Metapopulation Structure of CRISPR-Cas Immunity in Pseudomonas aeruginosa and Its Viruses

Abstract

Pseudomonas aeruginosa is a widespread opportunistic pathogen and a major cause of morbidity and mortality in cystic fibrosis patients. Microbe-virus interactions play a critical role in shaping microbial populations, as viral infections can kill microbial populations or contribute to gene flow among microbes. Investigating how P. aeruginosa uses its CRISPR immune system to evade viral infection aids our understanding of how this organism spreads and evolves alongside its viruses in humans and the environment. Here, we identify patterns of CRISPR targeting and immunity that indicate P. aeruginosa and its viruses evolve in both a broad global population and in isolated human “islands.” These data set the stage for exploring metapopulation dynamics occurring within and between isolated “island” populations associated with CF patients, an essential step to inform future work predicting the specificity and efficacy of virus therapy and the spread of invasive viral elements and pathogenic epidemic bacterial strains.

The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification

“…We had previously established such profiles of diversity in naturally occurring microbial populations [27,34,45] but had not tested their structure in relation to immunity and infection networks.…”

“…We use empirical data from three data sets in which both CRISPR alleles and virus strains have been carefully and manually assembled [27,34]. These represent lytic, chronic and temperate virus lifestyles and two different microorganisms from the two domains of life where CRISPR occurs (archaea and bacteria).…”

“…The first two data sets compare genomes resolved to individual strains of the thermoacidophilic crenarchaeon Sulfolobus islandicus sampled at a single time point from two different locations. The third data set is from the gamma proteobacteria Pseudomonas aeruginosa [27], isolated from the sputum of CF patients in a high resolution longitudinal dataset collected by Marvig et al [46], with virus genomes obtained from the mu-like viruses from the genomic database because these are the most highly targeted temperate phage genomes in P. aeruginosa. From each data set, the empirical immunity matrices were constructed by comparing CRISPR arrays from each individual host strain to virus genomes.…”

“…The predominant viral population in these hosts is the chronic Sulfolobus Spindle Shaped Virus (SSV) [34]. The third data set consists of longitudinal sampling of humanadapted P. aeruginosa isolates from sputum samples of Cystic Fibrosis patients collected at a hospital in Copenhagen, Denmark and a global set of temperate mu-like viruses from P. aeruginosa viruses extracted from NCBI to substitute for a lack of sequenced contemporary viruses [27,46].…”

“…This experimental and theoretical evidence for advantages of surface modification may entail strong fitness costs under natural conditions because mutations in surface receptors such as those in flagella or pili can be detrimental for microbial movement and biofilm formation [21]. Investigations of natural populations have indeed shown that surface resistance is costly in the wild [27,28]. These observations underlie the need for complementing experimental approaches by developing theory on the kinds of 'macroscopic', whole system, diversity patterns expected under 'microscopic' CRISPR-induced coevolutionary processes.…”