Survey of Genomes - Pseudomonas aeruginosa

A grape jelly smell and greenish blue pigments in an open wound are a sure sign of a serious infection that is hard to cure. Kiara Jeffrey from the 2019 Hiram College Genetics course introduces to the pathogen Pseudomonas aeruginosa.

Welcome back to Genomics Revolution, this is Kiara Jeffrey from the 2019 Hiram College Genetics course hosting this episode on the genome of Pseudomonas aeruginosa strain PAO1, which I will call P. aeruginosa from now on. This rod-shaped, gram-negative bacterium belongs to the Bacteria class gamma-Proteobacteria and the family Pseudomonadaceae (2). P. aeruginosa was first discovered in 1882 when a French bacteriologist and chemist, Carle Gessard, noticed a blue and green color develop on the bandages of two of his patients’ wounds. Through an experiment, he found that this odd color development was the result of the bacterium’s water-soluble pigments, which turn blue and green when subjected to UV light (3). However, the specific PAO1 strain was not identified until 1954, after it was isolated from a patient’s wound in Melbourne, Australia (2).
 
If you noticed, both extractions came from wounds, which is quite common for P. aeruginosa and also a major reason why it’s studied. This is because this bacterium is considered an opportunistic pathogen. As a result, it commonly causes infections in individuals with severe burns, UTIs in patients with catheters, and pneumonia in respirator patients (6). However, it is most infamous for its potentially lethal effect in cystic fibrosis patients. The lungs of these patients are similar to other environments that P. aeruginosa inhabits, like coastal marine habitats, soil and marshes, in that they contain moisture. This allows the pathogen to grow large colonies in the lungs of cystic fibrosis patients, which could lead to death (6). In addition to its ability to live in a diverse set of conditions, P.aeruginosa is also resistant to a wide variety of antibiotics and has even become resistant to new ones over the course of treatment (3). Given all of this, scientists decided to sequence its genome, which has since served as a reference for Pseudomonas genetics (2).

P.aeruginosa’s genome consists of 6,264,403 base pairs in a single, circular chromosome and, in total, encodes 5,570 proteins (6). Looking into this bacterium’s large genome has given scientists insight in regards to its abilities to resist antibiotics, to act as a pathogen, and to adapt.

Sequencing the genome gave scientists a better— yet still incomplete— understanding of how P. aeruginosa is resistant to many antibiotics. The pathogen is able to accomplish such a feat in part due to a combination of naturally encoded and imported resistance mechanisms and mutations. It was found that naturally, the pathogen’s genome codes for enzymes, like AmpC cephalosporinase, that break down antibiotics in such a way that they can no longer cause harm (1). P. aeruginosa also decreases the amount of non-specific porin proteins coded for and introduces more specific channels for importing essential nutrients, which serves as a way to limit antimicrobial substances from entering. There are also genes that code for components of outer membrane multi-drug efflux pumps that recognize specific antibiotics and pump them out of the cell. This gives its membrane a relatively low permeability to antibiotics (4). Lastly, it was found that mutations and changes in chromosomes can result in the over-expression of these resistance genes, greatly increasing the bacterium’s ability to be such a resilient organism (3). 

Another fascinating story scientists were able to piece together from sequencing its genome was some of the mechanisms by which this pathogen affects its host. In addition to the resistance genes previously mentioned, some of the 5,570 ORFs also account for a number of virulence factors including pili, flagella, quorum sensing proteins, exotoxin A and Type III secretion systems. The proteases mentioned can function in a variety of ways, which can range from breaking down proteins from the organism that it’s infecting and even killing off competing bacteria within the same vicinity. The Type III secretion systems produce toxins that can kill off some of its host’s cells (5). It’s no wonder these infections are so difficult to treat!

However, even more impressive is P. aeruginosa’s ability to grow in such a wide variety of environments. It can also live off of a wide array of organic carbon sources, but let’s take a look at additional encoded tools. Some of these include quorum sensing genes— which serve to pick up environmental signals and activate/deactivate other genes accordingly, motility switches— which control whether the pathogen remains stationary or moves, biofilm formation, and the regulation of the antibiotic resistance and virulence genes previously mentioned (4). Research has shown that deactivating motility and lowering virulency can actually help P. aeruginosa survive, as it helps to protect them from unfavorable environments. One may think the ability to move from less than optimal conditions would be more advantageous, but it turns out, switching off this gene allows the pathogen to form a colonized, biofilm structure, which— through a safety-in-numbers kind of logic— helps prevent damage from the host’s variety of immune responses and other competing species (4). Amazing.

Thanks for listening.

References:
(1) Hare, N.J. et al., 2012. J. Proteome Res 11:2. Proteomics of Pseudomonas aeruginosa Australian Epidemic Strain 1 (AES-1) Cultured under Conditions Mimicking the Cystic Fibrosis Lung Reveals Increased Iron Acquisition via the Siderophore Pyochelin.
(2) Klockgether, J. et al., 2010. J. Bacteriol 192:4. Genome Diversity of Pseudomonas aeruginosa PAO1 Laboratory Strains.
(3) Lister, P.D.; Wolter, D.J.; and Hanson N.D., 2009. Clin Microbial Rev 22:4. Antibacterial-Resistant Pseudomonas aeruginosa: Clinical Impact and Complex Regulation of Chromosomally Encoded Mechanisms.
(4) Moradali, M.F.; Ghods, S.; and Rehm, B.H.A., 2017. Frontiers in Cellular and Infection Microbiology 7:39. Pseudomonas aeruginosa Lifestyle: A Paradigm for Adaptation, Survival, and Persistence.
(5) Sood, U. et al., 2019. Front. Microbial. 10:53. Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa.
 (6) Stover, C.K. et al., 2000. Nature 406. Complete Genome Sequence of Pseudomonas aeruginosa PAO1, an Opportunistic Pathogen.