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Viral DNA in Genome of Bacteria Behind Fatal Cystic Fibrosis Lung Infections

NEW YORK (GenomeWeb News) – Clusters of genes — some from viruses — appear to contribute to the competitiveness of a Pseudomonas aeruginosa strain known to cause serious infections in humans, particularly cystic fibrosis patients, according to new research.
A team of investigators from Canada and the UK sequenced the genome of the P. aeruginosa strain LESB58, which was isolated from a hospitalized cystic fibrosis patient in Liverpool two decades ago. Along with the P. aeruginosa core genome, the researchers identified several clusters of sequence — derived from viral or prophage and non-prophage DNA — that are potentially involved in colonizing the lung and contributing to epidemics. Researchers say the insights could provide therapeutic targets for tackling the antibiotic-resistant strain. The work appears online today in Genome Research.
“It has been demonstrated that P. aeruginosa virulence is combinatorial,” senior author Roger Levesque, a molecular microbiologist at the University of Laval, and his colleagues wrote. “The studies described here indicate an ability to successfully establish colonization in what is usually a protected niche, the lung, [and] indicate that this too involves a combinatorial process and involves both the core genome and key prophage and genomic island genes from the ‘accessory’ genome to increase competitiveness.”
P. aeruginosa is found throughout the environment — in soil, water, and in associations with other organisms. Although it can be harmless, P. aeruginosa is also behind many opportunistic human infections and is the most common cause of persistent and sometimes fatal respiratory infections in those with cystic fibrosis.
For instance, a particularly virulent P. aeruginosa strain, dubbed the Liverpool Epidemic Strain, was identified in 1996 following an outbreak at a children’s cystic fibrosis unit. Since its discovery more than a decade ago, the strain has been implicated in infections in several centers in the UK.
Although other epidemic strains have also been detected in the UK and Australia, the Liverpool Epidemic Strain, which is resistant to β-lactam antibiotics and can cause so-called super-infection, is reportedly linked to the highest rates of patient morbidity.
In general, about 90 percent of the six- to seven-megabase genome tends to be highly conserved from one P. aeruginosa strain to the next. The other ten percent of the genome contains variable accessory genes and genomic islands that undergo rapid changes and diversifying selection.
In an effort to understand the genetic differences between epidemic and other P. aeruginosa strains, Levesque and his team used Sanger and BAC end sequencing to sequence the genome of the first known Liverpool Epidemic Strain isolate, called LESB58, to nine times coverage. The isolate was found in a Liverpool CF patient in 1988, eight years before research on the epidemic strain was first published.
The researchers reported that the LESB58 strain contained almost all of the virulence genes previously reported in other P. aeruginosa strains. In addition, they found that the LESB58 genome contains accessory genes in five prophase clusters, resembling viral DNA, five non-prophage islands, and one defective prophase cluster.
“The genome of LESB58, like those sequenced previously, carried the core genome, including the vast majority of recognized virulence genes of P. aeruginosa,” the authors wrote. “The genomic variations lie largely within five prophages and one defective prophage and five large genomic islands, a few of which are related to those found in other strains of P. aeruginosa.”
The researchers also compared LESB58 genes influencing motility, virulence, lipopolysaccharide serotypes, and antibiotic resistance with those found in other strains.
Next, the researchers used unbiased signature tagged mutagenesis to delve into the function of genes found in these clusters in rat lung models of cystic fibrosis. They found that mutations in the prophage genes led to strains that were defective for growth in vivo and/or less capable of infecting rat models of cystic fibrosis.
“We have shown that mutations within these novel prophages and genomic islands can prevent the strain from establishing infections,” lead author Craig Winstanley, a University of Liverpool researcher, said in a statement. “This indicates that bacterial viruses may contribute to the ability of bacterial pathogens to adapt to specific environments and to the emergence of particularly successful epidemic bacterial strains.”
In particular, the researchers noted that three prophages and one genomic island appear to contribute to the cystic fibrosis related infections caused by LESB58. That, in turn, should help researchers gather clues about the strategy that such epidemic strains use to colonize the human lung. And, researchers say, the results may provide insights into the P. aeruginosa LES strain that could eventually lead to new therapeutic targets to help combat the epidemic strain.
The annotated P. aeruginosa LES genome is available through the Pseudomonas Genome Database.

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