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Jean-Pierre V, Sorlin P, Pantel A, Chiron R, Lavigne JP, Jeannot K, Marchandin H. Cefiderocol susceptibility of Achromobacter spp.: study of an accurately identified collection of 230 strains. Ann Clin Microbiol Antimicrob 2024; 23:54. [PMID: 38886694 PMCID: PMC11184864 DOI: 10.1186/s12941-024-00709-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Achromobacter spp. are opportunistic pathogens, mostly infecting immunocompromised patients and patients with cystic fibrosis (CF) and considered as difficult-to-treat pathogens due to both intrinsic resistance and the possibility of acquired antimicrobial resistance. Species identification remains challenging leading to imprecise descriptions of resistance in each taxon. Cefiderocol is a broad-spectrum siderophore cephalosporin increasingly used in the management of Achromobacter infections for which susceptibility data remain scarce. We aimed to describe the susceptibility to cefiderocol of a collection of Achromobacter strains encompassing different species and isolation sources from CF or non-CF (NCF) patients. METHODS We studied 230 Achromobacter strains (67 from CF, 163 from NCF patients) identified by nrdA gene-based analysis, with available susceptibility data for piperacillin-tazobactam, meropenem and trimethoprim-sulfamethoxazole. Minimal inhibitory concentrations (MICs) of cefiderocol were determined using the broth microdilution reference method according to EUCAST guidelines. RESULTS Strains belonged to 15 species. A. xylosoxidans represented the main species (71.3%). MICs ranged from ≤ 0.015 to 16 mg/L with MIC50/90 of ≤ 0.015/0.5 mg/L overall and 0.125/2 mg/L against 27 (11.7%) meropenem-non-susceptible strains. Cefiderocol MICs were not related to CF/NCF origin or species although A. xylosoxidans MICs were statistically lower than those of other species considered as a whole. Considering the EUCAST non-species related breakpoint (2 mg/L), 228 strains (99.1%) were susceptible to cefiderocol. The two cefiderocol-resistant strains (A. xylosoxidans from CF patients) represented 3.7% of meropenem-non-susceptible strains and 12.5% of MDR strains. CONCLUSIONS Cefiderocol exhibited excellent in vitro activity against a large collection of accurately identified Achromobacter strains, irrespective of species and origin.
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Affiliation(s)
- Vincent Jean-Pierre
- HydroSciences Montpellier, Univ. Montpellier, CNRS, IRD, Service de Microbiologie et Hygiène Hospitalière, CHU de Nîmes, 34093, Montpellier, France
| | - Pauline Sorlin
- HydroSciences Montpellier, Univ. Montpellier, CNRS, IRD, Service de Microbiologie et Hygiène Hospitalière, CHU de Nîmes, 34093, Montpellier, France
| | - Alix Pantel
- VBIC, INSERM U1047, Univ. Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU de Nîmes, 30029, Nîmes Cedex 9, France
| | - Raphaël Chiron
- HydroSciences Montpellier, Univ. Montpellier, CNRS, IRD, Centre de Ressources et de Compétences de la Mucoviscidose, CHU de Montpellier, 34093, Montpellier, France
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Univ. Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU de Nîmes, 30029, Nîmes Cedex 9, France
| | - Katy Jeannot
- Laboratoire Associé Au Centre National de Référence de La Résistance Aux Antibiotiques, CHU de Besançon, 25000, Besançon, France
| | - Hélène Marchandin
- HydroSciences Montpellier, Univ. Montpellier, CNRS, IRD, Service de Microbiologie et Hygiène Hospitalière, CHU de Nîmes, 34093, Montpellier, France.
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Olbrecht M, Echahidi F, Piérard D, Peeters C, Vandamme P, Wybo I, Demuyser T. In Vitro Susceptibility of Achromobacter Species Isolated from Cystic Fibrosis Patients: a 6-Year Survey. Antimicrob Agents Chemother 2023; 67:e0037923. [PMID: 37310234 PMCID: PMC10353363 DOI: 10.1128/aac.00379-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/17/2023] [Indexed: 06/14/2023] Open
Abstract
We conducted in vitro antimicrobial susceptibility testing of 267 Achromobacter isolates for 16 antibiotics from 2017 to 2022. The highest susceptibility was found for piperacillin-tazobactam (70%) and ceftazidime-avibactam (62%). Between 30% and 49% of strains were susceptible to tigecycline, ceftazidime, and meropenem. We applied species-specific Achromobacter xylosoxidans breakpoints for piperacillin-tazobactam, meropenem, and trimethoprim-sulfamethoxazole and EUCAST pharmacokinetic/pharmacodynamic (PK/PD) breakpoints for the others. A. xylosoxidans was the most frequently isolated species, followed by Achromobacter insuavis and Achromobacter ruhlandii.
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Affiliation(s)
- Margo Olbrecht
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Fedoua Echahidi
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Denis Piérard
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Ingrid Wybo
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Thomas Demuyser
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- AIMS lab, Center for Neurosciences, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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3
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Winzig F, Gandhi S, Lee A, Würstle S, Stanley GL, Capuano I, Neuringer I, Koff JL, Turner PE, Chan BK. Inhaled Bacteriophage Therapy for Multi-Drug Resistant Achromobacter. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2022; 95:413-427. [PMID: 36568830 PMCID: PMC9765334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The rise of antimicrobial resistant (AMR) bacteria is a global public health threat. AMR Achromobacter bacteria pose a challenging clinical problem, particularly for those with cystic fibrosis (CF) who are predisposed to chronic bacterial lung infections. Lytic bacteriophages (phages) offer a potential alternative to treat AMR infections, with the possible benefit that phage selection for resistance in target bacteria might coincide with reduced pathogenicity. The result is a genetic "trade-off," such as increased sensitivity to chemical antibiotics, and/or decreased virulence of surviving bacteria that are phage resistant. Here, we show that two newly discovered lytic phages against Achromobacter were associated with stabilization of respiratory status when deployed to treat a chronic pulmonary infection in a CF patient using inhaled (nebulized) phage therapy. The two phages demonstrate traits that could be generally useful in their development as therapeutics, especially the possibility that the phages can select for clinically useful trade-offs if bacteria evolve phage resistance following therapy. We discuss the limitations of the current study and suggest further work that should explore whether the phages could be generally useful in targeting pulmonary or other Achromobacter infections in CF patients.
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Affiliation(s)
- Franziska Winzig
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Technische Universität München, München, Germany
| | - Shiv Gandhi
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Department of Internal Medicine, Section of Infectious
Disease, Yale School of Medicine, New Haven, CT, USA
| | - Alina Lee
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
| | - Silvia Würstle
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Department of Internal Medicine II, University Hospital
rechts der Isar, School of Medicine, Technische Universität München, München,
Germany
| | - Gail L. Stanley
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Department of Internal Medicine, Section of Pulmonary,
Critical Care, & Sleep Medicine, Yale School of Medicine, New Haven, CT,
USA
| | - Isabella Capuano
- Department of Internal Medicine, Section of Pulmonary,
Critical Care, & Sleep Medicine, Yale School of Medicine, New Haven, CT,
USA
- Cornell University, Ithaca, NY, USA
| | | | - Jonathan L. Koff
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Department of Internal Medicine, Section of Pulmonary,
Critical Care, & Sleep Medicine, Yale School of Medicine, New Haven, CT,
USA
- To whom all correspondence should be addressed:
Paul E. Turner, ; ORCID:
https://www.orcid.org/0000-0003-3490-7498. Benjamin K. Chan,
. Jonathan L. Koff,
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Program in Microbiology, Yale School of Medicine, New
Haven, CT, USA
- To whom all correspondence should be addressed:
Paul E. Turner, ; ORCID:
https://www.orcid.org/0000-0003-3490-7498. Benjamin K. Chan,
. Jonathan L. Koff,
| | - Benjamin K. Chan
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- To whom all correspondence should be addressed:
Paul E. Turner, ; ORCID:
https://www.orcid.org/0000-0003-3490-7498. Benjamin K. Chan,
. Jonathan L. Koff,
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Clinical outcomes associated with Achromobacter species infection in people with cystic fibrosis. J Cyst Fibros 2022; 22:334-343. [PMID: 36418214 DOI: 10.1016/j.jcf.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/28/2022] [Accepted: 11/07/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND Achromobacter species are emerging pathogens isolated from respiratory samples of Patients with cystic fibrosis (pwCF) causing growing concerns in the CF community. The epidemiology and the clinical impact of Achromobacter in CF is unclear since data are restricted to small case control studies or selected populations. AIM To characterize the effect of Achromobacter respiratory infection on CF lung disease. METHODS European CF Society Patient Registry data was analysed for association between Achromobacter infection and demographic/clinical characteristics and outcomes of pwCF. RESULTS Of eligible 38,795 patients, Achromobacter infection was reported in 2,093 (prevalence (95% CI) of 5.40% (5.17 - 5.62). The prevalence varied significantly between the countries and increased with age peaking at the age 20-30. Achromobacter infection was more prevalent in pwCF carrying class minimal function mutations, having worse nutrition or lower pulmonary function, and more patients inhaled antibiotics against P. aeruginosa. Patient infected with Achromobacter had similar pulmonary function and BMI to patients infected with P. aeruginosa at all age groups. Being infected with both bacteria was associated with significantly lower pulmonary function and BMI at all age groups. CONCLUSIONS Achromobacter infection was associated with disease severity similar to infection with P. aeruginosa. Being infected with both bacteria is associated with even more severe disease. This suggests to study if eradication will improve the outcome of pwCF.
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Achromobacter spp. prevalence and adaptation in cystic fibrosis lung infection. Microbiol Res 2022; 263:127140. [DOI: 10.1016/j.micres.2022.127140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/11/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022]
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Le Goff M, Vastel M, Lebrun R, Mansuelle P, Diarra A, Grandjean T, Triponney P, Imbert G, Gosset P, Dessein R, Garnier F, Durand E. Characterization of the Achromobacter xylosoxidans Type VI Secretion System and Its Implication in Cystic Fibrosis. Front Cell Infect Microbiol 2022; 12:859181. [PMID: 35782124 PMCID: PMC9245596 DOI: 10.3389/fcimb.2022.859181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteria of the genus Achromobacter are environmental germs, with an unknown reservoir. It can become opportunistic pathogens in immunocompromised patients, causing bacteremia, meningitis, pneumonia, or peritonitis. In recent years, Achromobacter xylosoxidans has emerged with increasing incidence in patients with cystic fibrosis (CF). Recent studies showed that A. xylosoxidans is involved in the degradation of the respiratory function of patients with CF. The respiratory ecosystem of patients with CF is colonized by bacterial species that constantly fight for space and access to nutrients. The type VI secretion system (T6SS) empowers this constant bacterial antagonism, and it is used as a virulence factor in several pathogenic bacteria. This study aimed to investigate the prevalence of the T6SS genes in A. xylosoxidans isolated in patients with CF. We also evaluated clinical and molecular characteristics of T6SS-positive A. xylosoxidans strains. We showed that A. xylosoxidans possesses a T6SS gene cluster and that some environmental and clinical isolates assemble a functional T6SS nanomachine. A. xylosoxidans T6SS is used to target competing bacteria, including other CF-specific pathogens. Finally, we demonstrated the importance of the T6SS in the internalization of A. xylosoxidans in lung epithelial cells and that the T6SS protein Hcp is detected in the sputum of patients with CF. Altogether, these results suggest for the first time a role of T6SS in CF-lung colonization by A. xylosoxidans and opens promising perspective to target this virulence determinant as innovative theranostic options for CF management.
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Affiliation(s)
- Mélanie Le Goff
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Marseille, France
| | - Manon Vastel
- Université de Limoges, INSERM, Centre Hospitalier Universitaire (CHU) Limoges, Unité Mixte de Recherche (UMR) 1092, Limoges, France
| | - Régine Lebrun
- Plateforme Protéomique de l’Institut de Microbiologie de la Méditerranée, Marseille Protéomique, Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS) FR 3479, Marseille, France
| | - Pascal Mansuelle
- Plateforme Protéomique de l’Institut de Microbiologie de la Méditerranée, Marseille Protéomique, Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS) FR 3479, Marseille, France
| | - Ava Diarra
- Université de Lille, Centre National de la Recherche Scientifique (CNRS), INSERM, Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017-CIIL-Centre d’Infection et d’Immunité de Lille, University of Lille, Lille, France
| | - Teddy Grandjean
- Université de Lille, Centre National de la Recherche Scientifique (CNRS), INSERM, Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017-CIIL-Centre d’Infection et d’Immunité de Lille, University of Lille, Lille, France
| | - Pauline Triponney
- Centre National de Référence de la Résistance aux Antibiotiques , Centre Hospitalier Universitaire de Besançon, Besançon, France
| | | | - Philippe Gosset
- Université de Lille, Centre National de la Recherche Scientifique (CNRS), INSERM, Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017-CIIL-Centre d’Infection et d’Immunité de Lille, University of Lille, Lille, France
| | - Rodrigue Dessein
- Université de Lille, Centre National de la Recherche Scientifique (CNRS), INSERM, Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017-CIIL-Centre d’Infection et d’Immunité de Lille, University of Lille, Lille, France
| | - Fabien Garnier
- Université de Limoges, INSERM, Centre Hospitalier Universitaire (CHU) Limoges, Unité Mixte de Recherche (UMR) 1092, Limoges, France
- *Correspondence: Eric Durand, ; ; Fabien Garnier,
| | - Eric Durand
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Marseille, France
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Unité Mixte de Recherche (UMR) 7255, INSERM, Marseille, France
- *Correspondence: Eric Durand, ; ; Fabien Garnier,
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Distribution of Achromobacter Species in 12 French Cystic Fibrosis Centers in 2020 by a Retrospective MALDI-TOF MS Spectrum Analysis. J Clin Microbiol 2022; 60:e0242221. [PMID: 35510500 DOI: 10.1128/jcm.02422-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Achromobacter 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.
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Rapid detection by MALDI-TOF MS of isolates from cystic fibrosis patients belonging to the epidemic clones Achromobacter xylosoxidans ST137 or Achromobacter ruhlandii DES. J Clin Microbiol 2021; 59:e0094621. [PMID: 34346714 DOI: 10.1128/jcm.00946-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Objective: Achromobacter 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 the multiresistant epidemic clones, especially A. xylosoxidans ST137 (AxST137) and the Danish Epidemic Strain A. ruhlandii (DES) are lacking. We recently developed and published a database for Achromobacter 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 Achromobacter species. Methods: All the spectra of A.xylosoxidans (n=1571) and A.ruhlandii (n=174) used to build the local database were analysed by ClinProTools™, MALDI Biotyper® PCA, MALDI Biotyper® dendrogram and flexAnalysis™ softwares for biomarker peaks detection. Two-hundred-two isolates (including 48 isolates of AxST137 and 7 of DES) were tested. Results: Specific biomarker peaks were identified: absent peak at m/z 6651 for AxST137 isolates and present peak at m/z 9438 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. Conclusions: The use of MALDI-TOF MS allowed identifying isolates of A. xylosoxidans belonging to the AxST137 clone which spread in France and Belgium (the Belgian epidemic clone) and of A. ruhlandii belonging to the DES clone. This tool will help implementation of segregation measures to avoid inter-patient transmission of these resistant clones.
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Sandri A, Haagensen JAJ, Veschetti L, Johansen HK, Molin S, Malerba G, Signoretto C, Boaretti M, Lleo MM. Adaptive Interactions of Achromobacter spp. with Pseudomonas aeruginosa in Cystic Fibrosis Chronic Lung Co-Infection. Pathogens 2021; 10:978. [PMID: 34451442 PMCID: PMC8400197 DOI: 10.3390/pathogens10080978] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/17/2021] [Accepted: 07/26/2021] [Indexed: 12/23/2022] Open
Abstract
In the lungs of patients with cystic fibrosis (CF), the main pathogen Pseudomonas aeruginosa is often co-isolated with other microbes, likely engaging in inter-species interactions. In the case of chronic co-infections, this cohabitation can last for a long time and evolve over time, potentially contributing to the clinical outcome. Interactions involving the emerging pathogens Achromobacter spp. have only rarely been studied, reporting inhibition of P. aeruginosa biofilm formation. To evaluate the possible evolution of such interplay, we assessed the ability of Achromobacter spp. isolates to affect the biofilm formation of co-isolated P. aeruginosa strains during long-term chronic co-infections. We observed both competition and cohabitation. An Achromobacter sp. isolate secreted exoproducts interfering with the adhesion ability of a co-isolated P. aeruginosa strain and affected its biofilm formation. Conversely, a clonal Achromobacter sp. strain later isolated from the same patient, as well as two longitudinal strains from another patient, did not show similar competitive behavior against its P. aeruginosa co-isolates. Genetic variants supporting the higher virulence of the competitive Achromobacter sp. isolate were found in its genome. Our results confirm that both inter-species competition and cohabitation are represented during chronic co-infections in CF airways, and evolution of these interplays can happen even at the late stages of chronic infection.
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Affiliation(s)
- Angela Sandri
- Department of Diagnostics and Public Health, Section of Microbiology, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy; (A.S.); (C.S.); (M.B.)
| | - Janus Anders Juul Haagensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; (J.A.J.H.); (S.M.)
| | - Laura Veschetti
- Laboratory of Computational Genomics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (G.M.)
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark;
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; (J.A.J.H.); (S.M.)
| | - Giovanni Malerba
- Laboratory of Computational Genomics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (G.M.)
| | - Caterina Signoretto
- Department of Diagnostics and Public Health, Section of Microbiology, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy; (A.S.); (C.S.); (M.B.)
| | - Marzia Boaretti
- Department of Diagnostics and Public Health, Section of Microbiology, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy; (A.S.); (C.S.); (M.B.)
| | - Maria M. Lleo
- Department of Diagnostics and Public Health, Section of Microbiology, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy; (A.S.); (C.S.); (M.B.)
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Veschetti L, Sandri A, Patuzzo C, Melotti P, Malerba G, Lleo MM. Genomic characterization of Achromobacter species isolates from chronic and occasional lung infection in cystic fibrosis patients. Microb Genom 2021; 7. [PMID: 34292148 PMCID: PMC8477391 DOI: 10.1099/mgen.0.000606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Achromobacter species are increasingly being detected in cystic fibrosis (CF) patients, where they can establish chronic infections by adapting to the lower airway environment. To better understand the mechanisms contributing to a successful colonization by Achromobacter species, we sequenced the whole genome of 54 isolates from 26 patients with occasional and early/late chronic lung infection. We performed a phylogenetic analysis and compared virulence and resistance genes, genetic variants and mutations, and hypermutability mechanisms between chronic and occasional isolates. We identified five Achromobacter species as well as two non-affiliated genogroups (NGs). Among them were the frequently isolated Achromobacter xylosoxidans and four other species whose clinical importance is not yet clear: Achromobacter insuavis, Achromobacter dolens, Achromobacter insolitus and Achromobacter aegrifaciens. While A. insuavis and A. dolens were isolated only from chronically infected patients and A. aegrifaciens only from occasionally infected patients, the other species were found in both groups. Most of the occasional isolates lacked functional genes involved in invasiveness, chemotaxis, type 3 secretion system and anaerobic growth, whereas the great majority (>60%) of chronic isolates had these genomic features. Interestingly, almost all (n=22/23) late chronic isolates lacked functional genes involved in lipopolysaccharide production. Regarding antibiotic resistance, we observed a species-specific distribution of blaOXA genes, confirming what has been reported in the literature and additionally identifying blaOXA-2 in some A. insolitus isolates and observing no blaOXA genes in A. aegrifaciens or NGs. No significant difference in resistance genes was found between chronic and occasional isolates. The results of the mutator genes analysis showed that no occasional isolate had hypermutator characteristics, while 60% of early chronic (<1 year from first colonization) and 78% of late chronic (>1 year from first colonization) isolates were classified as hypermutators. Although all A. dolens, A. insuavis and NG isolates presented two different mutS genes, these seem to have a complementary rather than compensatory function. In conclusion, our results show that Achromobacter species can exhibit different adaptive mechanisms and some of these mechanisms might be more useful than others in establishing a chronic infection in CF patients, highlighting their importance for the clinical setting and the need for further studies on the less clinically characterized Achromobacter species.
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Affiliation(s)
- Laura Veschetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Angela Sandri
- Department of Diagnostics and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy
| | - Cristina Patuzzo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Paola Melotti
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata Verona, 37126 Verona, Italy
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Maria M Lleo
- Department of Diagnostics and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy
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11
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Abstract
Cystic fibrosis patients frequently suffer from recurring respiratory infections caused by colonizing pathogenic and commensal bacteria. Although modern therapies can sometimes alleviate respiratory symptoms by ameliorating residual function of the protein responsible for the disorder, management of chronic respiratory infections remains an issue. In cystic fibrosis, dynamic and complex communities of microbial pathogens and commensals can colonize the lung. Cultured isolates from lung sputum reveal high inter- and intraindividual variability in pathogen strains, sequence variants, and phenotypes; disease progression likely depends on the precise combination of infecting lineages. Routine clinical protocols, however, provide a limited overview of the colonizer populations. Therefore, a more comprehensive and precise identification and characterization of infecting lineages could assist in making corresponding decisions on treatment. Here, we describe longitudinal tracking for four cystic fibrosis patients who exhibited extreme clinical phenotypes and, thus, were selected from a pilot cohort of 11 patients with repeated sampling for more than a year. Following metagenomics sequencing of lung sputum, we find that the taxonomic identity of individual colonizer lineages can be easily established. Crucially, even superficially clonal pathogens can be subdivided into multiple sublineages at the sequence level. By tracking individual allelic differences over time, an assembly-free clustering approach allows us to reconstruct multiple lineage-specific genomes with clear structural differences. Our study showcases a culture-independent shotgun metagenomics approach for longitudinal tracking of sublineage pathogen dynamics, opening up the possibility of using such methods to assist in monitoring disease progression through providing high-resolution routine characterization of the cystic fibrosis lung microbiome.
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12
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Longitudinal Surveillance and Combination Antimicrobial Susceptibility Testing of Multidrug-Resistant Achromobacter Species from Cystic Fibrosis Patients. Antimicrob Agents Chemother 2020; 64:AAC.01467-20. [PMID: 32816722 DOI: 10.1128/aac.01467-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 08/07/2020] [Indexed: 01/16/2023] Open
Abstract
Achromobacter spp. are recognized as emerging pathogens in patients with cystic fibrosis (CF). Though recent works have established species-level identification using nrdA sequencing, there is a dearth in knowledge relating to species-level antimicrobial susceptibility patterns and antimicrobial combinations, which hampers the use of optimal antimicrobial combinations for the treatment of chronic infections. The aims of this study were to (i) identify at species-level referred Achromobacter isolates, (ii) describe species-level antimicrobial susceptibility profiles, and (iii) determine the most promising antimicrobial combination for chronic Achromobacter infections. A total of 112 multidrug-resistant (MDR) Achromobacter species isolates from 39 patients were identified using nrdA sequencing. Antimicrobial susceptibility and combination testing were carried out using the Etest method. We detected six species of Achromobacter and found that Achromobacter xylosoxidans was the most prevalent species. Interestingly, sequence analysis showed it was responsible for persistent infection (18/28 patients), followed by Achromobacter ruhlandii (2/3 patients). Piperacillin-tazobactam (70.27%) and co-trimoxazole (69.72%) were the most active antimicrobials. Differences were observed in species-level susceptibility to ceftazidime, carbapenems, ticarcillin-clavulanate, and tetracycline. Antimicrobial combinations with co-trimoxazole or tobramycin demonstrate the best synergy, while co-trimoxazole gave the best susceptibility breakpoint index values. This study enriches the understanding of MDR Achromobacter spp. epidemiology and confirms prevalence and chronic colonization of A. xylosoxidans in CF lungs. It presents in vitro data to support the efficacy of new combinations for use in the treatment of chronic Achromobacter infections.
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13
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Pongchaikul P, Santanirand P, Antonyuk S, Winstanley C, Darby AC. AcGI1, a novel genomic island carrying antibiotic resistance integron In687 in multidrug resistant Achromobacter xylosoxidans in a teaching hospital in Thailand. FEMS Microbiol Lett 2020; 367:5863935. [PMID: 32592387 DOI: 10.1093/femsle/fnaa109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/25/2020] [Indexed: 12/21/2022] Open
Abstract
This study investigated the genetic basis of multidrug resistance in two strains of Achromobacter xylosoxidans isolated from patients attending a hospital in Thailand in 2012. These isolates were highly resistant to cephalosporins, aminoglycosides, fluoroquinolones, co-trimoxazole and carbapenems. Whole genome sequencing revealed that the two isolates were not clonally related and identified a carbapenem resistance gene-habouring integron (In687), residing in a novel genomic island, AcGI1. This In687 shares 100% identical nucleotide sequence with ones found in Acinetobacter baumannii Aci 16, isolated from the same hospital in 2007. We report the first analysis of multidrug-resistant A. xylosoxidans isolated in Thailand, and the first example of this island in A. xylosoxidans. Our data support the idea that resistance has spread in Thailand via horizontal gene transfer between species and suggest the possibility of A. xylosoxidans may serve as a reservoir of antibiotic resistance, especially in hospital setting.
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Affiliation(s)
- Pisut Pongchaikul
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bang Phli, Samut Prakan 10540, Thailand.,Institute of Infection and Global Health, University of Liverpool, Liverpool L69 3BE, UK
| | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
| | - Svetlana Antonyuk
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 3BE, UK
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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14
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Garrigos T, Neuwirth C, Chapuis A, Bador J, Amoureux L. Development of a database for the rapid and accurate routine identification of Achromobacter species by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Clin Microbiol Infect 2020; 27:126.e1-126.e5. [PMID: 32283265 DOI: 10.1016/j.cmi.2020.03.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 02/17/2020] [Accepted: 03/26/2020] [Indexed: 10/24/2022]
Abstract
OBJECTIVES Achromobacter spp. are emerging pathogens in respiratory samples from cystic fibrosis patients. The current reference methods (nrdA-sequencing or multilocus sequence typing) can identify 18 species which are often misidentified by conventional techniques as A. xylosoxidans. A few studies have suggested that matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) provides accurate identification of the genus but not of species. The aims of this study were (a) to generate a database for MALDI-TOF/MS Bruker including the 18 species, (b) to evaluate the suitability of the database for routine laboratory identification, and (c) to compare its performance with that of the currently available Bruker default database. METHODS A total of 205 isolates belonging to the 18 species identified by nrdA sequencing were used to build a local database. Main spectra profiles (MSPs) were created according to Bruker's recommendations for each isolate with the Biotyper software. Performance of the default Bruker database and ours for routine use were compared by testing 167 strains (including 38 isolates used from MSP creation) belonging to the 18 species identified by nrdA sequencing directly from colonies cultivated on various media. RESULTS Our new database accurately identified 99.4% (166/167) of the isolates from the 18 species (score ≥2.0) versus only 50.9% (85/167) with the Bruker database. In the Bruker database 17.3% of the isolates (29/167) were incorrectly identified as another species despite a score of ≥2.0. CONCLUSIONS The use of MALDI-TOF/MS in combination with a database developed with samples from 18 Achromobacter species provides rapid and accurate identification. This tool could be used to help future clinical studies.
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Affiliation(s)
- T Garrigos
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France
| | - C Neuwirth
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France; UMR/CNRS 6249 Chrono-environnement, University of Bourgogne- Franche-Comté, Besançon, France
| | - A Chapuis
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France
| | - J Bador
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France; UMR/CNRS 6249 Chrono-environnement, University of Bourgogne- Franche-Comté, Besançon, France
| | - L Amoureux
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France; UMR/CNRS 6249 Chrono-environnement, University of Bourgogne- Franche-Comté, Besançon, France.
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15
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Papalia M, Figueroa-Espinosa R, Steffanowski C, Barberis C, Almuzara M, Barrios R, Vay C, Gutkind G, Di Conza J, Radice M. Expansion and improvement of MALDI-TOF MS databases for accurate identification of Achromobacter species. J Microbiol Methods 2020; 172:105889. [PMID: 32171844 DOI: 10.1016/j.mimet.2020.105889] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
Abstract
Different MALDI-TOF MS databases were evaluated for the identification of Achromobacter species. The in-house and extended database generated in this study rendered more accurate identification (58/64 and 57/64 isolates, respectively) in comparison with the Bruker commercial database (42/64 isolates), especially in those infrequent species that are not available or poorly represented.
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Affiliation(s)
- Mariana Papalia
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Roque Figueroa-Espinosa
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina
| | - Carla Steffanowski
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina
| | - Claudia Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Laboratorio de Bacteriología Clínica, Av. Córdoba 2351, 1er. piso, Ciudad Autónoma de Buenos Aires CP1113, Argentina
| | - Marisa Almuzara
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Laboratorio de Bacteriología Clínica, Av. Córdoba 2351, 1er. piso, Ciudad Autónoma de Buenos Aires CP1113, Argentina
| | | | - Carlos Vay
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Laboratorio de Bacteriología Clínica, Av. Córdoba 2351, 1er. piso, Ciudad Autónoma de Buenos Aires CP1113, Argentina
| | - Gabriel Gutkind
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - José Di Conza
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Marcela Radice
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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16
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Papalia M, Steffanowski C, Traglia G, Almuzara M, Martina P, Galanternik L, Vay C, Gutkind G, Ramírez MS, Radice M. Diversity of Achromobacter species recovered from patients with cystic fibrosis, in Argentina. Rev Argent Microbiol 2019; 52:13-18. [PMID: 31253503 DOI: 10.1016/j.ram.2019.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/06/2019] [Accepted: 03/18/2019] [Indexed: 11/16/2022] Open
Abstract
Different phenotype-based techniques and molecular tools were used to describe the distribution of different Achromobacter species in patients with cystic fibrosis (CF) in Argentina, and to evaluate their antibiotic resistance profile. Phenotypic identification was performed by conventional biochemical tests, commercial galleries and MALDI-TOF MS. Genetic approaches included the detection of A. xylosoxidans specific marker blaoxa-114, the amplification and sequencing of the 16S rRNA gene, nrdA and blaOXA complete sequence, and MLST analysis. Phenotypic approaches, even MALDI-TOF, rendered inconclusive or misleading results. On the contrary, concordant results were achieved with the nrdA sequencing or sequence type (ST) analysis, and the complete blaOXA sequencing, allowing a reliable discrimination of different Achromobacter species. A. xylosoxidans accounted for 63% of Achromobacter infections and A. ruhlandii accounted for 17%. The remaining species corresponded to A. insuavis, A. dolens, A. marplatensis and A. pulmonis. Antimicrobial susceptibilities were determined by the agar dilution method according to CLSI guidelines. Piperacillin, piperacillin/tazobactam and carbapenems were the most active antibiotics. However, the emergence of carbapenem-resistant isolates was detected. In conclusion, prompt and accurate identification tools were necessary to determine that different Achromobacter species may colonize/infect the airways of patients with CF. Moreover, antimicrobial therapy should be administered based on the susceptibility profile of individual Achromobacter sp. isolates.
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Affiliation(s)
- Mariana Papalia
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Microbiología, Laboratorio de Resistencia Bacteriana, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Carla Steffanowski
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Microbiología, Laboratorio de Resistencia Bacteriana, Ciudad Autónoma de Buenos Aires, Argentina
| | - Germán Traglia
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Laboratorio de Bacteriología Clínica, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Marisa Almuzara
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Laboratorio de Bacteriología Clínica, Ciudad Autónoma de Buenos Aires, Argentina
| | - Pablo Martina
- Universidad Nacional De Misiones, Instituto de Biología Subtropical, Misiones, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Laura Galanternik
- Hospital de Niños Ricardo Gutiérrez, Ciudad Autónoma de Buenos Aires, Argentina
| | - Carlos Vay
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Laboratorio de Bacteriología Clínica, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gabriel Gutkind
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Microbiología, Laboratorio de Resistencia Bacteriana, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - María Soledad Ramírez
- California State University, Fullerton, Department of Biological Science, Fullerton, United States; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Marcela Radice
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Microbiología, Laboratorio de Resistencia Bacteriana, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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17
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Amoureux L, Sauge J, Sarret B, Lhoumeau M, Bajard A, Tetu J, Bador J, Neuwirth C. Study of 109 Achromobacter spp. isolates from 9 French CF centres reveals the circulation of a multiresistant clone of A. xylosoxidans belonging to ST 137. J Cyst Fibros 2019; 18:804-807. [PMID: 31104975 DOI: 10.1016/j.jcf.2019.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/12/2019] [Accepted: 04/04/2019] [Indexed: 12/21/2022]
Abstract
We previously reported the distribution of Achromobacter spp. (species and Sequence Types (ST)) in our French Cystic Fibrosis (CF) centre. In the present study we collected 109 Achromobacter isolates (1/patient) from 9 other French CF Centres for species identification, antimicrobial susceptibility testings and Multilocus-Sequence-Typing (MLST) analysis. Ten species were detected, A. xylosoxidans being the most predominant one (73.4% of the isolates). Piperacillin-tazobactam, ceftazidime, imipenem, meropenem and ciprofloxacin were respectively active against 88, 70, 79, 72 and 23% of the isolates. Among the 79 A. xylosoxidans isolates, 46 STs were detected. Interestingly, ST 137, recovered in 4 centres (5 patients), was previously detected in our centre (2 patients). The strains from the 7 patients belonged to the same pulsotype (pulsed-field-gel-electrophoresis analysis) and harboured acquired resistance to meropenem, ceftazidime, ciprofloxacin, and except for 2 isolates, to imipenem and piperacillin-tazobactam. This is the first description in France of a circulating multiresistant A. xylosoxidans strain.
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Affiliation(s)
- Lucie Amoureux
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France; UMR/CNRS 6249 Chrono-environnement, University of Franche-Comté, Besançon, France.
| | - Juliette Sauge
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France
| | - Benoit Sarret
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France
| | - Matthieu Lhoumeau
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France
| | - Audrey Bajard
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France
| | - Jennifer Tetu
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France
| | - Julien Bador
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France; UMR/CNRS 6249 Chrono-environnement, University of Franche-Comté, Besançon, France
| | - Catherine Neuwirth
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France; UMR/CNRS 6249 Chrono-environnement, University of Franche-Comté, Besançon, France
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18
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Chronic Airway Colonization by Achromobacter xylosoxidans in Cystic Fibrosis Patients Is Not Sustained by Their Domestic Environment. Appl Environ Microbiol 2018; 84:AEM.01739-18. [PMID: 30217850 DOI: 10.1128/aem.01739-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022] Open
Abstract
Achromobacter spp. are nonfermentative Gram-negative bacilli considered emergent pathogens in cystic fibrosis (CF). Although some cross-transmission events between CF patients have been described, Achromobacter strains were mostly patient specific, suggesting sporadic acquisitions from nonhuman reservoirs. However, sources of these emergent CF pathogens remain unknown. A large collection of specimens (n = 273) was sampled in the homes of 3 CF patients chronically colonized by Achromobacter xylosoxidans with the aim of evaluating the potential role of domestic reservoirs in sustaining airway colonization of the patients. Samples were screened for the presence of Achromobacter by using genus-specific molecular detection. Species identification, multilocus genotypes, and antimicrobial susceptibility patterns observed for environmental isolates were compared with those of clinical strains. Patient homes hosted a high diversity of Achromobacter species (n = 7), including Achromobacter mucicolens and A. animicus, two species previously isolated from human samples only, and genotypes (n = 15), all showing an overall susceptibility to antimicrobial agents. Achromobacter strains were mostly isolated from indoor moist environments and siphons, which are potential reservoirs for several CF emerging pathogens. A. xylosoxidans, the worldwide prevalent species colonizing CF patients, was not the major Achromobacter species inhabiting domestic environments. A. xylosoxidans genotypes chronically colonizing the patients were not detected in their household environments. These results support the notions that the domestic environment could not be incriminated in sustained patient colonization and that after initial colonization, the environmental survival of A. xylosoxidans clones adapted to the CF airways is probably impaired.IMPORTANCE Achromobacter spp. are worldwide emerging opportunistic pathogens in CF patients, able to chronically colonize the respiratory tract. Apart from regular consultations at the hospital CF center, patients spend most of their time at home. Colonization from nonhuman sources has been suggested, but the presence of Achromobacter spp. in CF patients' homes has not been explored. The domestic environments of CF patients chronically colonized by Achromobacter, especially wet environments, host several opportunistic pathogens, including a large diversity of Achromobacter species and genotypes. However, Achromobacter genotypes colonizing the patients were not detected in their domestic environments, making it unlikely that a shuttle between environment and CF airways is involved in persisting colonization. This also suggests that once the bacteria have adapted to the respiratory tract, their survival in the domestic environment is presumably impaired. Nevertheless, measures for reducing domestic patient exposure should be targeted on evacuation drains, which are frequently contaminated by CF opportunistic pathogens.
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Recio R, Brañas P, Martínez MT, Chaves F, Orellana MA. Effect of respiratory Achromobacter spp. infection on pulmonary function in patients with cystic fibrosis. J Med Microbiol 2018; 67:952-956. [DOI: 10.1099/jmm.0.000763] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- R. Recio
- Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - P. Brañas
- Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - M. T. Martínez
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Cystic Fibrosis Unit, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - F. Chaves
- Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - M. A. Orellana
- Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
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20
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Clinical Outcomes Associated with Achromobacter Species Infection in Patients with Cystic Fibrosis. Ann Am Thorac Soc 2018; 14:1412-1418. [PMID: 28406714 DOI: 10.1513/annalsats.201701-071oc] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RATIONALE Achromobacter species are increasingly identified in individuals with cystic fibrosis (CF), but the clinical outcomes in these patients remain poorly understood. OBJECTIVES We aimed to determine the association of Achromobacter infection on clinical outcomes in pediatric and adult patients with CF. METHODS A cohort study of pediatric and adult patients with CF was conducted from 1997 to 2014 in Toronto, Ontario, Canada. Achromobacter spp. infection was categorized as no history of infection, intermittent infection, and chronic infection (two or more positive cultures in the preceding 12 months). Cox models were used to estimate risk of death or transplantation. Mixed-effects models were used to assess odds of pulmonary exacerbations and effect on lung function (FEV1%) by Achromobacter spp. RESULTS A total of 1,103 patients were followed-up over the course of 18 years; 88 patients (7.3%) had one or more culture for Achromobacter species. Chronic Achromobacter infection was associated with a greater risk of death or transplantation compared with in patients with no history of infection (adjusted hazard ratio, 2.03; 95% confidence interval, 1.05-3.95; P = 0.036). Pulmonary exacerbations were more common in patients with chronic infection, but after adjusting for confounding factors, the effect was no longer significant. The chronic group had lower FEV1%, but it did not worsen after developing chronic infection. CONCLUSIONS Patients with CF and chronic Achromobacter infection are at increased risk of death or transplantation.
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Gade SS, Nørskov-Lauritsen N, Ridderberg W. Prevalence and species distribution of Achromobacter sp. cultured from cystic fibrosis patients attending the Aarhus centre in Denmark. J Med Microbiol 2017; 66:686-689. [DOI: 10.1099/jmm.0.000499] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Moremi N, Claus H, Hingi M, Vogel U, Mshana SE. Multidrug-resistant Achromobacter animicus causing wound infection in a street child in Mwanza, Tanzania. Diagn Microbiol Infect Dis 2017; 88:58-61. [DOI: 10.1016/j.diagmicrobio.2017.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/03/2017] [Accepted: 02/04/2017] [Indexed: 01/24/2023]
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Prevalence and Outcomes of Achromobacter Species Infections in Adults with Cystic Fibrosis: a North American Cohort Study. J Clin Microbiol 2017; 55:2074-2085. [PMID: 28446570 DOI: 10.1128/jcm.02556-16] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/20/2017] [Indexed: 02/07/2023] Open
Abstract
Achromobacter species are increasingly being detected in cystic fibrosis (CF) patients, with an unclear epidemiology and impact. We studied a cohort of patients attending a Canadian adult CF clinic who had positive sputum cultures for Achromobacter species in the period from 1984 to 2013. Infection was categorized as transient or persistent (≥50% positive cultures for 1 year). Those with persistent infection were matched 2:1 with age-, sex-, and time-matched controls without a history of Achromobacter infection, and mixed-effects models were used to assess pulmonary exacerbation (PEx) frequency and lung function decline. Isolates from a biobank were retrospectively assessed, identified to the species level by nrdA sequencing, and genotyped using pulsed-field gel electrophoresis (PFGE). Thirty-four patients (11% of those in our clinic), with a median age of 24 years (interquartile range [IQR], 20.3 to 29.8 years), developed Achromobacter infection. Ten patients (29%) developed persistent infection. Persistence did not denote permanence, as most patients ultimately cleared infection, often after years. Patients were more likely to experience PEx at incident isolation than at prior or subsequent visits (odds ratio [OR], 2.7 [95% confidence interval {CI}, 1.2 to 6.7]; P = 0.03). Following persistent infection, there was no difference in annual lung function decline (-1.08% [95% CI, -2.73 to 0.57%] versus -2.74% [95% CI, -4.02 to 1.46%]; P = 0.12) or the odds of PEx (OR, 1.21 [95% CI, 0.45 to 3.28]; P = 0.70). Differential virulence among Achromobacter species was not observed, and no cases of transmission occurred. We demonstrated that incident Achromobacter infection was associated with a greater risk of PEx; however, neither transient nor chronic infection was associated with a worsened long-term prognosis. Large, multicenter studies are needed to clarify the clinical impact, natural history, and transmissibility of Achromobacter.
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Achromobacter xylosoxidans is the predominant Achromobacter species isolated from diverse non-respiratory samples. Epidemiol Infect 2016; 144:3527-3530. [PMID: 27535588 DOI: 10.1017/s0950268816001564] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Achromobacter spp. are emerging opportunistic Gram-negative rods responsible for diverse nosocomial or community-acquired infections. We describe, for the first time, the distribution of Achromobacter spp., defined by nrdA gene sequencing, and their antimicrobial susceptibility in a variety of non-respiratory samples recovered from hospitalized patients from 2010 to 2015. Of the 63 isolates studied, A. xylosoxidans was the most prevalent (41 isolates), and with the exception of A. insuavis (four isolates), the remaining 10 species identified were represented by one or two isolates only. All isolates were uniformly susceptible to piperacillin and piperacillin-tazobactam and 97% to meropenem, but 76% showed resistance to ciprofloxacin. This study confirms the diversity of Achromobacter spp. in non-cystic fibrosis (CF) isolates and the predominance of A. xylosoxidans, as previously reported for CF sputum isolates. There was no apparent link between the clinical site of infection and the species of Achromobacter.
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Cools P, Ho E, Vranckx K, Schelstraete P, Wurth B, Franckx H, Ieven G, Van Simaey L, Van Daele S, Verhulst S, De Baets F, Vaneechoutte M. Epidemic Achromobacter xylosoxidans strain among Belgian cystic fibrosis patients and review of literature. BMC Microbiol 2016; 16:122. [PMID: 27342812 PMCID: PMC4919866 DOI: 10.1186/s12866-016-0736-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 06/08/2016] [Indexed: 12/11/2022] Open
Abstract
Background Achromobacter xylosoxidans is increasingly being recognized as an emerging pathogen in cystic fibrosis. Recent severe infections with A. xylosoxidans in some of our cystic fibrosis (CF) patients led to a re-evaluation of the epidemiology of CF-associated A. xylosoxidans infections in two Belgian reference centres (Antwerp and Ghent). Several of these patients also stayed at the Rehabilitation Centre De Haan (RHC). In total, 59 A. xylosoxidans isolates from 31 patients (including 26 CF patients), collected between 2001 and 2014, were studied. We evaluated Matrix Assisted Laser Desorption Ionisation -Time of Flight mass spectrometry (MALDI-TOF) as an alternative for McRAPD typing. Results Both typing approaches established the presence of a major cluster, comprising isolates, all from 21 CF patients, including from two patients sampled when staying at the RHC a decade ago. This major cluster was the same as the cluster established already a decade ago at the RHC. A minor cluster consisted of 13 isolates from miscellaneous origin. A further seven isolates, including one from a non-CF patient who had stayed recently at the RHC, were singletons. Conclusions Typing results of both methods were similar, indicating transmission of a single clone of A. xylosoxidans among several CF patients from at least two reference centres. Isolates of the same clone were already observed at the RHC, a decade ago. It is difficult to establish to what extent the RHC is the source of transmission, because the epidemic strain was already present when the first epidemiological study in the RHC was carried out. This study also documents the applicability of MALDI-TOF for typing of strains within the species A. xylosoxidans and the need to use the dynamic cutoff algorithm of the BioNumerics® software for correct clustering of the fingerprints. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0736-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Piet Cools
- Laboratory Bacteriology Research (LBR), Department of Microbiology, Immunology, and Clinical Chemistry, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Erwin Ho
- Cystic Fibrosis Centre, Antwerp University Hospital (AUH), Antwerp, Belgium
| | | | | | - Bettina Wurth
- Zeepreventorium (Rehabilitation Centre, RHC), De Haan, Belgium
| | - Hilde Franckx
- Zeepreventorium (Rehabilitation Centre, RHC), De Haan, Belgium
| | - Greet Ieven
- Department of Microbiology, Antwerp University Hospital, Antwerp, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research (LBR), Department of Microbiology, Immunology, and Clinical Chemistry, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Sabine Van Daele
- Cystic Fibrosis Centre, Ghent University Hospital (GUH), Ghent, Belgium
| | - Stijn Verhulst
- Cystic Fibrosis Centre, Antwerp University Hospital (AUH), Antwerp, Belgium
| | - Frans De Baets
- Cystic Fibrosis Centre, Ghent University Hospital (GUH), Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research (LBR), Department of Microbiology, Immunology, and Clinical Chemistry, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.
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Firmida MC, Pereira RHV, Silva EASR, Marques EA, Lopes AJ. Clinical impact of Achromobacter xylosoxidans colonization/infection in patients with cystic fibrosis. Braz J Med Biol Res 2016; 49:e5097. [PMID: 26909788 PMCID: PMC4792508 DOI: 10.1590/1414-431x20155097] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/17/2015] [Indexed: 12/20/2022] Open
Abstract
The rate of diagnosis of colonization/infection of the airways with
Achromobacter xylosoxidans has increased in cystic fibrosis
patients, but its clinical significance is still controversial. This retrospective,
case-control study aimed to evaluate the clinical impact of A.
xylosoxidans colonization/infection in cystic fibrosis patients.
Individuals who were chronically colonized/infected (n=10), intermittently
colonized/infected (n=15), and never colonized/infected with A.
xylosoxidans (n=18) were retrospectively evaluated during two
periods that were 2 years apart. Demographic characteristics, clinical data, lung
function, and chronic bacterial co-colonization data were evaluated. Of the total
study population, 87% were pediatric patients and 65.1% were female. Individuals
chronically colonized/infected with A. xylosoxidans had decreased
forced expiratory volume in 1 s (51.7% in the chronic colonization/infection group
vs 82.7% in the intermittent colonization/infection group
vs 76% in the never colonized/infected group). Compared with the
other two groups, the rate of co-colonization with methicillin-resistant
Staphylococcus aureus was higher in individuals chronically
colonized/infected with A. xylosoxidans (P=0.002).
Changes in lung function over 2 years in the three groups were not significant,
although a trend toward a greater decrease in lung function was observed in the
chronically colonized/infected group. Compared with the other two groups, there was a
greater number of annual hospitalizations in patients chronically colonized/infected
with A. xylosoxidans (P=0.033). In cystic fibrosis patients, there
was an increased frequency of A. xylosoxidans colonization/infection
in children, and lung function was reduced in patients who were chronically
colonized/infected with A. xylosoxidans. Additionally, there were no
differences in clinical outcomes during the 2-year period, except for an increased
number of hospitalizations in patients with A. xylosoxidans.
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Affiliation(s)
- M C Firmida
- Programa de Pós-Graduação em Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - R H V Pereira
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - E A S R Silva
- Laboratório de Bacteriologia, Hospital Universitário Pedro Ernesto, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - E A Marques
- Programa de Pós-Graduação em Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - A J Lopes
- Programa de Pós-Graduação em Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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Amoureux L, Bador J, Bounoua Zouak F, Chapuis A, de Curraize C, Neuwirth C. Distribution of the species of Achromobacter in a French Cystic Fibrosis Centre and multilocus sequence typing analysis reveal the predominance of A. xylosoxidans and clonal relationships between some clinical and environmental isolates. J Cyst Fibros 2016; 15:486-94. [PMID: 26778615 DOI: 10.1016/j.jcf.2015.12.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/01/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Achromobacter spp. are emerging pathogens in Cystic Fibrosis (CF) patients. Recent studies proposed Multilocus Sequence Typing (MLST) scheme and a species-level identification method by nrdA sequencing for this genus. Epidemiological data are needed to assess the species and/or the sequence types (STs) involved and their potential role in CF patients lung function degradation. The aims of this study were i) to describe the distribution of the different species of Achromobacter in our CF centre ii) to detect potential STs more involved in chronic colonisations iii) to detect a potential local or worldwide predominance of some STs among clinical and environmental isolates. METHODS All the isolates (477) collected in our CF centre from 2007 to 2014 among the 177 patients attending the centre were identified using nrdA sequencing. MLST analysis was performed for 37 clinical and 14 environmental isolates. RESULTS A total of 47 out of 177 patients presented positive culture(s) with Achromobacter spp., representing 12.7% of the patients of the centre each year. Eleven species were detected, A. xylosoxidans being the most prevalent species (27 patients). Only A. xylosoxidans (>80%) and A. insuavis were involved in chronic colonisation (6.7%). MLST analysis revealed a wide diversity among the isolates (36 STs for 51 isolates). Nevertheless, one third of the isolates belonged to STs previously detected in clinical isolates from other countries. CONCLUSIONS This study is a first approach in understanding the global epidemiology of Achromobacter species in CF. These results confirm the high prevalence of the species A. xylosoxidans among CF patients, reveal the worldwide distribution of some STs and point out the potential role of environmental sources of contamination. More studies are needed to search for relationships between species and/or ST and pathogenicity.
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Affiliation(s)
- Lucie Amoureux
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France.
| | - Julien Bador
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France
| | - Fatma Bounoua Zouak
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France
| | - Angélique Chapuis
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France
| | - Claire de Curraize
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France
| | - Catherine Neuwirth
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France
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Bador J, Neuwirth C, Liszczynski P, Mézier MC, Chrétiennot M, Grenot E, Chapuis A, de Curraize C, Amoureux L. Distribution of innate efflux-mediated aminoglycoside resistance among different Achromobacter species. New Microbes New Infect 2015; 10:1-5. [PMID: 26904200 PMCID: PMC4726742 DOI: 10.1016/j.nmni.2015.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/27/2015] [Accepted: 11/27/2015] [Indexed: 11/21/2022] Open
Abstract
Achromobacter spp. are emerging respiratory pathogens in cystic fibrosis patients. Since 2013 the genus Achromobacter includes 15 species for which innate antibiotic resistance is unknown. Previously the AxyXY-OprZ efflux system has been described to confer aminoglycoside (AG) resistance in A. xylosoxidans. Nevertheless, some Achromobacter spp. strains are susceptible to AG. This study including 49 Achromobacter isolates reveals that AG resistance is correlated with different Achromobacter spp. It is noteworthy that the axyXY-oprZ operon is detected only in AG-resistant species, including the most frequently encountered in cystic fibrosis patients: A. xylosoxidans, A. ruhlandii, A. dolens and A. insuavis.
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Affiliation(s)
| | - C. Neuwirth
- Corresponding author: C. Neuwirth, Laboratoire de Bactériologie, Hôpital Universitaire, Plateau technique de Biologie, BP 37013, 21070 Dijon, Cedex, France
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Abstract
Achromobacteria are ubiquitous environmental organisms that may also become opportunistic pathogens in certain conditions, such as cystic fibrosis, hematologic and solid organ malignancies, renal failure, and certain immune deficiencies. Some members of this genus, such as xylosoxidans, cause primarily nosocomially acquired infections affecting multiple organ systems, including the respiratory tract, urinary tract, and, less commonly, the cardiovascular and central nervous systems. Despite an increasing number of published case reports and literature reviews suggesting a global increase in achromobacterial disease, most clinicians remain uncertain of the organism's significance when clinically isolated. Moreover, effective treatment can be challenging due to the organism's inherent and acquired multidrug resistance patterns. We reviewed all published cases to date of non-cystic fibrosis achromobacterial lung infections to better understand the organism's pathogenic potential and drug susceptibilities. We found that the majority of these cases were community acquired, typically presenting as pneumonias (88%), and were most frequent in individuals with hematologic and solid organ malignancies. Our findings also suggest that achromobacterial lung infections are difficult to treat, but respond well to extended-spectrum penicillins and cephalosporins, such as ticarcillin, piperacillin, and cefoperazone.
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Coward A, Kenna DTD, Perry C, Martin K, Doumith M, Turton JF. Use of nrdA gene sequence clustering to estimate the prevalence of different Achromobacter species among Cystic Fibrosis patients in the UK. J Cyst Fibros 2015; 15:479-85. [PMID: 26412052 DOI: 10.1016/j.jcf.2015.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/03/2015] [Accepted: 09/09/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND We aimed to estimate the prevalence of different Achromobacter species among UK Cystic Fibrosis (CF) patients. METHODS nrdA sequence clustering was used to identify 147 Achromobacter isolates from 96 patients from 27 hospitals to species level. Potential cross-infection was investigated by MLST, pulsed-field gel electrophoresis and whole genome sequencing (WGS). RESULTS Achromobacter xylosoxidans was the most prevalent species affecting 59 of 96 (61%) patients, followed by Achromobacter insuavis and Achromobacter dolens (12.4% and 8%, respectively). Three novel nrdA clusters were identified. One was further characterised by sequencing the intrinsic blaOXA gene, revealing novel variants. WGS of A. insuavis 2a isolates from four patients attending the same paediatric unit revealed that three were ST144, but differed from one another by a minimum of 385 SNPs, suggesting cross-infection was unlikely. CONCLUSIONS nrdA sequence clustering permitted an estimation of UK Achromobacter species prevalence, highlighted additional novel species, and aided cross-infection investigations.
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Affiliation(s)
- Amy Coward
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom
| | - Dervla T D Kenna
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom.
| | - Claire Perry
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom
| | - Kate Martin
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom
| | - Michel Doumith
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; Bioinformatics Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom
| | - Jane F Turton
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom
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Llorca Otero L, Girón Moreno R, Buendía Moreno B, Valenzuela C, Guiu Martínez A, Alarcón Cavero T. Achromobacter xylosoxidans infection in an adult cystic fibrosis unit in Madrid. Enferm Infecc Microbiol Clin 2015; 34:184-7. [PMID: 26139304 DOI: 10.1016/j.eimc.2015.05.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 04/07/2015] [Accepted: 05/18/2015] [Indexed: 11/30/2022]
Abstract
BACKGROUND Achromobacter xylosoxidans is an emerging pathogen in cystic fibrosis (CF). Although the rate of colonization by this microorganism is variable, prevalence is increasing in CF units. METHODS A microbiological/clinical study was conducted on of adult CF patients harboring A. xylosoxidans. Identification and susceptibility testing were performed using MicroScan (Siemens). Decline in lung function was assessed using the variable, annual percentage loss of FEV1 (forced expiratory volume in 1s). RESULTS A. xylosoxidans was isolated in 18 (19.8%) of 91 patients over a 14-year period. Mean age was 26.6 years (18-39 years). Nine patients (9.8%) were chronically colonized. Piperacillin/tazobactam and imipenem were the most active antibiotics. Mean annual decline in lung function in chronically colonized patients was 2.49%. CONCLUSIONS A. xylosoxidans is a major pathogen in CF. A decreased lung function was observed among patients who were chronically colonized by A. xylosoxidans. Antibiotic therapy should be started early in order to prevent chronic colonization by this microorganism.
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Affiliation(s)
- Laura Llorca Otero
- Department of Microbiology, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, Diego de León, 62, Madrid, Spain.
| | - Rosa Girón Moreno
- Department of Pulmonology, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, Diego de León, 62, Madrid, Spain
| | - Buenaventura Buendía Moreno
- Department of Microbiology, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, Diego de León, 62, Madrid, Spain
| | - Claudia Valenzuela
- Department of Pulmonology, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, Diego de León, 62, Madrid, Spain
| | - Alba Guiu Martínez
- Department of Microbiology, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, Diego de León, 62, Madrid, Spain
| | - Teresa Alarcón Cavero
- Department of Microbiology, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, Diego de León, 62, Madrid, Spain
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Dupont C, Michon AL, Jumas-Bilak E, Nørskov-Lauritsen N, Chiron R, Marchandin H. Intrapatient diversity of Achromobacter spp. involved in chronic colonization of Cystic Fibrosis airways. INFECTION GENETICS AND EVOLUTION 2015; 32:214-23. [PMID: 25791931 DOI: 10.1016/j.meegid.2015.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/27/2015] [Accepted: 03/09/2015] [Indexed: 11/28/2022]
Abstract
Achromobacter spp. are increasingly identified in Cystic Fibrosis (CF) patients and their ability to persistently colonize the CF respiratory tract (CFRT) suggests that Achromobacter species possess adaptive characteristics. We studied genome dynamics in 118 isolates recovered from 13 patients with Achromobacter chronic colonization (5-26 isolates per patient recovered over 13-61 months). Isolates were identified to species level by nrdA gene sequencing, subjected to Pulsed-Field Gel Electrophoresis (PFGE) and multiplex rep-PCR (MR-PCR), and rrs intragenomic diversity was studied by PCR-Temporal Temperature Gel Electrophoresis (TTGE). Intrapatient diversity was assessed: (i) from dynamics of XbaI and/or SpeI-based pulsotypes, (ii) from comparison of MR-PCR profiles, and (iii) by longitudinal analysis of rrs intragenomic diversity. Patients were chronically colonized by Achromobacter xylosoxidans (n=10), Achromobacter dolens (n=1) or Achromobacter insuavis (n=2). All strains displayed genomic diversification over time but A. insuavis showed higher pulsotype diversity compared to other species. Intragenomic rrs heterogeneity was found in strains from 6 of 13 patients and may be persistently observed. Achromobacter genome evolution observed during chronic colonization of the CFRT warrants further investigation of the adaptation features of the different species, as well as of the selective forces driving this adaptation in the CFRT.
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Affiliation(s)
- Chloé Dupont
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Anne-Laure Michon
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France; Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Estelle Jumas-Bilak
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France; Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Saint-Eloi, Laboratoire d'Hygiène hospitalière, 80 avenue Augustin Fliche, 34295 Montpellier Cedex 5, France
| | - Niels Nørskov-Lauritsen
- Department of Clinical Microbiology, Aarhus University Hospital, Skejby, 8200 Aarhus, Denmark
| | - Raphaël Chiron
- Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Centre de Ressources et de Compétences de la Mucoviscidose, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Hélène Marchandin
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France; Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.
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Gomila M, Prince-Manzano C, Svensson-Stadler L, Busquets A, Erhard M, Martínez DL, Lalucat J, Moore ERB. Genotypic and phenotypic applications for the differentiation and species-level identification of achromobacter for clinical diagnoses. PLoS One 2014; 9:e114356. [PMID: 25474264 PMCID: PMC4256396 DOI: 10.1371/journal.pone.0114356] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 11/10/2014] [Indexed: 11/18/2022] Open
Abstract
The Achromobacter is a genus in the family Alcaligenaceae, comprising fifteen species isolated from different sources, including clinical samples. The ability to detect and correctly identify Achromobacter species, particularly A. xylosoxidans, and differentiate them from other phenotypically similar and genotypically related Gram-negative, aerobic, non-fermenting species is important for patients with cystic fibrosis (CF), as well as for nosocomial and other opportunistic infections. Traditional phenotypic profile-based analyses have been demonstrated to be inadequate for reliable identifications of isolates of Achromobacter species and genotypic-based assays, relying upon comparative 16S rRNA gene sequence analyses are not able to insure definitive identifications of Achromobacter species, due to the inherently conserved nature of the gene. The uses of alternative methodologies to enable high-resolution differentiation between the species in the genus are needed. A comparative multi-locus sequence analysis (MLSA) of four selected ‘house-keeping’ genes (atpD, gyrB, recA, and rpoB) assessed the individual gene sequences for their potential in developing a reliable, rapid and cost-effective diagnostic protocol for Achromobacter species identifications. The analysis of the type strains of the species of the genus and 46 strains of Achromobacter species showed congruence between the cluster analyses derived from the individual genes. The MLSA gene sequences exhibited different levels of resolution in delineating the validly published Achromobacter species and elucidated strains that represent new genotypes and probable new species of the genus. Our results also suggested that the recently described A. spritinus is a later heterotypic synonym of A. marplatensis. Strains were analyzed, using whole-cell Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF MS), as an alternative phenotypic profile-based method with the potential to support the identifications determined by the genotypic DNA sequence-based MLSA. The MALDI-TOF MS data showed good accordance in strain groupings and identifications by the MLSA data.
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Affiliation(s)
- Margarita Gomila
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Islas Baleares, Spain
- * E-mail:
| | - Claudia Prince-Manzano
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Islas Baleares, Spain
| | - Liselott Svensson-Stadler
- Department of Infectious Diseases, Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Antonio Busquets
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Islas Baleares, Spain
| | | | - Deny L. Martínez
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Islas Baleares, Spain
| | - Jorge Lalucat
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Islas Baleares, Spain
- Mediterranean Institute for Advanced Studies (IMEDEA) (CSIC-UIB), Palma de Mallorca, Islas Baleares, Spain
| | - Edward R. B. Moore
- Department of Infectious Diseases, Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
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Detection of Achromobacter xylosoxidans in hospital, domestic, and outdoor environmental samples and comparison with human clinical isolates. Appl Environ Microbiol 2013; 79:7142-9. [PMID: 24038696 DOI: 10.1128/aem.02293-13] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Achromobacter xylosoxidans is an aerobic nonfermentative Gram-negative rod considered an important emerging pathogen among cystic fibrosis (CF) patients worldwide and among immunocompromised patients. This increased prevalence remains unexplained, and to date no environmental reservoir has been identified. The aim of this study was to identify potential reservoirs of A. xylosoxidans in hospital, domestic, and outdoor environments and to compare the isolates with clinical ones. From 2011 to 2012, 339 samples were collected in Dijon's university hospital, in healthy volunteers' homes in the Dijon area, and in the outdoor environment in Burgundy (soil, water, mud, and plants). We designed a protocol to detect A. xylosoxidans in environmental samples based on a selective medium: MCXVAA (MacConkey agar supplemented with xylose, vancomycin, aztreonam, and amphotericin B). Susceptibility testing, genotypic analysis by pulsed-field gel electrophoresis, and blaOXA-114 sequencing were performed on the isolates. A total of 50 strains of A. xylosoxidans were detected in hospital (33 isolates), domestic (9 isolates), and outdoor (8 isolates) samples, mainly in hand washing sinks, showers, and water. Most of them were resistant to ciprofloxacin (49 strains). Genotypic analysis and blaOXA-114 sequencing revealed a wide diversity among the isolates, with 35 pulsotypes and 18 variants of oxacillinases. Interestingly, 10 isolates from hospital environment were clonally related to clinical isolates previously recovered from hospitalized patients, and one domestic isolate was identical to one recovered from a CF patient. These results indicate that A. xylosoxidans is commonly distributed in various environments and therefore that CF patients or immunocompromised patients are surrounded by these reservoirs.
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Current Approaches to the Management of Infection in Cystic Fibrosis. CURRENT PEDIATRICS REPORTS 2013. [DOI: 10.1007/s40124-013-0024-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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