Pseudomonas

# Overview
Pseudomonas is a genus of gamma proteobacteria, belonging to the larger family of pseudomonads. 
Recently, 16S rRNA sequence analysis has redefined the taxonomy of many bacterial species. As a result the genus Pseudomonas includes strains formerly classifed in the genera Chryseomonas and Flavimonas. Other strains previously classified in the genus Pseudomonas are now classified in the genera Burkholderia and Ralstonia.

# History
Pseudomonad literally means 'false unit', being derived from the Greek pseudo ( 'false') and monas ( /  'a single unit'). The term "monad" was used in the early history of microbiology to denote single-celled organisms.
Because of their widespread occurrence in nature, the pseudomonads were observed early in the history of microbiology. The generic name Pseudomonas created for these organisms was defined in rather vague terms in 1894 as a genus of Gram-negative, rod-shaped and polar-flagella bacteria. Soon afterwards, a very large number of species was assigned to the genus. Pseudomonads were isolated from many natural niches and a large number of species names was originally assigned to the genus. New methodology and the inclusion of approaches based on the studies of conservative macromolecules have reclassified many strains. 
Pseudomonas aeruginosa is increasingly recognized as an emerging opportunistic pathogen of clinical relevance. Several different epidemiological studies indicate that antibiotic resistance is increasing in clinical isolates.
In the year 2000, the complete genome sequence of a Pseudomonas species was determined; more recently the sequence of other strains have been determined including P. aeruginosa strains PAO1 (2000), P. putida KT2440 (2002), P. fluorescens Pf-5 (2005), P. syringae pathovar tomato DC3000 (2003), P. syringae pathovar syringae B728a (2005), P. syringae pathovar phaseolica 1448A (2005), P. fluorescens PfO-1 and P. entomophila L48.
An article published in the journal Science in 2008 showed that Pseudomanas may be the most common nucleator of ice crystals in clouds, thereby being of utmost importance to the formation of snow and rain around the world.

# Characteristics
Members of the genus display the following defining characteristics:
- Rod shaped
- Gram-negative
- One or more polar flagella, providing motility
- Aerobic, although some species have been found to be facultative anaerobes (e.g. P. aeruginosa)
- Nonspore forming
- Positive catalase test
Other characteristics which tend to be associated with Pseudomonas species (with some exceptions) include secretion of pyoverdin (fluorescein), a fluorescent yellow-green siderophore under iron-limiting conditions. Certain Pseudomonas species may also produce additional types of siderophore, such as pyocyanin by Pseudomonas aeruginosa and thioquinolobactin by Pseudomonas fluorescens,. Pseudomonas species also typically give a positive result to the oxidase test, the absence of gas formation from glucose, glucose is oxidised in oxidation/fermentation test using Hugh and Leifson O/F test, beta hemolytic (on blood agar), indole negative, methyl red negative, Voges Proskauer test negative, citrate positive.
The genus demonstrates a great deal of metabolic diversity, and consequently are able to colonise a wide range of niches. Their ease of culture in vitro and availability of an increasing number of Pseudomonas strain genome sequences has made the genus an excellent focus for scientific research; the best studied species include P. aeruginosa in its role as an opportunistic human pathogen, the plant pathogen P. syringae, the soil bacterium P. putida, and the plant growth promoting P. fluorescens.

# Diagnosis

## Physical Examination

### Skin
- Pseudomonas infection. With permission from Dermatology Atlas.

## Biofilm formation
All species and strains of Pseudomonas are Gram-negative rods, and have historically been classified as strict aerobes. Exceptions to this classification have recently been discovered in Pseudomonas biofilms. A significant number can produce exopolysaccharides that are known as slime layers. Secretion of exopolysaccharide makes it difficult for Pseudomonads to be phagocytosed by mammalian white blood cells. Slime production also contributes to surface-colonising biofilms which are difficult to remove from food preparation surfaces. Growth of Pseudomonads on spoiling foods can generate a "fruity" odor.
Pseudomonas have the ability to metabolise a variety of diverse nutrients. Combined with the ability to form biofilms, they are thus able to survive in a variety of unexpected places. For example, they have been found in areas where pharmaceuticals are prepared. A simple carbon source, such as soap residue or cap liner-adhesives is a suitable place for the Pseudomonads to thrive. Other unlikely places where they have been found include antiseptics such as quaternary ammonium compounds and bottled mineral water.

## Antibiotic resistance
Being Gram-negative bacteria, most Pseudomonas spp. are naturally resistant to penicillin and the majority of related beta-lactam antibiotics, but a number are sensitive to piperacillin, imipenem, tobramycin, or ciprofloxacin.
This ability to thrive in harsh conditions is a result of their hardy cell wall that contains porins. Their resistance to most antibiotics is attributed to efflux pumps called ABC transporters, which pump out some antibiotics before they are able to act.
Pseudomonas aeruginosa is a highly relevant opportunistic pathogen. One of the most worrisome characteristics of P. aeruginosa consists in its low antibiotic susceptibility. This low susceptibility is attributable to a concerted action of multidrug efflux pumps with chromosomally-encoded antibiotic resistance genes and the low permeability of the bacterial cellular envelopes. Besides intrinsic resistance, P. aeruginosa easily develop acquired resistance either by mutation in chromosomally-encoded genes, either by the horizontal gene transfer of antibiotic resistance determinants. Development of multidrug resistance by P. aeruginosa isolates requires several different genetic events that include acquisition of different mutations and/or horizontal transfer of antibiotic resistance genes. Hypermutation favours the selection of mutation-driven antibiotic resistance in P. aeruginosa strains producing chronic infections, whereas the clustering of several different antibiotic resistance genes in integrons favours the concerted acquisition of antibiotic resistance determinants. Some recent studies have shown that phenotypic resistance associated to biofilm formation or to the emergence of small-colony-variants may be important in the response of P. aeruginosa populations to antibiotics treatment.

# Taxonomy
The studies on the taxonomy of this complicated genus groped their way in the dark while following the classical procedures developed for the description and identification of the organisms involved in sanitary bacteriology during the first decades of the twentieth century. This situation sharply changed with the proposal to introduce as the central criterion the similarities in the composition and sequences of macromolecules components of the ribosomal RNA. The new methodology clearly showed that the genus Pseudomonas, as classical defined, consisted in fact of a conglomerate of genera that could clearly be separated into five so-called rRNA homology groups. Moreover, the taxonomic studies suggested an approach that might proved useful in taxonomic studies of all other prokaryotic groups. A few decades after the proposal of the new genus Pseudomonas by Migula in 1894, the accumulation of species names assigned to the genus reached alarming proportions. At the present moment, the number of species in the current list has contracted more than tenfold. In fact, this approximated reduction may be even more dramatic if one considers that the present list contains many new names, i.e., relatively few names of the original list survived in the process. The new methodology and the inclusion of approaches based on the studies of conservative macromolecules other than rRNA components, constitutes an effective prescription that helped to reduce Pseudomonas nomenclatural hypertrophy to a manageable size.

# Pathogenicity

## Animal pathogens
P. aeruginosa is an opportunistic human pathogen, most commonly affecting immunocompromised patients, such as those with cystic fibrosis or AIDS. Infection can affect many different parts of the body, but infections typically target the respiratory tract (e.g. patients with CF or those on mechanical ventillation), causing bacterial pneumonia. Treatment of such infections can be difficult due to multiple antibiotic resistance.
P. oryzihabitans can also be a human pathogen, although infections are rare. It can cause peritonitis, endophthalmitis, septicemia and bacteremia. Similar symptoms although also very rare can be seen by infections of P. luteola.
P. plecoglossicida is a fish pathogenic species, causing hemorrhagic ascites in the ayu (Plecoglossus altivelis). P. anguilliseptica is also a fish pathogen.
Due to their hemolytic activity, even non-pathogenic species of Pseudomonas can occasionally become a problem in clinical settings, where they have been known to infect blood transfusions.

# Use as biocontrol agents
Since the mid 1980s, certain members of the Pseudomonas genus have been applied to cereal seeds or applied directly to soils as a way of preventing the growth or establishment of crop pathogens. This practice is generically referred to as biocontrol. The biocontrol properties of P. fluorescens strains (CHA0 or Pf-5 for example) are currently best understood, although it is not clear exactly how the plant growth promoting properties of P. fluorescens are achieved. Theories include: that the bacteria might induce systemic resistance in the host plant, so it can better resist attack by a true pathogen; the bacteria might out compete other (pathogenic) soil microbes, e.g. by siderophores giving a competitive advantage at scavenging for iron; the bacteria might produce compounds antagonistic to other soil microbes, such as phenazine-type antibiotics or hydrogen cyanide. There is experimental evidence to support all of these theories, in certain conditions; a good review of the topic is written by Haas and Defago.
Other notable Pseudomonas species with biocontrol properties include P. chlororaphis which produces a phenazine type antibiotic active agent against certain fungal plant pathogens, and the closely related species P. aurantiaca which produces di-2,4-diacetylfluoroglucylmethan, a compound antibiotically active against Gram-positive organisms.

# Use as bioremediation agents
Some members of the genus Pseudomonas are able to metabolise chemical pollutants in the environment, and as a result can be used for bioremediation. Notable species demonstrated as suitable for use as bioremediation agents include:
- P. alcaligenes, which can degrade polycyclic aromatic hydrocarbons.
- P. mendocina, which is able to degrade toluene.
- P. pseudoalcaligenes is able to use cyanide as a nitrogen source.
- P. resinovorans can degrade carbazole.
- P. veronii has been shown to degrade a variety of simple aromatic organic compounds.
- P. putida has the ability to degrade organic solvents such as toluene. At least one strain of this bacterium is able to convert morphine in aqueous solution into the stronger and somewhat expensive to manufacture drug hydromorphone (Dilaudid).
- Strain KC of P. stutzeri is able to degrade carbon tetrachloride.

# Food spoilage agents
As a result of their metabolic diversity, ability to grow at low temperatures and ubiquitous nature, many Pseudomonas can cause food spoilage. Notable examples include dairy spoilage by P. fragi, mustiness in eggs caused by P. taetrolens and P. mudicolens, and P. lundensis, which causes spoilage of milk, cheese, meat, and fish.

# Species previously classified in the genus
Recently, 16S rRNA sequence analysis redefined the taxonomy of many bacterial species previously classified as being in the Pseudomonas genus. Species which moved from the Pseudomonas genus are listed below; clicking on a species will show its new classification. Note that the term 'Pseudomonad' does not apply strictly to just the Pseudomonas genus, and can be used to also include previous members such as the genera Burkholderia and Ralstonia.
 proteobacteria: P. abikonensis, P. aminovorans, P. azotocolligans, P. carboxydohydrogena, P. carboxidovorans, P. compransoris, P. diminuta, P. echinoides, P. extorquens, P. lindneri, P. mesophilica, P. paucimobilis, P. radiora, P. rhodos, P. riboflavina, P. rosea, P. vesicularis.
 proteobacteria: P. acidovorans, P. alliicola, P. antimicrobica, P. avenae, P. butanovorae, P. caryophylli, P. cattleyae, P. cepacia, P. cocovenenans, P. delafieldii, P. facilis, P. flava, P. gladioli, P. glathei, P. glumae, P. graminis, P. huttiensis, P. indigofera, P. lanceolata, P. lemoignei, P. mallei, P. mephitica, P. mixta, P. palleronii, P. phenazinium, P. pickettii, P. plantarii, P. pseudoflava, P. pseudomallei, P. pyrrocinia, P. rubrilineans, P. rubrisubalbicans, P. saccharophila]], P. solanacearum, P. spinosa, P. syzygii, P. taeniospiralis, P. terrigena, P. testosteroni.
- proteobacteria: P. beteli, P. boreopolis, P. cissicola, P. geniculata, P. hibiscicola, P. maltophilia, P. pictorum.
 proteobacteria: P. beijerinckii, P. diminuta, P. doudoroffii, P. elongata, P. flectens, P. halodurans, P. halophila, P. iners, P. marina, P. nautica, P. nigrifaciens, P. pavonacea, P. piscicida, P. stanieri.
 proteobacteria: P. formicans