Intraclonal competitive fitness of longitudinal cystic fibrosis Pseudomonas aeruginosa airway isolates in liquid cultures

Improved engineering of Pseudomonas aeruginosa to study the adaptation of pyoverdine production under intra- or inter- specific bacterial competition

Pseudomonas aeruginosa (PA) is a common cause of chronic infections, particularly feared by cystic fibrosis patients. PA colonizes the lung where it adapts to the local environment, and/or to treatments by drugs. This genotypic and phenotypic adaptation, in turns, influences its interaction with its environment, like bacteria from the microbiota. As an example, to access iron, PA produces and secretes two siderophores, pyoverdine and pyochelin that are iron chelators scavenging iron from the environment and bringing it back into the bacterial cells. Siderophores production depends on the level of iron starvation, on the presence of other bacteria, etc. this latter component being less well investigated. Even if studies on bacterial interactions, and their evolution, have been increasing since several years, we are still facing a lack of tools, for example, to specifically follow the growth of PA isolates in such competitive environments. We thus improved a cloning method to gain time in the cloning steps, to lower the polar effects, and to accurately follow the interactions of any PA isolate with other bacteria. For that, a fluorescent reporter gene was inserted between two genes, the glutamine-fructose-6-phosphate transaminase (glmS) and PA5548. This reporter was efficiently produced either from an inducible or a house-keeping promoter, and its expression did not lead to polar effects. We used this strain to study intra and inter-specific bacterial competitions for iron between different lung pathogens. We thus grew wild-type PA together either with an isogenic PA ΔpvdS variant, that does not produce the most efficient siderophore pyoverdine, or with Klebsiella pneumoniae or Acinetobacter baumanii, two other lung pathogens. We finally monitored the effect of the loss of pvdS on the competition between PA and the other bacterial species. These studies enabled us to differentiate intra from inter specific competitions, both arising in the lung environment, and pinpoint the importance of the bacterial specie for the adaptation of pyoverdine production.

Microevolution of Pseudomonas aeruginosa in the airways of people with cystic fibrosis

The chronic infections of cystic fibrosis (CF) airways with Pseudomonas aeruginosa are a paradigm of how environmental bacteria can conquer, adapt, and persist in an atypical habitat and successfully evade defense mechanisms and chemotherapy in a susceptible host. The within-host evolution of intraclonal diversity has been examined by whole-genome sequencing, phenotyping, and competitive fitness experiments of serial P. aeruginosa isolates collected from CF airways since onset of colonization for a period of up to 40 years. The spectrum of de novo mutations and the adaptation of phenotype and fitness of the bacterial progeny were more influenced by the living conditions in the CF lung than by the clone type of their ancestor and its genetic repertoire.

Competitive fitness of Pseudomonas aeruginosa isolates in human and murine precision-cut lung slices

Chronic respiratory infections with the gram-negative bacterium Pseudomonas aeruginosa are an important co-morbidity for the quality of life and prognosis of people with cystic fibrosis (CF). Such long-term colonization, sometimes lasting up to several decades, represents a unique opportunity to investigate pathogen adaptation processes to the host. Our studies aimed to resolve if and to what extent the bacterial adaptation to the CF airways influences the fitness of the pathogen to grow and to persist in the lungs. Marker-free competitive fitness experiments of serial P. aeruginosa isolates differentiated by strain-specific SNPs, were performed with murine and human precision cut lung slices (PCLS). Serial P. aeruginosa isolates were selected from six mild and six severe CF patient courses, respectively. MPCLS or hPCLS were inoculated with a mixture of equal numbers of the serial isolates of one course. The temporal change of the composition of the bacterial community during competitive growth was quantified by multi-marker amplicon sequencing. Both ex vivo models displayed a strong separation of fitness traits between mild and severe courses. Whereas the earlier isolates dominated the competition in the severe courses, intermediate and late isolates commonly won the competition in the mild courses. The status of the CF lung disease rather than the bacterial genotype drives the adaptation of P. aeruginosa during chronic CF lung infection. This implies that the disease status of the lung habitat governed the adaptation of P. aeruginosa more strongly than the underlying bacterial clone-type and its genetic repertoire.

From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment

Pseudomonas aeruginosa is one of the main microbial species colonizing the lungs of cystic fibrosis patients and is responsible for the decline in respiratory function. Despite the hostile pulmonary environment, P. aeruginosa is able to establish chronic infections thanks to its strong adaptive capacity. Various longitudinal studies have attempted to compare the strains of early infection with the adapted strains of chronic infection. Thanks to new '-omics' techniques, convergent genetic mutations, as well as transcriptomic and proteomic dysregulations have been identified. As a consequence of this evolution, the adapted strains of P. aeruginosa have particular phenotypes that promote persistent infection.

Genome-Based Analyses of Fitness Effects and Compensatory Changes Associated with Acquisition of bla CMY-, bla CTX-M-, and bla OXA-48/VIM-1-Containing Plasmids in Escherichia coli

(1) Background: Resistance plasmids are under selective conditions beneficial for the bacterial host, but in the absence of selective pressure, this carriage may cause fitness costs. Compensation of this fitness burden is important to obtain competitive ability under antibiotic-free conditions. In this study, we investigated fitness effects after a conjugative transfer of plasmids containing various beta-lactamase genes transferred into Escherichia coli. (2) Methods: Fourteen beta-lactamase-encoding plasmids were transferred from clinical donor strains to E. coli J53. Growth rates were compared for all transconjugants and the recipient. Selected transconjugants were challenged in long-term growth experiments. Growth rates were assessed at different time points during growth for 500 generations. Whole-genome sequencing (WGS) of initial and evolved transconjugants was determined. Results: Most plasmid acquisitions resulted in growth differences, ranging from -4.5% to 7.2%. Transfer of a single bla _CMY-16-carrying plasmid resulted in a growth burden and a growth benefit in independent mating. Long-term growth led to a compensation of fitness burdens and benefits. Analyzing WGS revealed genomic changes caused by Single Nucleotide Polymorphisms (SNPs) and insertion sequences over time. Conclusions: Fitness effects associated with plasmid acquisitions were variable. Potential compensatory mutations identified in transconjugants' genomes after 500 generations give interesting insights into aspects of plasmid-host adaptations.