Highly Diversified Pandoraea pulmonicola Population during Chronic Colonization in Cystic Fibrosis Chloé Dupont, Fabien Aujoulat, Raphaël Chiron, Pauline Condom, Estelle Jumas-Bilak, Hélène Marchandin To cite this version: Chloé Dupont, Fabien Aujoulat, Raphaël Chiron, Pauline Condom, Estelle Jumas-Bilak, et al.. Highly Diversified Pandoraea pulmonicola Population during Chronic Colonization in Cystic Fibrosis. Fron- tiers in Microbiology, Frontiers Media, 2017, 8, pp.1892. 10.3389/fmicb.2017.01892. hal-01891570 HAL Id: hal-01891570 https://hal.archives-ouvertes.fr/hal-01891570 Submitted on 6 Jan 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. 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Distributed under a Creative Commons Attribution - NonCommercial| 4.0 International License fmicb-08-01892 October 4, 2017 Time: 16:17 # 1 ORIGINAL RESEARCH published: 06 October 2017 doi: 10.3389/fmicb.2017.01892 Highly Diversified Pandoraea pulmonicola Population during Chronic Colonization in Cystic Fibrosis Chloé Dupont1, Fabien Aujoulat1, Raphaël Chiron2, Pauline Condom1, Estelle Jumas-Bilak1,3 and Hélène Marchandin1,4,5* 1 Equipe Pathogènes Hydriques, Santé, Environnements, UMR 5569 Hydrosciences Montpellier, U.F.R des Sciences Pharmaceutiques et Biologiques and Université Montpellier, Montpellier, France, 2 Centre de Ressources et de Compétences pour la Mucoviscidose, Hôpital Arnaud de Villeneuve, Centre Hospitalier Universitaire de Montpellier, Montpellier, France, 3 Laboratoire d’Hygiène Hospitalière, Hôpital Saint-Eloi, Centre Hospitalier Universitaire de Montpellier, Montpellier, France, 4 Service de Microbiologie, Hôpital Carémeau, Centre Hospitalier Universitaire de Nîmes, Nîmes, France, 5 Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Centre Hospitalier Universitaire de Montpellier, Montpellier, France Several environmental bacteria are considered as opportunistic pathogens in cystic fibrosis (CF) and are able to persistently colonize the CF respiratory tract (CFRT). Beside Pseudomonas aeruginosa and Burkholderia cepacia complex, Pandoraea spp. are defined as pathogenic. During chronic colonization, adaptive evolution and diversified population have been demonstrated, notably for P. aeruginosa. However, the persistence of Pandoraea in the CFRT remains largely unexplored. We studied genomic Edited by: and phenotypic traits of Pandoraea pulmonicola isolates successively recovered from Leonard Peruski, Centers for Disease Control and the airways of a single CF patient and relate the results to qualitative and quantitative Prevention (CDC), United States evolution of other cultivable pathogens and to patient clinical status. A total of 31 isolates Reviewed by: recovered from 18 sputum samples over a 7-year period in a single CF patient were Miklos Fuzi, studied. Genome dynamics was assessed by pulsed-field gel electrophoresis, ERIC- Semmelweis University, Hungary Dane Parker, PCR fingerprinting and 16S rRNA gene PCR-temporal temperature gel electrophoresis. Columbia University, United States Phenotypic features included antimicrobial susceptibility, motility, biofilm production, *Correspondence: and virulence in Caenorhabditis elegans model. Variability was observed for all the Hélène Marchandin [email protected] characteristics studied leading to highly diversified patterns (24 patterns) for the 31 clonally related isolates. Some of these modifications, mainly genomic events were Specialty section: concomitantly observed with CFRT microbiota composition shifts and with severe This article was submitted to Infectious Diseases, exacerbations. The diversity of P. pulmonicola population studied, observed for isolates a section of the journal recovered from successive samples but also within a sample suggested that existence Frontiers in Microbiology of a diversified population may represent a patho-adaptive strategy for host persistence Received: 14 February 2017 Accepted: 15 September 2017 in the heterogeneous and fluctuating CFRT environment. Published: 06 October 2017 Keywords: cystic fibrosis, Pandoraea, diversity, persistence, biofilm, motility, antimicrobial resistance, virulence Citation: Dupont C, Aujoulat F, Chiron R, Condom P, Jumas-Bilak E and INTRODUCTION Marchandin H (2017) Highly Diversified Pandoraea pulmonicola The genus Pandoraea was described in 2000, it belongs to the family Burkholderiaceae and Population during Chronic Colonization in Cystic Fibrosis. comprises 10 species mainly cultured from sputum of cystic fibrosis (CF) patients or soil Front. Microbiol. 8:1892. (Coenye et al., 2000). Currently, 20 Pandoraea genomes are totally sequenced, including a unique doi: 10.3389/fmicb.2017.01892 Pandoraea pulmonicola genome. Pandoraea species are considered as emerging pathogens and Frontiers in Microbiology| www.frontiersin.org 1 October 2017| Volume 8| Article 1892 fmicb-08-01892 October 4, 2017 Time: 16:17 # 2 Dupont et al. Diversity in CF Pandoraea pulmonicola Persisting Population infection led to the production of high levels of antibodies, were named with the same number followed by apostrophe(s). and to a worsened CF lung disease (Jørgensen et al., Selected co-colonizing P. aeruginosa (Pa13 isolated in September 2003; Mahenthiralingam, 2014; Degand et al., 2015; Martina 2013) and methicillin-resistant Staphylococcus aureus (Sa14 et al., 2017). After first colonization, Pandoraea spp. were isolated in January 2014) isolated at the time of or close to able to chronically colonize the CF respiratory tract (CFRT) the most severe pulmonary exacerbation experienced by the (Fernández-Olmos et al., 2012; Kokcha et al., 2013; Pugès patient during the study period, were also studied. Sputum et al., 2015; Martina et al., 2017), were transmissible between culture results (bacterial identification, load), clinical data patients (Jørgensen et al., 2003; Degand et al., 2015) and can [forced expiratory volume in 1 s (FEV1), body mass index, produce severe lung diseases and bacteremia (Pimentel and pulmonary exacerbations/stable status], and antibiotic courses MacLeod, 2008; Kokcha et al., 2013). The pathogenicity appears were recorded. mainly supported by a pro-inflammatory response induction significantly greater than with Pseudomonas aeruginosa (Caraher Antimicrobial Susceptibility Testing et al., 2008; Costello et al., 2014) and the treatment may be Antimicrobial susceptibility testing was performed according complicated by multidrug resistance conferred by carbapenem- to the 2016 recommendations of the Antibiogram Committee hydrolyzing oxacillinases (Caraher et al., 2008). P. pulmonicola of the French Society for Microbiology1. Disk diffusion method showed an ability to invade human lung epithelial cells, not was performed for amikacin, amoxicillin C/− clavulanic shared by other Pandoraea species (Caraher et al., 2008) acid, aztreonam, cefalotin, cefepime, cefoxitin, cefpirom, and was the most virulent species, being as virulent as cefotaxime, ceftazidime, chloramphenicol, ciprofloxacin, Burkholderia cenocepacia in the Galleria mellonella larvae colistin, cotrimoxazole, fosfomycin, gentamicin, imipenem, model (Costello et al., 2011). The potential involvement of isepamicin, levofloxacin, moxalactam, nalidixic acid, netilmicin, Pandoraea in complex interactions between microorganisms ofloxacin, piperacillin, piperacillin/tazobactam, tetracycline, within the CF airways was also suggested (Costello et al., ticarcillin C/− clavulanic acid, and tobramycin (Bio-Rad R ). 2014). E-test (bioMérieux R ) was performed when inhibition zone During long-term colonization, adaptive evolution was diameters were observed around disks, and minimal inhibitory found in most CF pathogens and was particularly studied concentration (MIC) results that differed by more than two for P. aeruginosa and Burkholderia spp. (Silva et al., 2011). dilutions were considered as different. For ciprofloxacin, MICs In P. aeruginosa, evolutionary adaptation and phenotype were determined by the agar dilution reference method. diversification occur during CFRT colonization (Hauser et al., 2011; Winstanley et al., 2016 for reviews). These variations Motility and Biofilm Formation generally lead to decreased immunogenicity and virulence while Motility of Pandoraea isolates was tested in semi-solid agar antibiotic resistance globally increases. In addition, some studies according to Kirov et al.(2004). Biofilm formation was evaluated revealed a diversified population within a sample and suggested after 72 h of growth for Pandoraea isolates and after 48 h of that this diversity may also represent an adaptive strategy for growth for P. aeruginosa and S. aureus at 37◦C in microtitre plates host persistence (Lieberman et al., 2014; Winstanley et al., NUNC R -polystyrene (Abdouchakour et al., 2015). Isolates were 2016). categorized as non-adherent or weakly, moderately, or strongly Adaptive behavior of other CF pathogens has received less adherent according to Stepanovic et al.(2000). Experiments were attention although an increased virulence has been suggested performed in triplicate. during chronic colonization for