Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated

Temperate phages enhance pathogen fitness in chronic lung infection

The Liverpool Epidemic Strain (LES) is a polylysogenic, transmissible strain of Pseudomonas aeruginosa, capable of superinfecting existing P. aeruginosa respiratory infections in individuals with cystic fibrosis (CF). The LES phages are highly active in the CF lung and may have a role in the competitiveness of the LES in vivo. In this study, we tested this by competing isogenic PAO1 strains that differed only by the presence or absence of LES prophages in a rat model of chronic lung infection. Lysogens invaded phage-susceptible populations, both in head-to-head competition and when invading from rare, in the spatially structured, heterogeneous lung environment. Appreciable densities of free phages in lung tissue confirmed active phage lysis in vivo. Moreover, we observed lysogenic conversion of the phage-susceptible competitor. These results suggest that temperate phages may have an important role in the competitiveness of the LES in chronic lung infection by acting as anti-competitor weapons

Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Abstract Background Chronic lung infections caused by Pseudomonas aeruginosa are a significant cause of morbidity and mortality in people with cystic fibrosis (CF). Shared P. aeruginosa strains, that can be transmitted between patients, are of concern and in Australia the AUST-02 shared strain is predominant in individuals attending CF centres in Queensland and Western Australia. M3L7 is a multidrug resistant sub-type of AUST-02 that was recently identified in a Queensland CF centre and was shown to be associated with poorer clinical outcomes. The main aim of this study was to resolve the relationship of the emergent M3L7 sub-type within the AUST-02 group of strains using whole genome sequencing. Results A whole genome core phylogeny of 63 isolates indicated that M3L7 is a monophyletic sub-lineage within the context of the broader AUST-02 group. Relatively short branch lengths connected all of the M3L7 isolates. A phylogeny based on nucleotide polymorphisms present across the genome showed that the chronological estimation of the most recent common ancestor was around 2001 (± 3 years). SNP differences between sequential non-hypermutator M3L7 isolates collected 3–4 years apart from five patients suggested both continuous infection of the same strain and cross-infection of some M3L7 variants between patients. The majority of polymorphisms that were characteristic of M3L7 (i.e. acquired after divergence from all other AUST-02 isolates sequenced) were found to produce non-synonymous mutations in virulence and antibiotic resistance genes. Conclusions M3L7 has recently diverged from a common ancestor, indicating descent from a single carrier at a CF treatment centre in Australia. Both adaptation to the lung and transmission of M3L7 between adults attending this centre may have contributed to its rapid dissemination. Further genomic investigations are required on multiple intra-sample isolates of this sub-type to decipher potential mechanisms which facilitates its epidemiological success

Clarifying the Intracellular and Extracellular Lifestyles of CF Microbes in Three Dimensions

Imaging of sputum smears and thin sections have suggested that P. aeruginosa persists as extracellular bacterial aggregates, or biofilms, during chronic CF infections. However, emerging evidence indicates that host cells may also provide a protective reservoir for P. aeruginosa during infection. While phagocytes that flood the CF airways normally kill infecting bacteria, CFTR-deficient murine macrophages fail to kill P. aeruginosa, raising the possibility that CF macrophages could house viable bacteria. Epithelial cells may also provide an intracellular home for P. aeruginosa, since P. aeruginosa can invade epithelial cells in tissue culture systems. Together, these results have led to our hypothesis that the intracellular environment is a protective reservoir for P. aeruginosa during chronic CF infections. We are using a state-of-the-art imaging technique termed MiPACT to study how bacteria are spatially organized and functioning in CF sputum in relation to host cells. MiPACT was previously developed for the characterization of growth rates and spatial organization of microbes in millimeter thick three-dimensional CF sputum specimens. A major advantage to MiPACT is that the sputum specimens are embedded in a hydrogel and passively cleared with a detergent, which renders the sputum optically transparent and maintains the original biogeography of the specimens. This represents a substantial advance over traditional techniques like smears and thin sections, which were essentially limited to analyses in two dimensions. In this study, we have further advanced MiPACT in two ways to study how P. aeruginosa interacts with host cells. First, we can now detect bacterial gene expression in situ with fluorescent nucleic acid probes, which will allow us to determine whether specific genes are expressed when bacteria associate with host cells. Second, we have combined MiPACT with immunofluorescence to label bacteria and host cell proteins with fluorescent antibodies. In these preliminary studies, we have developed probes to detect P. aeruginosa alginate gene expression in vitro and successfully used immunofluorescence to label neutrophils, macrophages, and P. aeruginosa in CF sputum in situ. The immunofluorescence revealed that P. aeruginosa can be detected as extracellular and intracellular aggregates in sputum. Ongoing work is being performed to determine which host cells are housing intracellular P. aeruginosa and whether intracellular bacteria are viable or in the process of being killed. These new methods will shed important light on how P. aeruginosa persists in the CF airways