User:Providencia rettgeri
Providencia rettgeri
Introduction
Bacteria that are considered opportunistic pathogens are able to associate with certain host organisms with no negative effects on the host, but in other organisms, their association can result in an infection. Providencia rettgeri found in reptilian and amphibian intestinal tracts appear harmless to the host but when these bacteria are seen in humans it is associated with urinary tract infections (Penner, 2015). They are Gram-negative, rod-shaped bacteria that have motility through peritrichous flagella (Penner, 2015). P. rettgeri are found in either aqueous environments or associated with a host either as a pathogen or as a non-pathogen interaction (Penner, 2015). The bacteria’s ability to produce urease allows for the breakdown of urea and the resulting products of this breakdown can raise the pH of the surrounding environment (Mekonnen, et al. 2021). Biofilm production also plays a crucial role in the bacteria’s ability to survive in their aqueous environments and their virulence ability in the colonization of a host (Sagar, Narasimhaswamy, & D'Souza, 2017). The images below show P. rettgeri under microscopes and growing on media.
Figure 1: Providencia rettgeri under a light microscope at 100x magnification with oil, a scanning electron microscope, and a transmission electron microscope (Salaskar D.A., Padwal M.K., Gupta A., Basu B., and Kale S.P., 2022). http://www.bacteriainphotos.com/providencia%20rettgeri.html
Figure 2: Providencia rettgeri colonies grown on Endo agar which gives the colonies a pinkish appearance rather than their typical white coloration. (“Providencia Rettgeri.” Available from: http://www.bacteriainphotos.com/providencia%20rettgeri.html.)
Classification
Higher order taxa: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Morganellaceae Species: Providencia rettgeri Taxonomy: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=587&lvl=3&lin=f&keep=1&srchmode=1&unlock GOLD Organism Information: https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2562617097
Phylogenetic Relatedness
16S rRNA sequencing has not been extensively done in the Enterobacter family due to the high amount of conservation in these closely related species, a way to remedy this is through comparison of housekeeping genes (Giammanco, et al. 2011). A common housekeeping gene found in bacteria is the rpoB gene which always has at least one copy present as it is essential for cellular metabolism (Giammanco, et al. 2011). The genomic DNA of the bacteria is extracted and a portion of the region coding for rpoB is amplified using primers. The amplified section of the genome is sequenced again using primers to obtain a partial sequence. Alignment and phylogenetic analysis of gene sequences is done using a CLUSTAL algorithm and MEGA software. Based on the phylogenetic tree generated from the results (Figure 3) it found that Providencia rettgeri is most closely related to Providencia vermicola and Providencia heimbachae with its closest relative from a non-Providencia genus being Morganella morganii (Giammanco, et al. 2011).
Figure 3: A phylogenetic analysis of bacteria from within the order Enterobacteria that shows the closest relatives of those within this order of bacteria (Giammanco, et al. 2011). https://www.microbiologyresearch.org/docserver/fulltext/ijsem/61/7/021964-f2.gif
Ecological Habitat
Providencia rettgeri was originally isolated from poultry in 1918 (Penner, 2015). Since then, it has been isolated in water samples and in the digestive and urinary tracts of a number of organisms including humans, insects, and reptiles (Penner, 2015). Typically, the environments that Providencia rettgeri are found in indicates that it is a neutrophile as its varying habitats have a pH range from around 6 (such as in the gut of insects) to upwards of 8 (such as in saltwater environments) (Libretexts). As for the temperature range for these bacteria, they can be found housed within organisms with a body temperature ranging from 35-37°C. The marine environments that they can live in however have a lower temperature range that is closer to 20-30°C. Oxygen requirements for these bacteria fit within the facultative anaerobe meaning that when it is in environments that have oxygen present, such as those found in aqueous environments, they will use the oxygen to respire. However, if there is little or no oxygen present in their habitat, such as in a host organism’s gut, they are able to switch to fermentation. Providencia rettgeri is most commonly reported in the intestines of the smaller organisms mentioned above. It is typically identified by growing the bacteria in a lab setting and performing characteristic tests. Some “field marks” of these bacteria in regards to their pathogenic strains in the silkworm Bombyx mori are first the worms will stop eating and slow in movement (Zhang, 2013).
Ecological Lifestyle and Interactions
Providencia rettgeri is an opportunistic pathogen, or a host-associated bacteria with its typically aqueous environment allowing for interactions with potential hosts. The most common host organisms for Providencia rettgeri are frogs, fish, and lizards (Penner, 2015). However, there are cases of this bacteria being found in insects and birds as well (Penner, 2015). In the case of insects, it is considered an opportunistic pathogen such as in the case of silkworms (Zhang, et al. 2013). There have also been cases of this bacteria causing infections in humans and is associated with patients with long-term catheters (Sagar, Narasimhaswamy, & D'Souza, 2017). Providencia rettgeri is able to produce urease and biofilms which results in this association as the bacteria are able to form biofilms in catheters and are often detected due to an increase in urea (Sagar, Narasimhaswamy, & D'Souza, 2017). There has also been a link between P. rettgeri and “purple bag syndrome” which results in purple-tinged urine in a patient due to the enzymatic activity of the bacteria (Sagar, Narasimhaswamy, & D'Souza, 2017). As P. rettgeri is often found in host organisms it is exposed to a number of other microbes. One example of this is the gut of the Drosophila fly where P. rettgeri has been isolated along with Lactobacillus and Acetobacter species (Galac, & Lazzaro, 2012). Biological interactions between these bacteria in the host’s gut can influence the health and well-being of the host. Lactobacillus and Acetobacter interactions in particular have been found to affect the fat content of the host fly (Ludington & Ja, 2020). In Providencia’s more aqueous environments its ability to produce urease, which in turn breaks down urea into ammonia and carbon dioxide, can provide a carbon source, in the form of CO2, for cyanobacteria and microalgae in the surrounding waters (Penner, 2015).
Significance to Humans
Providencia rettgeri is an opportunistic pathogen, and while it is rare for these bacteria to be associated with human disease when it does occur it is linked to patients with long-term catheters (Sagar, Narasimhaswamy, & D'Souza, 2017). This association is due to its ability to produce urease when in the presence of urea, hydrolyzing it and breaking it down into ammonia and carbon dioxide. A urinary catheter provides not only the urea needed for this but is also an ideal environment for creating and attaching a biofilm to. Previously, P. rettgeri has been associated with “purple bag syndrome” which gets its name from the resulting enzymatic activity of the bacteria that turns the urine to a purple-tinged color (Sagar, Narasimhaswamy, & D'Souza, 2017). Strains of P. rettgeri have been found to possess antibiotic resistance to penicillin and cephalosporins and is a result of their use treatment of urinary infections (Penner, 2015). They are still susceptible to antibiotics such as aminoglycosides (Penner, 2015). Another way that this microbe can be interrupted is by disrupting its ability to form biofilms, as it is key to P. rettgeri’s ability to cause infections.
Cell Structure
Providencia rettgeri are a Gram-negative, non-sporulating, rod-shaped bacteria that are motile (Penner, 2015). Motility and their ability to form biofilms assist in P. rettgeri’s ability to live in aqueous environments successfully (Sagar, Narasimhaswamy, & D’Souza, 2017). On media, the bacteria form white-colored, mucoid, circular colonies that are convex (Zhang, Shen, Tang, Xu, & Zhu, 2013). Many strains of Providencia rettgeri have resistance to antibiotics such as penicillin and cephalosporins but are susceptible to aminoglycosides (Penner, 2015). This resistance to certain antibiotics is due to their use in treating urinary tract infections and resulting in strains developing that are no longer susceptible to the more common antibiotics (Penner, 2015).
Cell Metabolism
Providencia rettgeri can be kept in the lab on a TSA plate at the optimal temperature of 37°C (Penner, 2015). They are facultative anaerobes capable of using carbon sources such as mannitol, rhamnose, and galactose for fermentation (Penner, 2015). Mannitol is commonly found in plants or algae and is one of the most abundant energy sources found in nature (Song & Vielle, 2009). P. rettgeri’s aqueous habitats offer algae as a mannitol source when it is free floating without a host. Galactose is a type of monosaccharide that’s breakdown results in the product of glucose and has been associated with biofilm formation in other bacteria (Chai, et al. 2012). P. rettgeri is distinguished from other Providencia species by its capability to hydrolyze urea and ferment mannitol (Penner, 2015). Their antibiotic resistance is facilitated by the bacteria’s ability to produce beta-lactamase, which is able to break certain antibiotic structures (Shin, Jeong, Lee, et al., 2018).
Genome Structure, Content, & Gene Expression
Metrics Genome size: 4.62 Mb (NIH) GC %: 40.4 (NIH) Number of Chromosomes/Plasmids: 1 chromosome & one plasmid (NIH) Circular or linear: Circular (NIH) Interesting Features: There are 3943 genes in the chromosome and 180 genes in the plasmid (NIH) Relevance This organism was sequenced at Washington University in St. Louis and was done so after being isolated from human feces as it was a human pathogenic strain (IMG). The sequenced genome shows that Providencia rettgeri provided new insight into the bacteria’s antimicrobial potential as it found lysozyme proteins associated with lysing Gram-negative bacteria and considered an antimicrobial enzyme (IMG). Within the sequenced genomes, the proteins for the bacteria’s ability to produce urease are found and include a urea transporter, urease accessory proteins, and urease subunits (IMG). There were also colicin immunity proteins which are associated with toxins produced by the bacteria itself and are related to pore formation in membranes (Nardi, Corda, Baty, & Duché, 2001). Some more proteins of note that were found that are crucial to the bacteria’s survival in its habitat are those associated with flagella and biofilm regulation which assists in the ability to survive in aqueous environments (IMG). In comparison, the sequenced genome of a strain of P. rettgeri from a Drosophila fly had similar statistics to the one isolated from human feces. Both had one plasmid and a GC% of approximately 40 (Galac & Lazzaro, 2012). The differences between the two appear in the size and number of genes, with the Drosophila strain having a smaller genome size of 4.3 Mb, but a higher gene count of 4532 (Galac, & Lazzaro, 2012). When compared to other Providencia species in this study P. rettgeri had 800 unique genes.
Interesting Feature
Providencia rettgeri has genes capable of promoting rhamnose metabolic processes, which is seen in only one other Providencia species (Galac, & Lazzaro, 2012). This metabolic process is associated with the breakdown of pectin from the cell walls of plants as rhamnose is a sugar found in abundance in two out of the four structural elements of pectin (Chroumpi, et al, 2020). This allows for the bacteria to break down rhamnose from plant matter into pyruvate as an energy supply. This can be beneficial for strains living as host-associated organisms, as often these hosts are ingesting plant matter which the bacteria in the gut will have access to as a potential carbon source.
References
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