1
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Polymyxin Resistance and Heteroresistance Are Common in Clinical Isolates of Achromobacter Species and Correlate with Modifications of the Lipid A Moiety of Lipopolysaccharide. Microbiol Spectr 2023; 11:e0372922. [PMID: 36519943 PMCID: PMC9927164 DOI: 10.1128/spectrum.03729-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The Achromobacter genus includes opportunistic pathogens that can cause chronic infections in immunocompromised patients, especially in people with cystic fibrosis (CF). Treatment of Achromobacter infections is complicated by antimicrobial resistance. In this study, a collection of Achromobacter clinical isolates, from CF and non-CF sources, was investigated for polymyxin B (PmB) resistance. Additionally, the effect of PmB challenge in a subset of isolates was examined and the presence of PmB-resistant subpopulations within the isolates was described. Further, chemical and mass spectrometry analyses of the lipid A of Achromobacter clinical isolates enabled the determination of the most common structures and showed that PmB challenge was associated with lipid A modifications that included the addition of glucosamine and palmitoylation and the concomitant loss of the free phosphate at the C-1 position. This study demonstrates that lipid A modifications associated with PmB resistance are prevalent in Achromobacter and that subresistant populations displaying the addition of positively charged residues and additional acyl chains to lipid A can be selected for and isolated from PmB-sensitive Achromobacter clinical isolates. IMPORTANCE Achromobacter species can cause chronic and potentially severe infections in immunocompromised patients, especially in those with cystic fibrosis. Bacteria cannot be eradicated due to Achromobacter's intrinsic multidrug resistance. We report that intrinsic resistance to polymyxin B (PmB), a last-resort antimicrobial peptide used to treat infections by multiresistant bacteria, is prevalent in Achromobacter clinical isolates; many isolates also display increased resistance upon PmB challenge. Analysis of the lipopolysaccharide lipid A moiety of several Achromobacter species reveals a penta-acylated lipid A, which in the PmB-resistant isolates was modified by the incorporation of glucosamine residues, an additional acyl chain, loss of phosphates, and hydroxylation of acyl chains, all of which can enhance PmB resistance in other bacteria. We conclude that PmB resistance, particularly in Achromobacter isolates from chronic respiratory infections, is a common phenomenon, and that Achromobacter lipid A displays modifications that may confer increased resistance to polymyxins and potentially other antimicrobial peptides.
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2
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Blanchard AC, Waters VJ. Opportunistic Pathogens in Cystic Fibrosis: Epidemiology and Pathogenesis of Lung Infection. J Pediatric Infect Dis Soc 2022; 11:S3-S12. [PMID: 36069904 DOI: 10.1093/jpids/piac052] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022]
Abstract
Cystic fibrosis (CF) is one of the most common life-shortening genetic diseases in Caucasians. Due to abnormal accumulation of mucus, respiratory failure caused by chronic infections is the leading cause of mortality in this patient population. The microbiology of these respiratory infections includes a distinct set of opportunistic pathogens, including Pseudomonas aeruginosa, Burkholderia spp., Achromobacter spp., Stenotrophomonas maltophilia, anaerobes, nontuberculous mycobacteria, and fungi. In recent years, culture-independent methods have shown the polymicrobial nature of lung infections, and the dynamics of microbial communities. The unique environment of the CF airway predisposes to infections caused by opportunistic pathogens. In this review, we will highlight how the epidemiology and role in disease of these pathogens in CF differ from that in individuals with other medical conditions. Infectious diseases (ID) physicians should be aware of these differences and the specific characteristics of infections associated with CF.
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Affiliation(s)
- Ana C Blanchard
- Department of Pediatrics, Division of Infectious Diseases, CHU Sainte-Justine, Université de Montréal, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, Quebec, H3T 1C5, Canada
| | - Valerie J Waters
- Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, Ontario, M5G 1X8, Canada
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3
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Elborn JS, Flume PA, Van Devanter DR, Procaccianti C. Management of chronic Pseudomonas aeruginosa infection with inhaled levofloxacin in people with cystic fibrosis. Future Microbiol 2021; 16:1087-1104. [PMID: 34384254 DOI: 10.2217/fmb-2021-0150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
People with cystic fibrosis (CF) are highly susceptible to bacterial infections of the airways. By adulthood, chronic Pseudomonas aeruginosa (Pa) is the most prevalent infective organism and is difficult to eradicate owing to its adaptation to the CF lung microenvironment. Long-term suppressive treatment with inhaled antimicrobials is the standard care for reducing exacerbation frequency, improving quality of life and increasing measures of lung function. Levofloxacin (a fluoroquinolone antimicrobial) has been approved as an inhaled solution in Europe and Canada, for the treatment of adults with CF with chronic P. aeruginosa pulmonary infections. Here, we review the clinical principles relating to the use of inhaled antimicrobials and inhaled levofloxacin for the management of P. aeruginosa infections in patients with CF.
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Affiliation(s)
- J Stuart Elborn
- Faculty of Medicine, Health & Life Sciences, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Patrick A Flume
- Departments of Medicine & Pediatrics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Donald R Van Devanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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4
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Menetrey Q, Sorlin P, Jumas-Bilak E, Chiron R, Dupont C, Marchandin H. Achromobacter xylosoxidans and Stenotrophomonas maltophilia: Emerging Pathogens Well-Armed for Life in the Cystic Fibrosis Patients' Lung. Genes (Basel) 2021; 12:genes12050610. [PMID: 33919046 PMCID: PMC8142972 DOI: 10.3390/genes12050610] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
In patients with cystic fibrosis (CF), the lung is a remarkable ecological niche in which the microbiome is subjected to important selective pressures. An inexorable colonization by bacteria of both endogenous and environmental origin is observed in most patients, leading to a vicious cycle of infection–inflammation. In this context, long-term colonization together with competitive interactions among bacteria can lead to over-inflammation. While Pseudomonas aeruginosa and Staphylococcus aureus, the two pathogens most frequently identified in CF, have been largely studied for adaptation to the CF lung, in the last few years, there has been a growing interest in emerging pathogens of environmental origin, namely Achromobacter xylosoxidans and Stenotrophomonas maltophilia. The aim of this review is to gather all the current knowledge on the major pathophysiological traits, their supporting mechanisms, regulation and evolutionary modifications involved in colonization, virulence, and competitive interactions with other members of the lung microbiota for these emerging pathogens, with all these mechanisms being major drivers of persistence in the CF lung. Currently available research on A. xylosoxidans complex and S. maltophilia shows that these emerging pathogens share important pathophysiological features with well-known CF pathogens, making them important members of the complex bacterial community living in the CF lung.
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Affiliation(s)
- Quentin Menetrey
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Pauline Sorlin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Raphaël Chiron
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Centre de Ressources et de Compétences de la Mucoviscidose, CHU de Montpellier, 34093 Montpellier, France;
| | - Chloé Dupont
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 34093 Nîmes, France
- UMR 5151 HydroSciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université de Montpellier, 15, Avenue Charles Flahault, BP 14491, CEDEX 5, 34093 Montpellier, France
- Correspondence:
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First Documented Case of Percutaneous Endoscopic Gastrostomy (PEG) Tube-Associated Bacterial Peritonitis due to Achromobacter Species with Literature Review. Case Rep Gastrointest Med 2020; 2020:4397930. [PMID: 32047677 PMCID: PMC7007964 DOI: 10.1155/2020/4397930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/24/2019] [Accepted: 11/11/2019] [Indexed: 01/25/2023] Open
Abstract
Introduction. Achromobacter species (spp.) peritonitis has seldom been identified in medical literature. Scarce cases of Achromobacter peritonitis described previously have been correlated with peritoneal dialysis and more sparingly with spontaneous bacterial peritonitis. Achromobacter exhibits intrinsic and acquired resistance, especially in chronic infections, to most antibiotics. This article conducts a literature review of all previously reported Achromobacter spp. peritonitis and describes the first reported case of Achromobacter peritonitis as a complication of percutaneous endoscopic gastrostomy (PEG) tube placement. Discussion. Achromobacter peritonitis as a complication of PEG-tube placement has not been previously reported. In our patients' case, the recently placed PEG-tube with ascitic fluid leakage was identified as the most plausible infection source. Although a rare bacterial peritonitis pathogen, Achromobacter may be associated with wide antimicrobial resistance and unfavorable outcomes. Conclusion. No current guidelines provide significant guidance on treatment of PEG-tube peritonitis regardless of microbial etiology. Infectious Disease Society of America identifies various broad-spectrum antibiotics targeting nosocomial intra-abdominal coverage; some of these antimicrobial selections (such as cefepime and metronidazole combination) may yet be inadequate for widely resistant Achromobacter spp. Recognizably, the common antibiotics utilized for spontaneous bacterial peritonitis, i.e., third generation cephalosporins and fluoroquinolones, to which Achromobacter is resistant and variably susceptible, respectively, would be extensively insufficient. Piperacillin/tazobactam (P/T) and carbapenem were identified to provide the most reliable coverage in vitro; clinically, 5 out of the 8 patients who received either P/T or a carbapenem, or both, eventually experienced clinical improvement.
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6
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Abstract
Cystic fibrosis (CF) is a genetic, multisystem disease due to defects in the cystic fibrosis transmembrane conductance regulator (CFTR) protein, an anion channel responsible for chloride and bicarbonate trafficking. Although this channel is expressed in many tissues, its impaired function in airway epithelial cells leads to hyperviscous mucous secretions impeding effective mucociliary clearance. Impaired clearance of inhaled microorganisms results in the establishment of chronic infection, triggering an overexaggerated inflammatory response. The resulting release of inflammatory cytokines and enzymes causes pulmonary damage in the form of bronchiectasis, further impairing mucociliary action, forming a vicious cycle. Subsequent respiratory failure remains the leading cause of death in individuals with CF.
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Affiliation(s)
- Stephanie Duggins Davis
- The University of North Carolina at Chapel Hill, Department of Pediatrics, UNC Children’s Hospital, Chapel Hill, NC USA
| | - Margaret Rosenfeld
- Department of Pediatrics, University of Washington School of Medicine, Division of Pulmonary and Sleep Medicine Seattle Children’s Hospital, Seattle, WA USA
| | - James Chmiel
- Department of Pediatrics, Indiana University School of Medicine, Division of Pediatric Pulmonology, Allergy and Sleep Medicine, Riley Hospital for Children at IU Health, Indianapolis, IN USA
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7
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Abstract
Although survival of individuals with cystic fibrosis (CF) has been continuously improving for the past 40 years, respiratory failure secondary to recurrent pulmonary infections remains the leading cause of mortality in this patient population. Certain pathogens such as Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and species of the Burkholderia cepacia complex continue to be associated with poorer clinical outcomes including accelerated lung function decline and increased mortality. In addition, other organisms such as anaerobes, viruses, and fungi are increasingly recognized as potential contributors to disease progression. Culture-independent molecular methods are also being used for diagnostic purposes and to examine the interaction of microorganisms in the CF airway. Given the importance of CF airway infections, ongoing initiatives to promote understanding of the epidemiology, clinical course, and treatment options for these infections are needed.
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Affiliation(s)
- Ana C Blanchard
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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8
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Cameron LC, Bonis B, Phan CQ, Kent LA, Lee AK, Hunter RC. A putative enoyl-CoA hydratase contributes to biofilm formation and the antibiotic tolerance of Achromobacter xylosoxidans. NPJ Biofilms Microbiomes 2019; 5:20. [PMID: 31396394 PMCID: PMC6684605 DOI: 10.1038/s41522-019-0093-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023] Open
Abstract
Achromobacter xylosoxidans has attracted increasing attention as an emerging pathogen in patients with cystic fibrosis. Intrinsic resistance to several classes of antimicrobials and the ability to form robust biofilms in vivo contribute to the clinical manifestations of persistent A. xylosoxidans infection. Still, much of A. xylosoxidans biofilm formation remains uncharacterized due to the scarcity of existing genetic tools. Here we demonstrate a promising genetic system for use in A. xylosoxidans; generating a transposon mutant library which was then used to identify genes involved in biofilm development in vitro. We further described the effects of one of the genes found in the mutagenesis screen, encoding a putative enoyl-CoA hydratase, on biofilm structure and tolerance to antimicrobials. Through additional analysis, we find that a fatty acid signaling compound is essential to A. xylosoxidans biofilm ultrastructure and maintenance. This work describes methods for the genetic manipulation of A. xylosoxidans and demonstrated their use to improve our understanding of A. xylosoxidans pathophysiology.
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Affiliation(s)
- Lydia C. Cameron
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN 55455 USA
| | - Benjamin Bonis
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN 55455 USA
| | - Chi Q. Phan
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN 55455 USA
- Present Address: Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195 USA
| | - Leslie A. Kent
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN 55455 USA
| | - Alysha K. Lee
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN 55455 USA
- Present Address: Department of Earth System Science, Stanford University, Stanford, CA 94305 USA
| | - Ryan C. Hunter
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN 55455 USA
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9
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Beaudoin T, Stone TA, Glibowicka M, Adams C, Yau Y, Ahmadi S, Bear CE, Grasemann H, Waters V, Deber CM. Activity of a novel antimicrobial peptide against Pseudomonas aeruginosa biofilms. Sci Rep 2018; 8:14728. [PMID: 30283025 PMCID: PMC6170476 DOI: 10.1038/s41598-018-33016-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/17/2018] [Indexed: 11/09/2022] Open
Abstract
With the increasing recognition of biofilms in human disease, the development of novel antimicrobial therapies is of critical importance. For example, in patients with cystic fibrosis (CF), the acquisition of host-adapted, chronic Pseudomonas aeruginosa infection is associated with a decline in lung function and increased mortality. Our objective was to test the in vitro efficacy of a membrane-active antimicrobial peptide we designed, termed 6K-F17 (sequence: KKKKKK-AAFAAWAAFAA-NH2), against multidrug resistant P. aeruginosa biofilms. This peptide displays high antimicrobial activity against a range of pathogenic bacteria, yet is non-hemolytic to human erythrocytes and non-toxic to human bronchial epithelial cells. In the present work, P. aeruginosa strain PAO1, and four multidrug resistant (MDR) isolates from chronically infected CF individuals, were grown as 48-hour biofilms in a static biofilm slide chamber model. These biofilms were then exposed to varying concentrations of 6K-F17 alone, or in the presence of tobramycin, prior to confocal imaging. Biofilm biovolume and viability were assessed. 6K-F17 was able to kill biofilms - even in the presence of sputum - and greatly reduce biofilm biovolume in PAO1 and MDR isolates. Strikingly, when used in conjunction with tobramycin, low doses of 6K-F17 significantly potentiated tobramycin killing, leading to biofilm destruction.
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Affiliation(s)
- Trevor Beaudoin
- Division of Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Tracy A Stone
- Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Miroslawa Glibowicka
- Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Christina Adams
- Division of Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Yvonne Yau
- Division of Microbiology, Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Saumel Ahmadi
- Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Christine E Bear
- Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Hartmut Grasemann
- Division of Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Division of Respiratory Medicine, Department of Pediatrics, Hospital for Sick Children, Toronto, Canada
| | - Valerie Waters
- Division of Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, M5G 1X8, Canada
| | - Charles M Deber
- Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada. .,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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10
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Staphylococcus aureus interaction with Pseudomonas aeruginosa biofilm enhances tobramycin resistance. NPJ Biofilms Microbiomes 2017; 3:25. [PMID: 29062489 PMCID: PMC5648753 DOI: 10.1038/s41522-017-0035-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance is a significant threat to the treatment of infectious disease. Multiple mechanisms of resistance to different classes of antibiotics have been identified and well-studied. However, these mechanisms are studied with bacteria in isolation, whereas often, infections have a polymicrobial basis. Using a biofilm slide chamber model, we visualized the formation and development of clinical Pseudomonas aeruginosa biofilms in the presence of secreted Staphylococcus aureus exoproducts, two bacteria that commonly co-infect pediatric patients with cystic fibrosis. We showed that, over time, certain isolates of P. aeruginosa can form different biofilm architecture in the presence of S. aureus exoproducts. We further determined that this interaction was dependent on Psl produced by P. aeruginosa and staphylococcal protein A from S. aureus. Importantly, we identified a mechanism of antibiotic resistance to tobramycin that is dependent on the polymicrobial interactions between these two bacteria. This interaction occurred in isolates of P. aeruginosa recovered from children with cystic fibrosis who failed to clear P. aeruginosa following inhaled tobramycin treatment. The interaction between two different bacterial species can enhance the antibiotic resistance of biofilms. Resistance to antimicrobial therapy is usually studied using individual bacterial species, but many infections involve more than one species. Researchers in Canada, led by Trevor Beaudoin at The Hospital for Sick Children in Toronto, studied the effect of products secreted by Staphylococcus aureus bacteria on biofilms of Pseudomonas aeruginosa. They worked with biofilms that had resisted treatment, isolated from patients with cystic fibrosis. The co-infection altered the biofilm structure and increased its resistance to the antibiotic tobramycin. The effect depended on bacterial aggregation stimulated by the interaction between a large carbohydrate from P. aeruginosa and a protein secreted by S. aureus. The research highlights the need to study bacterial interactions to understand and treat infections involving different bacteria.
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11
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Jeukens J, Freschi L, Vincent AT, Emond-Rheault JG, Kukavica-Ibrulj I, Charette SJ, Levesque RC. A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter. Genome Biol Evol 2017; 9:1030-1046. [PMID: 28383665 PMCID: PMC5405338 DOI: 10.1093/gbe/evx061] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2017] [Indexed: 12/13/2022] Open
Abstract
Over the past decade, there has been a rising interest in Achromobacter sp., an emerging opportunistic pathogen responsible for nosocomial and cystic fibrosis lung infections. Species of this genus are ubiquitous in the environment, can outcompete resident microbiota, and are resistant to commonly used disinfectants as well as antibiotics. Nevertheless, the Achromobacter genus suffers from difficulties in diagnosis, unresolved taxonomy and limited understanding of how it adapts to the cystic fibrosis lung, not to mention other host environments. The goals of this first genus-wide comparative genomics study were to clarify the taxonomy of this genus and identify genomic features associated with pathogenicity and host adaptation. This was done with a widely applicable approach based on pan-genome analysis. First, using all publicly available genomes, a combination of phylogenetic analysis based on 1,780 conserved genes with average nucleotide identity and accessory genome composition allowed the identification of a largely clinical lineage composed of Achromobacter xylosoxidans, Achromobacter insuavis, Achromobacter dolens, and Achromobacter ruhlandii. Within this lineage, we identified 35 positively selected genes involved in metabolism, regulation and efflux-mediated antibiotic resistance. Second, resistome analysis showed that this clinical lineage carried additional antibiotic resistance genes compared with other isolates. Finally, we identified putative mobile elements that contribute 53% of the genus's resistome and support horizontal gene transfer between Achromobacter and other ecologically similar genera. This study provides strong phylogenetic and pan-genomic bases to motivate further research on Achromobacter, and contributes to the understanding of opportunistic pathogen evolution.
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Affiliation(s)
- Julie Jeukens
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Luca Freschi
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), Quebec City, Quebec, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Quebec City, Quebec, Canada
| | | | - Irena Kukavica-Ibrulj
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), Quebec City, Quebec, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Quebec City, Quebec, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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12
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Beaudoin T, Kennedy S, Yau Y, Waters V. Visualizing the Effects of Sputum on Biofilm Development Using a Chambered Coverglass Model. J Vis Exp 2016. [PMID: 28060284 DOI: 10.3791/54819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Biofilms consist of groups of bacteria encased in a self-secreted matrix. They play an important role in industrial contamination as well as in the development and persistence of many health related infections. One of the most well described and studied biofilms in human disease occurs in chronic pulmonary infection of cystic fibrosis patients. When studying biofilms in the context of the host, many factors can impact biofilm formation and development. In order to identify how host factors may affect biofilm formation and development, we used a static chambered coverglass method to grow biofilms in the presence of host-derived factors in the form of sputum supernatants. Bacteria are seeded into chambers and exposed to sputum filtrates. Following 48 hr of growth, biofilms are stained with a commercial biofilm viability kit prior to confocal microscopy and analysis. Following image acquisition, biofilm properties can be assessed using different software platforms. This method allows us to visualize key properties of biofilm growth in presence of different substances including antibiotics.
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Affiliation(s)
- Trevor Beaudoin
- Physiology and Experimental Medicine, Hospital for Sick Children;
| | - Sarah Kennedy
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland
| | - Yvonne Yau
- Department of Laboratory Medicine and Pathobiology, University of Toronto
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13
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Patterns of virulence factor expression and antimicrobial resistance in Achromobacter xylosoxidans and Achromobacter ruhlandii isolates from patients with cystic fibrosis. Epidemiol Infect 2016; 145:600-606. [PMID: 27873565 DOI: 10.1017/s0950268816002624] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Achromobacter spp. are opportunistic pathogens increasingly recovered from adult patients with cystic fibrosis (CF). We report the characterization of 122 Achromobacter spp. isolates recovered from 39 CF patients by multilocus sequence typing, virulence traits, and susceptibility to antimicrobials. Two species, A. xylosoxidans (77%) and A. ruhlandii (23%) were identified. All isolates showed a similar biofilm formation ability, and a positive swimming phenotype. By contrast, 4·3% and 44·4% of A. xylosoxidans and A. ruhlandii, respectively, exhibited a negative swarming phenotype, making the swimming and swarming abilities of A. xylosoxidans significantly higher than those of A. ruhlandii. A. xylosoxidans isolates from an outbreak clone also exhibited significantly higher motility. Both species were generally susceptible to ceftazidime, ciprofloxacin, imipenem and trimethoprim/sulphamethoxazole and there was no significant difference in susceptibility between isolates from chronic or sporadic infection. However, A. xylosoxidans isolates from chronic and sporadic cases were significantly more resistant to imipenem and ceftazidime than isolates of the outbreak clone.
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14
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Nielsen SM, Nørskov-Lauritsen N, Bjarnsholt T, Meyer RL. Achromobacter Species Isolated from Cystic Fibrosis Patients Reveal Distinctly Different Biofilm Morphotypes. Microorganisms 2016; 4:microorganisms4030033. [PMID: 27681927 PMCID: PMC5039593 DOI: 10.3390/microorganisms4030033] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/19/2016] [Accepted: 09/01/2016] [Indexed: 11/16/2022] Open
Abstract
Achromobacter species have attracted attention as emerging pathogens in cystic fibrosis. The clinical significance of Achromobacter infection is not yet fully elucidated; however, their intrinsic resistance to antimicrobials and ability to form biofilms renders them capable of establishing long-term chronic infections. Still, many aspects of Achromobacter biofilm formation remain uncharacterized. In this study, we characterized biofilm formation in clinical isolates of Achromobacter and investigated the effect of challenging the biofilm with antimicrobials and/or enzymes targeting the extracellular matrix. In vitro biofilm growth and subsequent visualization by confocal microscopy revealed distinctly different biofilm morphotypes: a surface-attached biofilm morphotype of small aggregates and an unattached biofilm morphotype of large suspended aggregates. Aggregates consistent with our in vitro findings were visualized in sputum samples from cystic fibrosis patients using an Achromobacter specific peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) probe, confirming the presence of Achromobacter biofilms in the CF lung. High antibiotic tolerance was associated with the biofilm phenotype, and biocidal antibiotic concentrations were up to 1000 fold higher than for planktonic cultures. Treatment with DNase or subtilisin partially dispersed the biofilm and reduced the tolerance to specific antimicrobials, paving the way for further research into using dispersal mechanisms to improve treatment strategies.
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Affiliation(s)
- Signe M Nielsen
- Department of Clinical Medicine, Aarhus University, DK-8200 Aarhus, Denmark.
- Department of Clinical Microbiology, Aarhus University Hospital, DK-8200 Aarhus, Denmark.
| | | | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Clinical Microbiology, Rigshospitalet, DK-2100 Copenhagen, Denmark.
| | - Rikke L Meyer
- Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus, Denmark.
- Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark.
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