή, staphylē, "grape" and κόκκος, kókkos, "granule") is a genus (a group of species) of Gram-positive bacteria. Their name comes from their appearance under a microscope - they appear round (cocci)), and form in grape-like clusters. The genus name is commonly shortened to "Staph". 
The Staphylococcus genus includes at least 40 species. Of these, nine have two subspecies, one has three subspecies, and one has four subspecies. Most of the species are harmless and reside normally on the skin and mucous membranes of humans and other organisms. Found worldwide, they are a small component of soil microbial flora.
Most of the species are remarkably hardy and can survive dry environments, hot environments and salty conditions that would kill most bacteria and even some viruses. As such, when a patient develops a staph infection, it is usually from bacteria that they have been carrying around for a considerable period of time on their skin, clothing or inside their nose. Several species are a common cause of infections of the skin, blood, and stomach of humans. The immune system, in most cases, can easily deal with staph infections. It is easily killed outside the body by antiseptics or even soap and water. However, it can be remarkably opportunistic even in an otherwise healthy individual. It can infect even the smallest puncture or scratch in the skin and, when established, can multiply rapidly. It's a common hospital acquired infection particularly among the immunocompromised, individuals who have had surgery or people with an intravenous line. Hospital acquired infections are more common than those acquired outside hospitals. Good hygiene practices can effectively reduce the chance of hospital infection. Transmission of staph infections from person to person is a healthy population is rare and it cannot be considered contagious. However, it can spread from an infected person to other patients in a hospital environment through health care workers, visitors or contaminated surfaces (including clothing such as ties and lab coats).
A staph infection usually starts with an abscess, usually just below the surface of the skin. Although these abcesses are often self-limiting, the infection can spread from the abscess into the bloodstream, where it can spread throughout the body. Typical symptoms include high fever and clotting. At this point, the growth of the bacteria can often continue unabated and can result in the death of the patient unless they are treated promptly. Luckily, the majority of infections can be treated with common antibiotics although in many cases, abscesses will have to be drained. However, resistant strains are becoming more common and can only be treated with a single very expensive antibiotic - vancomycin. such infections were once restricted to hospital acquired infections, but due to overuse of such powerful antibiotics, they are now becoming increasingly common in non-hospital acquired cases. One common complication is that in addition to the bacteria themselves, many species also secrete a toxin that can be fatal in and of itself. This toxin is also what causes food poisoning in staph infected foods.
Staph can manifest in many different ways in humans and, as such, several diseases where the underlying cause is a staph infection are often used for diagnostic purposes. However, in the vast majority of cases, it can be diagnosed solely by visual examination of the affected area without blood cultures.
==Taxonomy==
Most staph species are named after the source from where they were isolated, although some are named to honor people or places as well. A few are named after their physical characteristics. The taxonomy (species classification) is based on 16s rRNA sequences,and most of the staphylococcal species fall into 11 clusters:
#S. aureus group – S. aureus ("golden"), S. simiae ("of a monkey"). S. aureus is, by far, the most common cause of infection in humans.
#S. auricularis group – S. auricularis ("of the ear")
#S. carnosus group – S. carnosus ("of flesh"), S. condimenti ("of a spice"), S. massiliensis ("of Marseilles", [Roman Masillia]), S. piscifermentans ("fermenting fish"), S. simulans ("imitating")
#S. epidermidis group – S. capitis ("of the head"), S. caprae ("of a goat"), S. epidermidis ("of the epidermis" - skin), S. saccharolyticus ("sugar digesting")
#S. haemolyticus group – S. devriesei (after its discoverer Luc A DeVriesei), S. haemolyticus ("blood dissolving"), S. hominis ("of a man/human")
#S. hyicus-intermedius group – S. agnetis ("magnet"), S. chromogenes ("producing color"), S. felis ("of a cat"), S. delphini ("of a dolphin"), S. hyicus, S. intermedius ("intermediate"), S. lutrae ("otters"), S. microti ("of the vole species Microtus arvalis), S. muscae ("of a fly"), S. pseudintermedius ("false intermediate"), S. rostri ("of a pig snout"), S. schleiferi (after microbiologist Karl Heinz Schleifer)
#S. lugdunensis group – S. lugdunensis ("from Lyon" [Roman Lugdunum])
#S. saprophyticus group – S. arlettae (after microbiologist Arlette van de Kerckhove), S. cohnii (after biologist Ferdinand Cohn), S. equorum ("of horses"), S. gallinarum ("of hens"), S. kloosii (after biologist Wesley E. Kloos), S. leei ("says"), S. nepalensis ("of Nepal"), S. saprophyticus ("putrid plant"), S. succinus ("of amber"), S. xylosus ("of wood sugar")
#S. sciuri group – S. fleurettii (after microbiologist Jean Fleurette), S. lentus ("slow"), S. sciuri ("of the squirrel"), S. stepanovicii (for microbiologist Srdjan Stepanović), S. vitulinus ("of a calf")
#S. simulans group – S. simulans ("imitating")
#S. warneri group – S. pasteuri (after Louis Pasteur), S. warneri (named for Arthur Warner, the source of the strain)
A 12th group – that of S. caseolyticus – has now been moved to a new genus, Macrococcus, the species of which are currently the closest known relatives of Staphylococcus.
===Subspecies===
:S. aureus subsp. aureus
:S. aureus subsp. anaerobius ("not living in air")
:S. capitis subsp. capitis
:S. capitis subsp. urealyticus ("urine dissolving")
:S. carnosus subsp. carnosus
:S. carnosus subsp. utilis ("useful")
:S. cohnii subsp. cohnii
:S. cohnii subsp. urealyticus
:S. equorum subsp. equorum
:S. equorum subsp. linens ("smearing")
:S. hominis subsp. hominis
:S. hominis subsp. novobiosepticus ("resistant to [the antibiotic] novobiocin")
:S. petrasii subsp. croceilyticus ("saffron colored" from the Crocus)
:S. petrasii subsp. jettensis
:S. petrasii subsp. petrasii
:S. petrasii subsp. pragensis (from Prague [Roman Praga])
:S. saprophyticus subsp. bovis ("of a cow")
:S. saprophyticus subsp. saprophyticus
:S. schleiferi subsp. coagulans ("curdling" or "coagulating")
:S. schleiferi subsp. schleiferi
:S. sciuri subsp. carnaticus ("pertaining to meat")
:S. sciuri subsp. rodentium ("of rodents")
:S. sciuri subsp. sciuri
:S. succinus subsp. casei ("of cheese")
:S. succinus subsp. succinus
===Notes===
As with all generic names in binomial nomenclature, Staphylococcus is capitalized when used alone or with a specific species. Also, the abbreviations Staph and S. when used with a species (S. aureus) are correctly italicized and capitalized (though often errors in this are seen in popular literature). However, Staphylococcus is not capitalized or italicized when used in adjectival forms, as in a "staphylococcal infection", or as the informal plural "staphylococci".
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 group of species with a common ancestry 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 groups of species that appear to descend from a common ancestor, 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, produces catalase, has an appropriate cell wall structure (including peptidoglycan type and teichoic acid presence) and Guanine + Cytosine content of DNA in a range of 30–40% of molecular weight.
Staphylococcus species can be differentiated from other aerobic and facultative anaerobic, Gram-positive cocci by several simple tests. Staphylococcus species are capable of growth both aerobically (in oxygen) and anaerobically (without oxygen). All species grow in the presence of bile salts.
All species were once thought to be coagulase-positive, but this has since been disproven.
Growth can also occur in a 6.5% sodium chloride (table salt) solution. On Baird-Parker agar, Staphylococcus species grow fermentatively (without oxygen), except for S. saprophyticus, which grows oxidatively. Staphylococcus species are resistant to bacitracin and susceptible to furazolidone. Further biochemical testing is needed to identify to the species level.
When these bacteria divide, they do so along two axes, so form clumps of bacteria. This is as opposed to streptococci, which divide along one axis, so form chains (strep meaning twisted or pliant).
===Coagulase production===
One of the most important observable features used in the classification of staphylococci is their ability to produce coagulase, an enzyme that causes blood clot formation. This characteristic is what leads to clotting as a symptom of infection of some species of staph, but not others.
Six 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). S. aureus can also be found as being coagulase-negative.
A seventh 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 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 (a disease that naturally passes from other animals to humans).
S. epidermidis, a coagulase-negative species, is a natural and beneficial part of the skin's biological flora, 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 urinary 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 behavior (etiology) 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. 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
:S. aureus - humans
:S. auricularis – deer, dogs, humans
:S. capitis – humans
:S. caprae – goats, humans
:S. cohnii – chickens, humans
:S. delphini – dolphins
:S. devriesei – cattle
:S. epidermidis – humans
:S. equorum – horses
:S. felis – cats
:S. fleurettii – goats
:S. gallinarum – chickens, goats, pheasants
:S. haemolyticus – humans, mangabey monkeys, patus monkey, lemurs, mouse lemurs, macca plant, chimpanzees
:S. hyicus – pigs
:S. leei – humans
:S. lentus – goats, rabbits, sheep
:S. lugdunensis – humans, goats
:S. lutrae – otters
:S. microti – voles
: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
:S. simulans – humans
:S. warneri – humans, old world monkeys, gorillas, chimpanzees, orangutans
:S. xylosus – humans
==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 are also known to be a cause of bacterial conjunctivitis.S. aureus can cause a number of different skin diseases. Among neurosurgical patients, it can cause community-acquired meningitis.
==Types==
Main Staphylococcus aureus infections	Main Staphylococcus aureus infections
Type 	Examples
Localized skin infections 	
*Stye and other small, superficial abscesses in sweat or sebaceous glands
*Subcutaneous abscesses (boils) around foreign bodies
*Large, deep infections (carbuncles) possibly causing bacteremia
*Folliculitis; an infection of a hair follicle
*Ear infections
Diffuse skin infection 	
*Impetigo
Deep, localized infections 	
*Acute and chronic osteomyelitis
*Septic arthritis
Other infections 	
*Asthma and rhinitis
*Acute and chronic sinusitis
*Acute endocarditis
*Septicemia
*Necrotizing pneumonia
Toxinoses 	
*Toxic shock syndrome
*Gastroenteritis
*Scalded skin syndrome
 	
Other infections include:
*Closed-space infections of the fingertips, known as paronychia.
==Coagulase-positive==
The main coagulase-positive staphylococcus is S. aureus, although not all strains of S. aureus are coagulase positive. These bacteria can survive on dry surfaces, increasing the chance of transmission. S. aureus is also implicated in toxic shock syndrome; during the 1980s some tampons allowed the rapid growth of S. aureus, which released toxins that were absorbed into the bloodstream. Any S. aureus infection can cause the scalded skin syndrome, a cutaneous reaction to exotoxin absorbed into the bloodstream. It can also cause a type of septicemia called pyaemia. The infection can be life-threatening. Problematically, MRSA has become a major cause of hospital-acquired infections, and is being, MRSA has also been recognized with increasing frequency in community-acquired infections. The symptoms of a Staph Infection include a collection of pus, such as a boil or furuncle, or abscess. The area is typically tender or painful and may be reddened or swollen.
==On the series==
Staph is hardly a zebra. It's a fairly common infection and an infectologist like Gregory House should be able to recognize it right away. In addition the "morons" that work at the hospital should probably be considering it. However, it has still turned up twice on the series, so an unusual presentation can still trip up the best of doctors. It's also responsible for one of the few patient deaths on the series.
===The Big Con===
In House Training, Lupe presents with TIA which manifests as various neurological symptoms. Her tox screen is completely clean. She soon progresses to respiratory arrest. Tests indicate a lot of dead white blood cells, pointing to an autoimmune condition. Foreman points to steroids as the obvious choice. However, when Foreman notes that she has jaundice, it most likely points to cancer. He recommends radiation therapy as, even if it's an autoimmune condition, it will help by suppressing her immune system.
However, when she screams in pain while her blood pressure is being tested after the radiation treatment, House realizes there is only one diagnosis that fits - sepsis - an autoimmune reaction to a runaway infection. With her immune system suppressed from the treatment, she has only hours to live.
After she passes away, House does an autopsy and finds a small pus filled sore on Lupe's back, right next to a small scratch from her bra hook. He realizes she had a septic reaction to a runaway staph infection.
===Shrapnel===
In Bombshells, Ryan comes to the hospital spitting up blood, and the bleeding soon spreads to his urine. He soon loses all feeling in his right arm. Further testing finds clots. Treatment with blood thinners doesn't work. When they try to remove it with surgery, it instantly disintegrates. However, the patient keeps getting worse and liver failure is the next symptom.
Finally, House puts the pieces together and realizes it is a staph infection. He was treated for it, which means he has a hidden abscess. Taub suddenly realizes Ryan's fondness for making pipe bombs is medically relevant. Ryan used plastic pipe and, if he got to close to an explosion, some of the small pieces might have been driven into his body. That would also explain the scars on his abdomen. The plastic pieces wouldn't show up on imaging. They perform more surgery and find the pieces to remove the infection.
====Other appearances====
*Staph is one of the differentials in Euphoria (Part 1). It is ruled out when the brain biopsy is negative.
*Staph is one of the differentials in Maternity, but is ruled out when none of the patients respond to even the most powerful antibiotics.
*When second-opinion website patient Deedee shows up at the hospital in Let Them Eat Cake, Taub and Kutner are sure she just has staph. In fact, she's a plant by House and is faking her symptoms with help from Chase and Cameron.
*When Sir William develops blisters and red eyes, Thirteen suggests resistant staph. However, the cultures are negative.
*Staph was suggested in the differential for President Dibala, but it was ruled out because his fever wasn't high enough.
*Staph was the initial diagnosis for Mr. Plutus in 5 to 9
*A rash can be a sign of staph, but House ruled it out right away with Carnell Hall in Daddy's Boy.
*Staph was part of the differential for Sophia Isabel Velez in Emancipation, but it was ruled out because her white blood cell count was normal.
*In Words and Deeds, Chase suggested Derek Hoyt may have a staph infection from his previous hospital stay for his burns. However, Derek developed new symptoms which ruled it out.
*When Nick Greenwald developed a high fever in The Social Contract, staph was one of the possibilities, but a medical history pointed to leptospirosis.
*In Twenty Vicodin, House realizes that staph would explain Nick's bone weakness, but then instantly realizes it wouldn't have acted that quickly.
*In a bit of irony, Peter Treiber's attempts to avoid staph wind up causing his illness when he has an adverse reaction to the antiseptic in his soap.
*In other media, staph was a differential in four different episodes of House M.D. - Critical Cases.
==Coagulase-negative==
*S. epidermidis, a coagulase-negative staphylococcus species, is a natural and beneficial part of the skin's flora, but can cause severe infections in immune-suppressed 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 urinary tract infections in sexually-active young women.
*In recent years, several other staphylococcal species have been implicated in human infections, notably S. lugdunensis, S. schleiferi, and S. caprae.
==See also==
*MRSA
*VRSA
Staphylococcus at Wikipedia
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