Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients

Abstract

In many human infections, hosts and pathogens coexist for years or decades. Important examples include HIV, herpes viruses, tuberculosis, leprosy, and malaria. With the exception of intensively studied viral infections such as HIV͞AIDs, little is known about the extent to which the clonal expansion that occurs during long-term infection by pathogens involves important genetic adaptations. We report here a detailed, whole-genome analysis of one such infection, that of a cystic fibrosis (CF) patient by the opportunistic bacterial pathogen Pseudomonas aeruginosa. The bacteria underwent numerous genetic adaptations during 8 years of infection, as evidenced by a positive-selection signal across the genome and an overwhelming signal in specific genes, several of which are mutated during the course of most CF infections. Of particular interest is our finding that virulence factors that are required for the initiation of acute infections are often selected against during chronic infections. It is apparent that the genotypes of the P. aeruginosa strains present in advanced CF infections differ systematically from those of ''wild-type'' P. aeruginosa and that these differences may offer new opportunities for treatment of this chronic disease.chronic infection ͉ positive selection ͉ virulence ͉ antibiotic resistance M ost cystic fibrosis (CF) patients acquire chronic Pseudomonas aeruginosa infections by their teenage years, if not earlier, and these respiratory infections are responsible for much of the morbidity and mortality caused by CF (1, 2). It has been established that most of these infections are clonal (3), and even among groups of CF patients treated in specific clinics the infections are acquired independently, presumably from diverse environmental reservoirs (4). Previous studies, particularly of the O-antigen biosynthetic locus and the transcriptional regulator mucA, indicate that some P. aeruginosa genes commonly incur loss-of-function mutations as the infections progress (5-7). Mutator phenotypes also arise frequently (8).The overall picture is reminiscent of typical cancers: a clone of cells, albeit in this instance one of exogenous origin, experiences selection for an accumulation of genetic variants that promote long-term survival and clonal expansion. Our data validate this model for P. aeruginosa infections in CF and provide strong evidence for the role of selection in shaping the genotypes of the bacteria that are present during the late, life-threatening phase of the infections. Our data also focus attention on particular aspects of P. aeruginosa metabolism that are premier targets of selection, both in the patient we studied in most detail and in other, independently evolving, P. aeruginosa infections in additional CF patients.

Bacterial competition and quorum‐sensing signalling shape the eco‐evolutionary outcomes of model in vitro phage therapy

“…This suggests that QS may play an important role for P. aeruginosa competition against other bacterial species. For example, the proportion of lasR mutants typically increases during chronic polymicrobial CF infections (Ghoul et al., 2015; Marvig et al., 2014; Smith et al., 2006) and this could be potentially partly explained with QS‐mediated competitive interactions with other bacteria (Harrison, Paul, Massey, & Buckling, 2008). There are several mutually nonexclusive explanations for reduced P. aeruginosa growth in the presence of competitors.…”

“…Competition could thus enhance the phage efficacy when treating acute CF and burn infections that are commonly co‐infected by QS signalling P. aeruginosa , S. aureus and S. maltophilia (Harrison, 2007; Turner et al., 2014). However, in contrary, P. aeruginosa resistance evolution to phages could be a more severe problem in chronic polymicrobial CF infections that are often dominated by P. aeruginosa mutants that have lost QS signalling ability during the long‐term adaptation (Andersen et al., 2015; Marvig et al., 2014; Smith et al., 2006). Interestingly, we found that higher levels of lasR strain resistance evolution were correlated with the higher rate of phage infectivity evolution, which could open up avenues for pre‐adapting phages to be more infective before clinical phage therapy treatments (Betts et al., 2013; Friman et al., 2016).…”

“…Apart from the mutation in QS signalling pathway, the two isolates were otherwise isogenic (Fletcher et al., 2007). The lasR mutation is often associated with isolates from the later stages of long‐term infections in patients with CF (Andersen et al., 2015; Marvig et al., 2014), and its weakened virulence is due to inability to detect and produce quorum‐sensing signalling molecules that activate the expression of P. aeruginosa virulence factors (Smith et al., 2006). A lytic bacteriophage, PT7, which obligately kills P. aeruginosa , was used as a phage (Friman et al., 2016).…”

Évolution adaptative des bactéries

“…Chez 14 d'entre eux, dont le premier à avoir été infecté, on a pu, pendant 16 ans, prélever et conserver 112 isolats séquencés récemment, l'ensemble des séquences obtenues couvrant le temps de l'évolution. On a identifié 492 SNP (single nucleotide polymorphism), soit environ deux par an, taux déjà décrit chez certains pathogènes au cours d'infections prolongées [3]. La construction d'un arbre phylogénétique suggérait un réseau de transmission entre patients et permettait de reconstruire la structure du dernier ancêtre commun.…”

“…Quelle est la base génétique de l'évasion immunitaire, de la résistance aux antibiotiques ? Cette question, soulevée depuis des années, a été explorée en laboratoire, soit dans des expériences d'évolution expérimentale utilisant des souches microbiennes définies que l'on repique pendant de nombreuses généra-tions dans des milieux liquides contrôlés [1,2], soit par l'étude de souches isolées au cours de processus pathologiques [3]. Ces travaux ont, cependant, été longtemps limités par les conditions techniques, essentiellement la difficulté à obtenir un nombre suffisant de séquences de génomes bactériens pour des résultats statistiquement valables.…”