Achromobacter : mechanisms of acquired resistance to fluoroquinolones

Achromobacter est un pathogène opportuniste émergent, rencontré principalement chez les patients atteints de mucoviscidose. Ce sont des bacilles à Gram négatif non fermentaires présentant des résistances naturelles à de nombreux antibiotiques ainsi que des résistances acquises fréquentes notamment aux fluoroquinolones pouvant rendre le traitement complexe. Les mécanismes de résistance acquise aux fluoroquinolones n’ont cependant pas été étudiés dans des souches cliniques chez Achromobacter avant ce travail. La modification de la cible, plus précisément des QRDR, est le mécanisme le plus fréquemment en cause dans la résistance bactérienne aux fluoroquinolones. La surexpression de systèmes d’efflux est également impliquée dans la résistance chez les bacilles à Gram négatif non fermentaires. L’objectif de ce travail était donc l’étude des mécanismes de résistance acquise aux fluoroquinolones chez Achromobacter.Nous avons tout d’abord pu montrer qu’à la différence d’autres bacilles à Gram négatif comme E. coli ou P. aeruginosa, l’altération de la cible est peu impliquée dans la résistance aux fluoroquinolones chez Achromobacter. Nous avons ensuite mis en évidence l’importante implication via une surexpression des systèmes d’efflux de type RND déjà connus : AxyEF-OprN, AxyABM, ainsi que de deux systèmes décrits dans ce travail AxySUV et AinSUV. L’implication d’AxyXY-OprZ a également été retrouvée, confirmant et complétant les résultats antérieurs le concernant. La surexpression de l’efflux était associée le plus souvent à des substitutions dans la séquence protéique des régulateurs locaux de ces systèmes. Ces systèmes d’efflux ne sont pas spécifiques d’un antibiotique ni même d’une classe en particulier. Ce travail a permis de préciser le spectre des molécules prises en charge par les systèmes qu’ils soient surexprimés ou non. L’activité de ces différents substrats peut être compromise par la surexpression des systèmes d’efflux après exposition aux fluoroquinolones, par exemple le méropénème en cas de surexpression d’AxyABM.Nos travaux ont permis une avancée significative dans la compréhension des mécanismes de résistance d’Achromobacter aux fluoroquinolones et par extension à d’autres classes d’antibiotiques d’intérêt majeur pour la prise en charge des infections chez les patients atteints de mucoviscidose.Achromobacter is an emerging opportunistic pathogen, mainly encountered in patients with cystic fibrosis. They are non-fermentative Gram-negative bacilli with natural resistance to many antibiotics as well as frequent acquired resistance, particularly to fluoroquinolones, which can make treatment complex. However, the mechanisms of acquired resistance to fluoroquinolones have not been studied in clinical strains of Achromobacter before this work. Target modification, specifically QRDRs, is the most common mechanism involved in bacterial resistance to fluoroquinolones. Overexpression of efflux systems has also been implicated in resistance in non-fermenting Gram-negative bacilli. The objective of this work was therefore to study the mechanisms of acquired fluoroquinolone resistance in Achromobacter.We have first demonstrated that, unlike other Gram-negative bacilli such as E. coli or P. aeruginosa, target alteration is rarely involved in fluoroquinolone resistance in Achromobacter. We then highlighted the important involvement via overexpression of the already known RND-type efflux systems: AxyEF-OprN, AxyABM, as well as two systems described in this work AxySUV and AinSUV. The involvement of AxyXY-OprZ was also observed, confirming and completing previous results. Overexpression of efflux was most often associated with substitutions in the protein sequence of local regulators of these systems. These efflux systems are not specific to any particular antibiotic or even class. This work has enabled us to specify the spectrum of molecules extruded by the systems, whether or not they are overexpressed. The activity of these different substrates can be compromised by overexpression of the efflux systems after exposure to fluoroquinolones, e.g. meropenem in the case of overexpression of AxyABM.Our work has led to a significant advance in the understanding of the mechanisms of resistance of Achromobacter to fluoroquinolones and by extension to other classes of antibiotics of major interest for the management of infections in cystic fibrosis patients

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Rapid Detection of Isolates Belonging to the Epidemic Clones Achromobacter xylosoxidans ST137 and Achromobacter ruhlandii DES from Cystic Fibrosis Patients.

spp. are increasingly reported among cystic fibrosis patients. Genotyping requires time-consuming methods such as multilocus sequence typing or pulsed-field gel electrophoresis. Therefore, data on the prevalence of multiresistant epidemic clones, especially A. xylosoxidans ST137 (AxST137) and the Danish epidemic strain (DES), are lacking. We recently developed and published a database for species identification by matrix-assisted laser desorption-ionization-time of flight mass spectrometry (MALDI-TOF MS; Bruker Daltonics). The aim of this study was to evaluate the ability of the MALDI-TOF MS to distinguish these multiresistant epidemic clones within species. All the spectra of A. xylosoxidans ( = 1,571) and ( = 174) used to build the local database were analyzed by ClinProTools, MALDI Biotyper PCA, MALDI Biotyper dendrogram, and flexAnalysis software for biomarker peak detection. Two hundred two isolates (including 48 isolates of AxST137 and 7 of DES) were tested. Specific biomarker peaks were identified: absent peak at 6,651 for AxST137 isolates and present peak at 9,438 for DES isolates. All tested isolates were well typed by our local database and clustered within distinct groups (ST137 or non-ST137 and DES or non-DES) no matter the MALDI-TOF software or only by simple visual inspection of the spectra by any user. The use of MALDI-TOF MS allowed us to identify isolates of A. xylosoxidans belonging to the AxST137 clone that spread in France and Belgium (the Belgian epidemic clone) and of belonging to the DES clone. This tool will help the implementation of segregation measures to avoid interpatient transmission of these resistant clones

Distribution of Achromobacter species in 12 French cystic fibrosis centers in 2020 by a retrospective MALDI-TOF MS spectrum analysis

International audienceAchromobacter spp. are nonfermenting Gram-negative bacilli mainly studied among cystic fibrosis (CF) patients. The identification of the 19 species within the genus is time-consuming (nrdA-sequencing), thus data concerning the distribution of the species are limited to specific studies. Recently, we built a database using MALDI-TOF mass spectrometry (MS) (Bruker) that allows rapid and accurate species identification and detection of the multiresistant epidemic clones: A xylosoxidans ST137 spreading among CF patients in various French and Belgium centers, and A. ruhlandii DES in Denmark. Here, we first assessed whether species identification could be achieved with our database solely by analysis of MS spectra without availability of isolates. Then, we conducted a multicentric study describing the distribution of Achromobacter species and of the clone ST137 among French CF centers. We collected and analyzed with our local database the spectra of Achromobacter isolates from 193 patients (528 samples) from 12 centers during 2020. In total, our approach enabled to conclude for 502/528 samples (95.1%), corresponding to 181 patients. Eleven species were detected, only five being involved in chronic colonization, A. xylosoxidans (86.4%), A. insuavis (9.1%), A. mucicolens (2.3%), A. marplatensis (1.1%) and A. genogroup 3 (1.1%). This study confirmed the high prevalence of A. xylosoxidans in chronic colonizations and the circulation of the clone A. xylosoxidans ST137 in France: four patients in two centers. The present study is the first to report the distribution of Achromobacter species from CF patients samples using retrospective MALDI-TOF/MS data. This easy approach could enable future large-scale epidemiological studies

Cyclamen: time, sea and speciation biogeography using a temporally calibrated phylogeny

Aim The Mediterranean region is a species-rich area with a complex geographical history. Geographical barriers have been removed and restored due to sea level changes and local climatic change. Such barriers have been proposed as a plausible mechanism driving the high levels of speciation and endemism in the Mediterranean basin. This raises the fundamental question: is allopatric isolation the mechanism by which speciation occurs? This study explores the potential driving influence of palaeo-geographical events on the speciation of Cyclamen (Myrsinaceae), a group with most species endemic to the Mediterranean region. Cyclamen species have been shown experimentally to have few genetic barriers to hybridization. Location The Mediterranean region, including northern Africa, extending eastwards to the Black Sea coast. Methods A generic level molecular phylogeny of Myrsinaceae and Primulaceae is constructed, using Bayesian approximation, to produce a secondary age estimate for the stem lineage of Cyclamen. This estimate is used to calibrate temporally an infrageneric phylogeny of Cyclamen, built with nrDNA ITS, cpDNA trnL-F and cpDNA rps16 sequences. A biogeographical analysis of Cyclamen is performed using dispersal-vicariance analysis. Results The emergence of the Cyclamen stem lineage is estimated at 30.1-29.2 Ma, and the crown divergence at 12.9-12.2 Ma. The average age of Cyclamen species is 3.7 Myr. Every pair of sister species have mutually exclusive, allopatric distributions relative to each other. This pattern appears typical of divergence events throughout the evolutionary history of the genus. Main conclusions Geographical barriers, such as the varying levels of the Mediterranean Sea, are the most plausible explanation for speciation events throughout the phylogenetic history of Cyclamen. The genus demonstrates distributional patterns congruent with the temporally reticulate palaeogeography of the Mediterranean region