Research Article: Accessory genome of the multi-drug resistant ocular isolate of Pseudomonas aeruginosa PA34

Date Published: April 15, 2019

Publisher: Public Library of Science

Author(s): Dinesh Subedi, Gurjeet Singh Kohli, Ajay Kumar Vijay, Mark Willcox, Scott A. Rice, Finbarr Hayes.


Bacteria can acquire an accessory genome through the horizontal transfer of genetic elements from non-parental lineages. This leads to rapid genetic evolution allowing traits such as antibiotic resistance and virulence to spread through bacterial communities. The study of complete genomes of bacterial strains helps to understand the genomic traits associated with virulence and antibiotic resistance. We aimed to investigate the complete accessory genome of an ocular isolate of Pseudomonas aeruginosa strain PA34. We obtained the complete genome of PA34 utilising genome sequence reads from Illumina and Oxford Nanopore Technology followed by PCR to close any identified gaps. In-depth genomic analysis was performed using various bioinformatics tools. The susceptibility to heavy metals and cytotoxicity was determined to confirm expression of certain traits. The complete genome of PA34 includes a chromosome of 6.8 Mbp and two plasmids of 95.4 Kbp (pMKPA34-1) and 26.8 Kbp (pMKPA34-2). PA34 had a large accessory genome of 1,213 genes and had 543 unique genes not present in other strains. These exclusive genes encoded features related to metal and antibiotic resistance, phage integrase and transposons. At least 24 genomic islands (GIs) were predicated in the complete chromosome, of which two were integrated into novel sites. Eleven GIs carried virulence factors or replaced pathogenic genes. A bacteriophage carried the aminoglycoside resistance gene (AAC(3)-IId). The two plasmids carried other six antibiotic resistance genes. The large accessory genome of this ocular isolate plays a large role in shaping its virulence and antibiotic resistance.

Partial Text

Pseudomonas aeruginosa is associated with many opportunistic and nosocomial human infections such as pneumonia, septicaemia, corneal ulcers (microbial keratitis) and chronic infections in cystic fibrotic lungs [1, 2]. Antibiotic resistance in this bacterium is alarmingly on the rise and P. aeruginosa has been included in one of the top three priority pathogens urgently requiring new antimicrobial therapies for treatment by the World Health Organization [3]. Resistance to different antimicrobials in P. aeruginosa is due to its inherent capacity to oppose the action of antibiotics and its capacity to acquire genetic elements that often carry antibiotic resistance genes [4].

The large accessory genome of P. aeruginosa strain PA34 indicates that this strain has a diverse genomic structure. The strain harbours twenty-four genomic islands and two plasmids that carry various metal and antibiotic resistance genes as well as several genes associated with virulence. This may be associated with the observance of higher antibiotic resistance, mercury tolerance and in-vitro cytotoxicity of PA34. The in-silico analysis showed that six antibiotic resistance genes were present in two different plasmids and one antibiotic resistance gene plus various mercury resistance genes were integrated into different GIs and these resistance genes have sequence similarities with that of either other environmental or enteric bacteria. Furthermore, the genome of the PA34 has been integrated by phage element (gp37) that has its origin in enteric bacteria and carried aminoglycoside resistance gene (AAC(3)-IId). These findings suggest that resistance and virulence in PA34 may have evolved due to environmental selection pressure where organisms acquire traits to survive predation by other inhabitants. Thus acquired traits enhance the pathogenesis process in human. Given the eye is susceptible to being infected by environmental strains of P. aeruginosa, examination of a larger number of eye isolates may be necessary to uncover any additional acquired genetic features associated with microbial keratitis. This will help our understanding of different aspects of Pseudomonas keratitis.