Whole genome sequencing of bacteria in cystic fibrosis as a model for bacterial genome adaptation and evolution

Abstract

Cystic fibrosis (CF) airways harbor a wide variety of new and/or emerging multidrug resistant bacteria which impose a heavy burden on patients. These bacteria live in close proximity with one another, which increases the frequency of lateral gene transfer. The exchange and movement of mobile genetic elements and genomic islands facilitate the spread of genes between genetically diverse bacteria, which seem to be advantageous to the bacterium as it allows adaptation to the new niches of the CF lungs. Niche adaptation is one of the major evolutionary forces shaping bacterial genome composition and in CF the chronic strains adapt and become less virulent. The purpose of this review is to shed light on CF bacterial genome alterations. Next-generation sequencing technology is an exciting tool that may help us to decipher the genome architecture and the evolution of bacteria colonizing CF lungs.

Keywords::

• adaptive evolution
• Burkholderia cepacia complex
• cystic fibrosis
• phage
• Pseudomonas aeruginosa
• Staphylococcus aureus

Acknowledgements

We thank American Journal Experts for carefully reviewing the English.

Financial & competing interests disclosure

The author has no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending or royalties.

No writing assistance was utilized in the production of this manuscript.

Key issues

• This study on the genomes of the most pathogenic bacteria found in cystic fibrosis infections revealed that the bacteria have undergone evolution and adaptation.

• Chimeric repertoires of the genome sequence can be considered to be the result of adaptation in response to the recurrent antibiotic pressure.

• The advent of next-generation sequencing technologies have led to the availability of whole-genome sequences of several species found in cystic fibrosis, which in turn allowed the identification and functional analysis of genomic regions that reflect differences in lifestyle.

• Genetic exchanges occurring by horizontal gene transfer are mainly due to the antimicrobial treatment and selective pressure which promote the emergence and selection of multidrug-resistant bacteria.

• The information obtained from the genomic data will enable predictions to be made regarding the bacterial adaptations in each patient, which would further enable to design and optimize new antibiotic therapy.

• Whole-genome sequencing will also help in predicting or co-relating phenotypic characteristics and the relationship between pathogen and host.

• Metagenomic studies of phages will help to decode the relationship between these mobile elements and the evolution of virulence.