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Brochet T, Tonnelier M, Justinien E, Lecapitaine AL, Bouras A. A case of community-acquired spondylodiscitis caused by Achromobacter xylosoxidans. IDCases 2024; 36:e01980. [PMID: 38737915 PMCID: PMC11088332 DOI: 10.1016/j.idcr.2024.e01980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
Achromobacter xylosoxidans is a Gram-negative, aerobic, non-fermenting bacillus mainly responsible for nosocomial infections. We report the first case of community-acquired spondylodiscitis caused by Achromobacter xylosoxidans in a 61-year-old woman, immunocompromised with necrotizing dermohypodermitis of the right lower limb successfully treated with ertapenem and ciprofloxacin.
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Affiliation(s)
- T. Brochet
- Infectious Diseases Department, CH Compiègne, Noyon, France
| | - M. Tonnelier
- Infectious Diseases Department, CH Compiègne, Noyon, France
| | - E. Justinien
- Endocrinology Department, CH Compiègne, Noyon, France
| | | | - A. Bouras
- Infectious Diseases Department, CH Compiègne, Noyon, France
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2
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Zhang S, Liu Y, Wang H, Xu Z, Peng J, Xu Q, Li K, Wang H, Guo Y. Achromobacter seleniivolatilans sp. nov. and Buttiauxella selenatireducens sp. nov., isolated from the rhizosphere of selenium hyperaccumulator Cardamine hupingshanesis. Int J Syst Evol Microbiol 2024; 74. [PMID: 38619980 DOI: 10.1099/ijsem.0.006334] [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] [Indexed: 04/17/2024] Open
Abstract
Two Gram-stain-negative bacterial strains, R39T and R73T, were isolated from the rhizosphere soil of the selenium hyperaccumulator Cardamine hupingshanesis in China. Strain R39T transformed selenite into elemental and volatile selenium, whereas strain R73T transformed both selenate and selenite into elemental selenium. Phylogenetic and phylogenomic analyses indicated that strain R39T belonged to the genus Achromobacter, while strain R73T belonged to the genus Buttiauxella. Strain R39T (genome size, 6.68 Mb; G+C content, 61.6 mol%) showed the closest relationship to Achromobacter marplatensis LMG 26219T and Achromobacter kerstersii LMG 3441T, with average nucleotide identity (ANI) values of 83.6 and 83.4 %, respectively. Strain R73T (genome size, 5.22 Mb; G+C content, 50.3 mol%) was most closely related to Buttiauxella ferragutiae ATCC 51602T with an ANI value of 86.4 %. Furthermore, strain A111 from the GenBank database was found to cluster with strain R73T within the genus Buttiauxella through phylogenomic analyses. The ANI and digital DNA-DNA hybridization values between strains R73T and A111 were 97.5 and 80.0% respectively, indicating that they belong to the same species. Phenotypic characteristics also differentiated strain R39T and strain R73T from their closely related species. Based on the polyphasic analyses, strain R39T and strain R73T represent novel species of the genera Achromobacter and Buttiauxella, respectively, for which the names Achromobacter seleniivolatilans sp. nov. (type strain R39T=GDMCC 1.3843T=JCM 36009T) and Buttiauxella selenatireducens sp. nov. (type strain R73T=GDMCC 1.3636T=JCM 35850T) are proposed.
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Affiliation(s)
- Sasa Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Yi Liu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Hao Wang
- Division of Biology and Biological Engineering, California Institute of Technology, California, 91125, USA
| | - Zhongnan Xu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Jing Peng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Qiaolin Xu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Kui Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Haoyang Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Yanbin Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
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3
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Impact of N-Acetylcysteine and Antibiotics Against Single and Dual Species Biofilms of Pseudomonas aeruginosa and Achromobacter xylosoxidans. Curr Microbiol 2022; 80:5. [PMID: 36434296 DOI: 10.1007/s00284-022-03122-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
Abstract
Lungs of cystic fibrosis patients are often colonized or infected with organisms, such as Pseudomonas aeruginosa and other emerging pathogenic bacteria such as Achromobacter xylosoxidans. Further, it is well established that infections of the cystic fibrosis lung airways are caused by polymicrobial infections, although its composition and diversity may change throughout the patient's life. In the present study, we investigated the effects of N-acetylcysteine (NAC) and amikacin, aztreonam, ciprofloxacin, and tobramycin alone and in combination against single- and dual-species biofilms of P. aeruginosa and A. xylosoxidans, in vitro and in the Caenorhabditis elegans infection model. Results showed that tobramycin and ciprofloxacin were the most effective antibiotics, while aztreonam was the least effective antibiotic against both single- and dual-species biofilms of P. aeruginosa and A. xylosoxidans. However, NAC showed little effect on both single- and dual-species, even with a combination of antibiotics. Increased survival was observed in C. elegans when treated with NAC in combination with tobramycin or ciprofloxacin, compared to no treatment or NAC alone. Tobramycin and ciprofloxacin were found effective in biofilms, but more research is needed to better understand the effects of NAC and antibiotics against single- and dual-species biofilms.
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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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Holgersen MG, Marthin JK, Johansen HK, Nielsen KG. A retrospective review of Achromobacter species and antibiotic treatments in patients with primary ciliary dyskinesia. Chron Respir Dis 2021; 18:14799731211061600. [PMID: 34854775 PMCID: PMC8646779 DOI: 10.1177/14799731211061600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Objectives: Primary ciliary dyskinesia (PCD) is a rare congenital disease with defective mucociliary clearance causing frequent and often persistent pulmonary infections. Achromobacter species are opportunistic pathogens renowned for the difficulty of effective treatments and deteriorating effects on lung function. We aimed to describe the occurrence, treatment, and rate of successful eradication of Achromobacter species in patients with PCD. Methods: We retrospectively reviewed 18 years of historical microbiological samples and 10 years of electronic health records for PCD patients in Denmark. Results: We included 136 patients. Twenty-six patients had isolates of Achromobacter species. On average, 5% of the cohort had at least one annual isolate. Infections became persistent in 38% with a median length of 6.6 years leading to a significant number of antibiotic treatments. Resistance toward tobramycin and ciprofloxacin was prevalent. Overall, successful eradication was achieved in 62% of patients. We found the course of lung function significantly worse during persistent Achromobacter species infection than during the two preceding years, but not different to the course in unaffected age-matched controls. Conclusion The prevalence of Achromobacter species in patients with PCD is in line with what has been reported in cystic fibrosis and can occur transiently, intermittently, or develop into a serious persistent lung infection associated with long-term antibiotic treatment.
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Affiliation(s)
- Mathias G Holgersen
- Danish Paediatric Pulmonary Service, 53146Copenhagen University Hospital, Rigshospitalet, Copenhagen E, Denmark
| | - June K Marthin
- Danish Paediatric Pulmonary Service, 53146Copenhagen University Hospital, Rigshospitalet, Copenhagen E, Denmark
| | - Helle K Johansen
- Department of Clinical Microbiology, 53146Copenhagen University Hospital, Rigshospitalet, Copenhagen E, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
| | - Kim G Nielsen
- Danish Paediatric Pulmonary Service, 53146Copenhagen University Hospital, Rigshospitalet, Copenhagen E, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
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6
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Mulinganya GM, Claeys M, Balolebwami SZ, Bamuleke BA, Mongane JI, Boelens J, Delanghe J, De Vos D, Kambale RM, Maheshe GB, Mateso GM, Bisimwa GB, Malembaka EB, Vaneechoutte M, Cools P, Callens S. Etiology of Early-Onset Neonatal Sepsis and Antibiotic Resistance in Bukavu, Democratic Republic of the Congo. Clin Infect Dis 2021; 73:e976-e980. [PMID: 33575791 DOI: 10.1093/cid/ciab114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The Democratic Republic of the Congo (DRC) has one of the highest neonatal death rates (between 14% and 28%) in the world. In the DRC, neonatal sepsis causes 15.6% of this mortality, but data on the bacterial etiology and associated drug susceptibility are lacking. METHODS Hemocultures of 150 neonates with possible early-onset neonatal sepsis (pEOS) were obtained at the Hôpital Provincial Général de Référence de Bukavu (Bukavu, DRC). The newborns with pEOS received an empirical first-line antimicrobial treatment (ampicillin, cefotaxime, and gentamicin) based on the synopsis of international guidelines for the management of EOS that are in line with World Health Organization (WHO) recommendations. Isolates were identified using matrix-assisted laser desorption/ ionization time-of-flight mass spectrophotometry. Antibiotic resistance was assessed using the disk diffusion method. RESULTS Fifty strains were obtained from 48 patients and identified. The 3 most prevalent species were Enterobacter cloacae complex (42%), Klebsiella pneumoniae (18%), and Serratia marcescens (12%). Enterobacter cloacae isolates were resistant to all first-line antibiotics. All K. pneumoniae and S. marcescens isolates were resistant to ampicillin, and the majority of the K. pneumoniae and half of the S. marcescens isolates were resistant to both cefotaxime and gentamicin. All E. cloacae complex strains, 89% of K. pneumoniae, and half of S. marcescens had an extended-spectrum ß-lactamase phenotype. CONCLUSIONS The most prevalent pathogens causing EOS in Bukavu were E. cloacae complex, K. pneumoniae, and S. marcescens. Most of these isolates were resistant to the WHO-recommended antibiotics.
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Affiliation(s)
- Guy M Mulinganya
- Department of Obstetrics and Gynecology, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of the Congo.,Faculty of Medicine, Catholic University of Bukavu, Bukavu, Democratic Republic of the Congo.,Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Maud Claeys
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Serge Z Balolebwami
- Faculty of Medicine, Catholic University of Bukavu, Bukavu, Democratic Republic of the Congo.,Department of Pediatrics, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of the Congo
| | - Bertrand A Bamuleke
- Faculty of Medicine, Catholic University of Bukavu, Bukavu, Democratic Republic of the Congo.,Department of Internal Medicine, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of the Congo
| | - Jules I Mongane
- Department of Obstetrics and Gynecology, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of the Congo
| | - Jerina Boelens
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Joris Delanghe
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Burn Wound Center, Queen Astrid Military Hospital, Brussels, Belgium
| | - Richard M Kambale
- Faculty of Medicine, Catholic University of Bukavu, Bukavu, Democratic Republic of the Congo.,Department of Pediatrics, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of the Congo
| | - Ghislain B Maheshe
- Faculty of Medicine, Catholic University of Bukavu, Bukavu, Democratic Republic of the Congo.,Department of Internal Medicine, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of the Congo
| | - Guy M Mateso
- Faculty of Medicine, Catholic University of Bukavu, Bukavu, Democratic Republic of the Congo.,Department of Internal Medicine, Hôpital Provincial Général de Référence de Bukavu, Bukavu, Democratic Republic of the Congo
| | - Ghislain B Bisimwa
- Faculty of Medicine, Catholic University of Bukavu, Bukavu, Democratic Republic of the Congo.,Catholic University of Bukavu, School of Public Health, Democratic Republic of the Congo
| | - Espoir B Malembaka
- Faculty of Medicine, Catholic University of Bukavu, Bukavu, Democratic Republic of the Congo.,Catholic University of Bukavu, School of Public Health, Democratic Republic of the Congo
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Piet Cools
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Steven Callens
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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7
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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: 2] [Impact Index Per Article: 0.7] [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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Marthin JK, Lucas JS, Boon M, Casaulta C, Crowley S, Destouches DMS, Eber E, Escribano A, Haarman E, Hogg C, Maitre B, Marsh G, Martinu V, Moreno-Galdó A, Mussaffi H, Omran H, Pohunek P, Rindlisbacher B, Robinson P, Snijders D, Walker WT, Yiallouros P, Johansen HK, Nielsen KG. International BEAT-PCD consensus statement for infection prevention and control for primary ciliary dyskinesia in collaboration with ERN-LUNG PCD Core Network and patient representatives. ERJ Open Res 2021; 7:00301-2021. [PMID: 34350277 PMCID: PMC8326680 DOI: 10.1183/23120541.00301-2021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/16/2021] [Indexed: 12/02/2022] Open
Abstract
Introduction In primary ciliary dyskinesia (PCD) impaired mucociliary clearance leads to recurrent airway infections and progressive lung destruction, and concern over chronic airway infection and patient-to-patient transmission is considerable. So far, there has been no defined consensus on how to control infection across centres caring for patients with PCD. Within the BEAT-PCD network, COST Action and ERS CRC together with the ERN-Lung PCD core a first initiative has now been taken towards creating such a consensus statement. Methods A multidisciplinary international PCD expert panel was set up to create a consensus statement for infection prevention and control (IP&C) for PCD, covering diagnostic microbiology, infection prevention for specific pathogens considered indicated for treatment and segregation aspects. Using a modified Delphi process, consensus to a statement demanded at least 80% agreement within the PCD expert panel group. Patient organisation representatives were involved throughout the process. Results We present a consensus statement on 20 IP&C statements for PCD including suggested actions for microbiological identification, indications for treatment of Pseudomonas aeruginosa, Burkholderia cepacia and nontuberculous mycobacteria and suggested segregation aspects aimed to minimise patient-to-patient transmission of infections whether in-hospital, in PCD clinics or wards, or out of hospital at meetings between people with PCD. The statement also includes segregation aspects adapted to the current coronavirus disease 2019 (COVID-19) pandemic. Conclusion The first ever international consensus statement on IP&C intended specifically for PCD is presented and is targeted at clinicians managing paediatric and adult patients with PCD, microbiologists, patient organisations and not least the patients and their families. For the first time ever, an international consensus statement for infection prevention and control in PCD is presented. A total of 20 statements were developed in a collaboration of BEAT-PCD, COST Action, ERS CRC and ERN-LUNG PCD Core Network.https://bit.ly/3yuahKt
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Affiliation(s)
- June K Marthin
- Danish PCD Centre Copenhagen, Paediatric Pulmonary Service, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Jane S Lucas
- Primary Ciliary Dyskinesia Centre, NIHR Respiratory Biomedical Research Centre, Clinical and Experimental Science, University of Southampton, Southampton, UK
| | - Mieke Boon
- Dept of Paediatrics, University Hospital Gasthuisberg, Leuven, Belgium
| | - Carmen Casaulta
- Division of Paediatric Respiratory Medicine, University Children's Hospital, Bern, Switzerland
| | - Suzanne Crowley
- Paediatric Dept of Allergy and Lung Diseases, Oslo University Hospital, Oslo, Norway
| | - Damien M S Destouches
- Association des Patients Ayant une Dyskinésie Ciliaire Primitive, Limeil-Brevannes, France.,Patient representative
| | - Ernst Eber
- Division of Paediatric Pulmonology and Allergology, Dept of Paediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Amparo Escribano
- Pediatric Pulmonology Unit, Hospital Clínico Universitario de Valencia, University of Valencia, Valencia, Spain
| | - Eric Haarman
- Dept of Pediatric Pulmonology, VU University Medical Center, Amsterdam, The Netherlands
| | - Claire Hogg
- Depts of Paediatrics and Paediatric Respiratory Medicine, Imperial College and Royal Brompton Hospital, London, UK
| | - Bernard Maitre
- Pulmonary Service, Centre constitutif Respirare, Centre Hospitalier intercommunal de Créteil, Univ Paris Est Creteil, INSERM, IMRB, Creteil, France
| | - Gemma Marsh
- Depts of Paediatrics and Paediatric Respiratory Medicine, Imperial College and Royal Brompton Hospital, London, UK
| | - Vendula Martinu
- Paediatric Pulmonology, Paediatric Dept, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Antonio Moreno-Galdó
- Dept of Pediatrics, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain.,CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Huda Mussaffi
- Schneider Children's Medical Center of Israel, Petach-Tikva, Sackler School of Medicine, Tel-Aviv, Israel
| | - Heymut Omran
- Dept of General Paediatrics and Adolescent Medicine, University Hospital Muenster, Muenster, Germany
| | - Petr Pohunek
- Paediatric Pulmonology, Paediatric Dept, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Bernhard Rindlisbacher
- Kartagener Syndrom und Primäre Ciliäre Dyskinesie, Steffisburg, Switzerland.,Patient representative
| | - Phil Robinson
- Dept of Respiratory and Sleep Medicine, Royal Children's Hospital, Parkville, Australia.,Dept of Paediatrics, University of Melbourne, Parkville, Australia.,Murdoch Children's Research Institute, Parkville, Australia
| | - Deborah Snijders
- Primary Ciliary Dyskinesia Centre, Dept of Woman and Child Health (SDB), University of Padova, Padua, Italy
| | - Woolf T Walker
- Primary Ciliary Dyskinesia Centre, NIHR Respiratory Biomedical Research Centre, Clinical and Experimental Science, University of Southampton, Southampton, UK
| | | | - Helle Krogh Johansen
- Dept of Clinical Microbiology, University Hospital Rigshospitalet, Copenhagen, Denmark.,Dept of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kim G Nielsen
- Danish PCD Centre Copenhagen, Paediatric Pulmonary Service, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Dept of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Biernat MM, Wróbel T. Bacterial Infection and Non-Hodgkin B-Cell Lymphoma: Interactions between Pathogen, Host and the Tumor Environment. Int J Mol Sci 2021; 22:ijms22147372. [PMID: 34298992 PMCID: PMC8305669 DOI: 10.3390/ijms22147372] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/23/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
Non-Hodgkin B-cell lymphomas (NHL) are a heterogeneous group of lymphoid neoplasms with complex etiopathology, rich symptomatology, and a variety of clinical courses, therefore requiring different therapeutic approaches. The hypothesis that an infectious agent may initiate chronic inflammation and facilitate B lymphocyte transformation and lymphogenesis has been raised in recent years. Viruses, like EBV, HTLV-1, HIV, HCV and parasites, like Plasmodium falciparum, have been linked to the development of lymphomas. The association of chronic Helicobacter pylori (H. pylori) infection with mucosa-associated lymphoid tissue (MALT) lymphoma, Borrelia burgdorferi with cutaneous MALT lymphoma and Chlamydophila psittaci with ocular adnexal MALT lymphoma is well documented. Recent studies have indicated that other infectious agents may also be relevant in B-cell lymphogenesis such as Coxiella burnettii, Campylobacter jejuni, Achromobacter xylosoxidans, and Escherichia coli. The aim of the present review is to provide a summary of the current literature on infectious bacterial agents associated with B-cell NHL and to discuss its role in lymphogenesis, taking into account the interaction between infectious agents, host factors, and the tumor environment.
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MESH Headings
- Bacterial Infections/complications
- Bacterial Infections/immunology
- Burkitt Lymphoma/complications
- Burkitt Lymphoma/microbiology
- Burkitt Lymphoma/pathology
- Carcinogenesis/genetics
- Carcinogenesis/immunology
- Carcinogenesis/metabolism
- Helicobacter Infections/complications
- Helicobacter Infections/microbiology
- Helicobacter pylori/pathogenicity
- Host-Pathogen Interactions/genetics
- Host-Pathogen Interactions/immunology
- Humans
- Lymphoma, B-Cell, Marginal Zone/complications
- Lymphoma, B-Cell, Marginal Zone/microbiology
- Lymphoma, B-Cell, Marginal Zone/pathology
- Lymphoma, Large B-Cell, Diffuse/complications
- Lymphoma, Large B-Cell, Diffuse/microbiology
- Lymphoma, Large B-Cell, Diffuse/pathology
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
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10
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Toro F, Alarcón J, Márquez S, Capella J, Bahamonde P, Esperón F, Moreno-Switt A, Castro-Nallar E. Composition and structure of the skin microbiota of rorquals off the Eastern South Pacific. FEMS Microbiol Ecol 2021; 97:6179854. [PMID: 33749784 DOI: 10.1093/femsec/fiab050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/18/2021] [Indexed: 01/04/2023] Open
Abstract
Recent advances in high-throughput sequencing have enabled the large-scale interrogation of microbiota in the most diverse environments, including host-associated microbiota. This has led to the recognition that the skin microbiota of rorquals is specific and structurally different from that of the ocean. This study reveals the skin microbiome of 85 wild individuals along the Chilean coast belonging to Megaptera novaeangliae, Balaenoptera musculus and Balaenoptera physalus. Alpha diversity analysis revealed significant differences in richness and phylogenetic diversity, particularly among humpback whales from different locations and between blue and humpback whales. Beta diversity was partially explained by host and location but only accounting for up to 17% of microbiota variability (adjusted VPA). Overall, we found that microbiota composition was dominated by bacterial genera such as Cardiobacter, Moraxella, Tenacibaculum, Stenotrophomonas, Flavobacteria and Pseudomonas. We also found that no ASVs were associated with the three rorqual species. Up to four ASVs were specific of a location, indicating a great variability in the microbiota. To the best of our knowledge, this is the first report on the composition and structure of the skin microbiota of whales off the coast of Chile, providing a foundational dataset to understand the microbiota's role in rorquals.
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Affiliation(s)
- Frederick Toro
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile.,Doctorate in Conservation Medicine, Facultad de Ciencias de la Vida, Universidad Andres Bello, Departamento de Ecologia y Recursos Naturales, Avenida Republica 330, Santiago 8370186, Chile.,Panthalassa, Red de Estudios de Vertebrados Marinos de Chile Toesca 2002 P6, Santiago, Chile.,Facultad de Medicina Veterinaria y Recursos Naturales, Universidad Santo Tomás, Escuela de Medicina Veterinaria, Avenida Limonares 190, Viña del Mar, Chile
| | - Jaime Alarcón
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile
| | - Sebastián Márquez
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile
| | - Juan Capella
- Whalesound Ltda., Lautaro Navarro 1163, 2do piso. Punta Arenas, Chile.,Fundación Yubarta, Apartado Aéreo 33141, Cali, Colombia
| | - Paulina Bahamonde
- Melimoyu Ecosystem Research Institute, Avenida Kennedy 5682, Vitacura, Chile.,Universidad de Playa Ancha, HUB AMBIENTAL UPLA - Centro de Estudios Avanzados, Playa Ancha 850, Valparaíso, Chile
| | - Fernando Esperón
- Animal Health Research Center, INIA-CISA, Valdeolmos, Carretera Algete-El Casar de Talamanca, Km. 8,1, 28130 Valdeolmos, Madrid, Spain
| | - Andrea Moreno-Switt
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Avenida Las Condes 12.461, torre 3, oficina 205. Las Condes, Chile.,Facultad de Medicina Veterinaria, Pontificia Universidad Católica de Chile
| | - Eduardo Castro-Nallar
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile
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11
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Menetrey Q, Sorlin P, Jumas-Bilak E, Chiron R, Dupont C, Marchandin H. Achromobacter xylosoxidans and Stenotrophomonas maltophilia: Emerging Pathogens Well-Armed for Life in the Cystic Fibrosis Patients' Lung. Genes (Basel) 2021; 12:genes12050610. [PMID: 33919046 PMCID: PMC8142972 DOI: 10.3390/genes12050610] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
In patients with cystic fibrosis (CF), the lung is a remarkable ecological niche in which the microbiome is subjected to important selective pressures. An inexorable colonization by bacteria of both endogenous and environmental origin is observed in most patients, leading to a vicious cycle of infection–inflammation. In this context, long-term colonization together with competitive interactions among bacteria can lead to over-inflammation. While Pseudomonas aeruginosa and Staphylococcus aureus, the two pathogens most frequently identified in CF, have been largely studied for adaptation to the CF lung, in the last few years, there has been a growing interest in emerging pathogens of environmental origin, namely Achromobacter xylosoxidans and Stenotrophomonas maltophilia. The aim of this review is to gather all the current knowledge on the major pathophysiological traits, their supporting mechanisms, regulation and evolutionary modifications involved in colonization, virulence, and competitive interactions with other members of the lung microbiota for these emerging pathogens, with all these mechanisms being major drivers of persistence in the CF lung. Currently available research on A. xylosoxidans complex and S. maltophilia shows that these emerging pathogens share important pathophysiological features with well-known CF pathogens, making them important members of the complex bacterial community living in the CF lung.
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Affiliation(s)
- Quentin Menetrey
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Pauline Sorlin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Raphaël Chiron
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Centre de Ressources et de Compétences de la Mucoviscidose, CHU de Montpellier, 34093 Montpellier, France;
| | - Chloé Dupont
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 34093 Nîmes, France
- UMR 5151 HydroSciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université de Montpellier, 15, Avenue Charles Flahault, BP 14491, CEDEX 5, 34093 Montpellier, France
- Correspondence:
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12
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Luo YH, Lai YS, Zheng C, Ilhan ZE, Ontiveros-Valencia A, Long X, Krajmalnik-Brown R, Rittmann BE. Increased expression of antibiotic-resistance genes in biofilm communities upon exposure to cetyltrimethylammonium bromide (CTAB) and other stress conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:144264. [PMID: 33418325 DOI: 10.1016/j.scitotenv.2020.144264] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/12/2020] [Accepted: 11/28/2020] [Indexed: 06/12/2023]
Abstract
Quaternary ammonium compounds (QAC, e.g., cetyltrimethylammonium bromide, (CTAB)) are widely used as surfactants and disinfectants. QAC already are commonly found in wastewaters, and their concentration could increase, since QAC are recommended to inactivate the SARS-CoV-2 (COVID-19) virus. Exposure of bacteria to QAC can lead to proliferation of antibiotic resistance genes (ARG). In particular, O2-based membrane biofilm reactors (O2-MBfRs) achieved excellent CTAB biodegradation, but ARG increased in their biofilms. Here, we applied meta-transcriptomic analyses to assess the impacts of CTAB exposure and operating conditions on microbial community's composition and ARG expression in the O2-MBfRs. Two opportunistic pathogens, Pseudomonas aeruginosa and Stenotrophomonas maltophilia, dominated the microbial communities and were associated with the presence of ARG. Operating conditions that imposed stress on the biofilms, i.e., limited supplies of O2 and nitrogen or a high loading of CTAB, led to large increases in ARG expression, particularly for genes conferring antibiotic-target protection. Important within the efflux pumps was the Resistance-Nodulation-Division (RND) family, which may have been active in exporting CTAB from cells. Oxidative stress appeared to be the key factor that triggered ARG proliferation by selecting intrinsically resistant species and accentuating the expression of ARG. Our findings suggest that means to mitigate the spread of ARG, such as shown here in a O2-based membrane biofilm reactor, need to consider the impacts of stressors, including QAC exposure and stressful operating conditions.
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Affiliation(s)
- Yi-Hao Luo
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA
| | - YenJung Sean Lai
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA.
| | - Chenwei Zheng
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA
| | - Zehra Esra Ilhan
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA; INRAE, Micalis Institute, Université Paris-Saclay, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Aura Ontiveros-Valencia
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA; Division de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa de San José 2055, ZC 78216 San Luis Potosí, Mexico
| | - Xiangxing Long
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-5306, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA
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13
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Transmission and Antibiotic Resistance of Achromobacter in Cystic Fibrosis. J Clin Microbiol 2021; 59:JCM.02911-20. [PMID: 33472899 PMCID: PMC8092725 DOI: 10.1128/jcm.02911-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/11/2021] [Indexed: 12/22/2022] Open
Abstract
Achromobacter species are increasingly being detected in patients with cystic fibrosis (CF), and this emerging pathogen is associated with antibiotic resistance and more-severe disease outcomes. Nonetheless, little is known about the extent of transmission and antibiotic resistance development in Achromobacter infections. We sequenced the genomes of 101 Achromobacter clinical isolates (identified as Achromobacter xylosoxidans based on matrix-assister laser desorption ionization-time of flight [MALDI-TOF] or API N20 typing) collected from 51 patients with CF-the largest longitudinal data set to date. We performed phylogenetic analysis on the genomes and combined this with epidemiological and antibiotic resistance data to identify patient-to-patient transmission and the development of antibiotic resistance. We confirmed that the MALDI-TOF or API N20 method was not sufficient for Achromobacter species-level typing and that the population of Achromobacter isolates was composed of five different species, among which A. xylosoxidans accounted for 52% of infections. Most patients were infected by unique Achromobacter clone types; nonetheless, suspected patient-to-patient transmission cases identified by shared clone types were observed in 35% (n = 18) of patients. In 15 of 16 cases, the suspected transmissions were further supported by genome- or clinic visit-based epidemiological analysis. Finally, we found that resistance developed over time. We show that whole-genome sequencing (WGS) is essential for Achromobacter species typing and identification of patient-to-patient transmission, which was revealed for Achromobacter ruhlandii, A. xylosoxidans, and, for the first time, Achromobacter insuavis Furthermore, we show that the development of antibiotic resistance is associated with chronic Achromobacter infections. Our findings emphasize that transmission and antibiotic resistance should be considered in future treatment strategies.
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14
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Lebeaux D, Merabishvili M, Caudron E, Lannoy D, Van Simaey L, Duyvejonck H, Guillemain R, Thumerelle C, Podglajen I, Compain F, Kassis N, Mainardi JL, Wittmann J, Rohde C, Pirnay JP, Dufour N, Vermeulen S, Gansemans Y, Van Nieuwerburgh F, Vaneechoutte M. A Case of Phage Therapy against Pandrug-Resistant Achromobacter xylosoxidans in a 12-Year-Old Lung-Transplanted Cystic Fibrosis Patient. Viruses 2021; 13:v13010060. [PMID: 33466377 PMCID: PMC7824836 DOI: 10.3390/v13010060] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022] Open
Abstract
Bacteriophages are a promising therapeutic strategy among cystic fibrosis and lung-transplanted patients, considering the high frequency of colonization/infection caused by pandrug-resistant bacteria. However, little clinical data are available regarding the use of phages for infections with Achromobacter xylosoxidans. A 12-year-old lung-transplanted cystic fibrosis patient received two rounds of phage therapy because of persistent lung infection with pandrug-resistant A. xylosoxidans. Clinical tolerance was perfect, but initial bronchoalveolar lavage (BAL) still grew A. xylosoxidans. The patient's respiratory condition slowly improved and oxygen therapy was stopped. Low-grade airway colonization by A. xylosoxidans persisted for months before samples turned negative. No re-colonisation occurred more than two years after phage therapy was performed and imipenem treatment was stopped. Whole genome sequencing indicated that the eight A. xylosoxidans isolates, collected during phage therapy, belonged to four delineated strains, whereby one had a stop mutation in a gene for a phage receptor. The dynamics of lung colonisation were documented by means of strain-specific qPCRs on different BALs. We report the first case of phage therapy for A. xylosoxidans lung infection in a lung-transplanted patient. The dynamics of airway colonization was more complex than deduced from bacterial culture, involving phage susceptible as well as phage resistant strains.
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Affiliation(s)
- David Lebeaux
- Université de Paris, F-75006 Paris, France; (I.P.); (F.C.); (J.-L.M.)
- Service de Microbiologie, Unité Mobile d’Infectiologie, AP-HP, Hôpital Européen Georges Pompidou, 20 rue Leblanc, 75015 Paris, France
- Correspondence: ; Tel.: +33-1-56-09-29-69; Fax: +33-1-56-09-24-46
| | - Maia Merabishvili
- Laboratory Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, B-1120 Brussels, Belgium; (M.M.); (J.-P.P.)
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (L.V.S.); (H.D.); (M.V.)
| | - Eric Caudron
- Service de Pharmacie, Hôpital européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris Centre Université-Paris, 20 rue Leblanc, 75015 Paris, France;
- Lipides, Systèmes Analytiques et Biologiques, Université Paris-Saclay, 92296 Châtenay-Malabry, France
| | - Damien Lannoy
- CHU Lille, Institut de Pharmacie, F-59000 Lille, France;
- ULR7365—GRITA—Groupe de Recherche Sur Les Formes Injectables et Les Technologies Associées, Universit Lille, F-59000 Lille, France
| | - Leen Van Simaey
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (L.V.S.); (H.D.); (M.V.)
| | - Hans Duyvejonck
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (L.V.S.); (H.D.); (M.V.)
- Research Center Health & Water Technology, University College Ghent, Keramiekstraat 80, B-9000 Gent, Belgium;
| | - Romain Guillemain
- Service d’Anesthésie-Réanimation, Hôpital Européen Georges Pompidou, 75015 Paris, France;
| | - Caroline Thumerelle
- Pediatric Pulmonology and Allergy Unit, Hôpital Jeanne de Flandre, University Lille, CHU Lille, F-59000 Lille, France;
| | - Isabelle Podglajen
- Université de Paris, F-75006 Paris, France; (I.P.); (F.C.); (J.-L.M.)
- Service de Microbiologie, AP-HP, Hôpital Européen Georges Pompidou, 20 rue Leblanc, 75015 Paris, France
| | - Fabrice Compain
- Université de Paris, F-75006 Paris, France; (I.P.); (F.C.); (J.-L.M.)
- Service de Microbiologie, AP-HP, Hôpital Européen Georges Pompidou, 20 rue Leblanc, 75015 Paris, France
| | - Najiby Kassis
- Unité d'Hygiène Hospitalière, Service de Microbiologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France;
| | - Jean-Luc Mainardi
- Université de Paris, F-75006 Paris, France; (I.P.); (F.C.); (J.-L.M.)
- Service de Microbiologie, AP-HP, Hôpital Européen Georges Pompidou, 20 rue Leblanc, 75015 Paris, France
| | - Johannes Wittmann
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (J.W.); (C.R.)
| | - Christine Rohde
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (J.W.); (C.R.)
| | - Jean-Paul Pirnay
- Laboratory Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, B-1120 Brussels, Belgium; (M.M.); (J.-P.P.)
| | - Nicolas Dufour
- Service de Réanimation Médico-Chirurgicale, Centre Hospitalier René Dubos, 95300 Pontoise, France;
| | - Stefan Vermeulen
- Research Center Health & Water Technology, University College Ghent, Keramiekstraat 80, B-9000 Gent, Belgium;
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium; (Y.G.); (F.V.N.)
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium; (Y.G.); (F.V.N.)
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (L.V.S.); (H.D.); (M.V.)
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15
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Holgersen MG, Marthin JK, Johansen HK, Nielsen KG. A retrospective review of Achromobacter species and antibiotic treatments in patients with primary ciliary dyskinesia. Chron Respir Dis 2021. [DOI: 10.1177/14799731211061600
expr 938379187 + 801163930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Objectives: Primary ciliary dyskinesia (PCD) is a rare congenital disease with defective mucociliary clearance causing frequent and often persistent pulmonary infections. Achromobacter species are opportunistic pathogens renowned for the difficulty of effective treatments and deteriorating effects on lung function. We aimed to describe the occurrence, treatment, and rate of successful eradication of Achromobacter species in patients with PCD. Methods: We retrospectively reviewed 18 years of historical microbiological samples and 10 years of electronic health records for PCD patients in Denmark. Results: We included 136 patients. Twenty-six patients had isolates of Achromobacter species. On average, 5% of the cohort had at least one annual isolate. Infections became persistent in 38% with a median length of 6.6 years leading to a significant number of antibiotic treatments. Resistance toward tobramycin and ciprofloxacin was prevalent. Overall, successful eradication was achieved in 62% of patients. We found the course of lung function significantly worse during persistent Achromobacter species infection than during the two preceding years, but not different to the course in unaffected age-matched controls. Conclusion The prevalence of Achromobacter species in patients with PCD is in line with what has been reported in cystic fibrosis and can occur transiently, intermittently, or develop into a serious persistent lung infection associated with long-term antibiotic treatment.
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Affiliation(s)
- Mathias G Holgersen
- Danish Paediatric Pulmonary Service, Copenhagen University Hospital, Rigshospitalet, Copenhagen E, Denmark
| | - June K Marthin
- Danish Paediatric Pulmonary Service, Copenhagen University Hospital, Rigshospitalet, Copenhagen E, Denmark
| | - Helle K Johansen
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen E, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
| | - Kim G Nielsen
- Danish Paediatric Pulmonary Service, Copenhagen University Hospital, Rigshospitalet, Copenhagen E, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
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16
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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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Achromobacter xylosoxidans Cellular Pathology Is Correlated with Activation of a Type III Secretion System. Infect Immun 2020; 88:IAI.00136-20. [PMID: 32366575 DOI: 10.1128/iai.00136-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023] Open
Abstract
Achromobacter xylosoxidans is increasingly recognized as a colonizer of cystic fibrosis (CF) patients, but the role that A. xylosoxidans plays in pathology remains unknown. This knowledge gap is largely due to the lack of model systems available to study the toxic potential of this bacterium. Recently, a phospholipase A2 (PLA2) encoded by a majority of A. xylosoxidans genomes, termed AxoU, was identified. Here, we show that AxoU is a type III secretion system (T3SS) substrate that induces cytotoxicity to mammalian cells. A tissue culture model was developed showing that a subset of A. xylosoxidans isolates from CF patients induce cytotoxicity in macrophages, suggestive of a pathogenic or inflammatory role in the CF lung. In a toxic strain, cytotoxicity is correlated with transcriptional activation of axoU and T3SS genes, demonstrating that this model can be used as a tool to identify and track expression of virulence determinants produced by this poorly understood bacterium.
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18
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Huang R, Liu Y, Zheng Y, Ye M. Optical frequency and phase information-based fusion approach for image rotation symmetry detection. OPTICS EXPRESS 2020; 28:18577-18595. [PMID: 32672156 DOI: 10.1364/oe.390224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
Detecting an object using rotation symmetry property is widely applicable as most artificial objects have this property. However, current known techniques often fail due to using single symmetry energy. To tackle this problem, this paper proposes a novel method which consists of two steps: 1) Based on an optical image, two independent symmetry energies are extracted from the optical frequency space (RSS - Rotation Symmetry Strength) and phase space (SSD - Symmetry Shape Density). And, an optimized symmetry-energy-based fusion algorithm is creatively applied to these two energies to achieve a more comprehensive reflection of symmetry information. 2) In the fused symmetry energy map, the local region detection algorithm is used to realize the detection of multi-scale symmetry targets. Compared with known methods, the proposed method can get more multiple-scale (skewed, small-scale, and regular) rotation symmetry centers, and can significantly boost the performance of detecting symmetry properties with better accuracy. Experimental results confirm the performance of the proposed method, which is superior to the state-of-the-art methods.
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19
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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: 4] [Impact Index Per Article: 1.0] [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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Dumolin C, Peeters C, Ehsani E, Tahon G, De Canck E, Cnockaert M, Boon N, Vandamme P. Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production. Int J Syst Evol Microbiol 2020; 70:530-536. [PMID: 31613739 DOI: 10.1099/ijsem.0.003786] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Strain LMG 30378T was isolated from a hydrogen-oxidizing bacteria enrichment reactor inoculated with forest soil. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Achromobacter. Multilocus sequence analysis combined with sequence analysis of a 765 bp nrd A gene fragment both showed Achromobacter agilis LMG 3411T and Achromobacter denitrificans LMG 1231T to be the closest-related neighbours to strain LMG 30378T. Genome sequence analysis revealed a draft genome of 6.81 Mb with a G+C content of 67.2 mol%. In silico DNA-DNA hybridization with A. denitrificans LMG 1231T and A. agilis LMG 3411T showed 42.7 and 42.5% similarity, respectively, confirming that strain LMG 30378T represented a novel Achromobacter species. Phenotypic and metabolic characterization revealed acid phosphatase activity and the absence of phosphoamidase activity as distinctive features. The draft genome composes all necessary metabolic components to fix carbon dioxide and to oxidize molecular hydrogen, suggesting that strain LMG 30378T is a key organism in the enrichment reactor. Together, these data demonstrate that strain LMG 30378T represents a novel species of the genus Achromobacter, for which the name Achromobacter veterisilvae sp. nov. is proposed. The type strain is LMG 30378T (=CCUG 71558T).
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Affiliation(s)
- Charles Dumolin
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Elham Ehsani
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Guillaume Tahon
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Dantam J, Subbaraman LN, Jones L. Adhesion of Pseudomonas aeruginosa, Achromobacter xylosoxidans, Delftia acidovorans, Stenotrophomonas maltophilia to contact lenses under the influence of an artificial tear solution. BIOFOULING 2020; 36:32-43. [PMID: 31973583 DOI: 10.1080/08927014.2019.1710832] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 12/25/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Corneal infection is a devastating sight-threatening complication that is associated with contact lens (CL) wear, commonly caused by Pseudomonas aeruginosa. Lately, Achromobacter xylosoxidans, Delftia acidovorans, and Stenotrophomonas maltophilia have been associated with corneal infection. This study investigated the adhesion of these emerging pathogens to CLs, under the influence of an artificial tear solution (ATS) containing a variety of components commonly found in human tears. Two different CL materials, etafilcon A and senofilcon A, either soaked in an ATS or phosphate buffered saline, were exposed to the bacteria. Bacterial adhesion was investigated using a radio-labeling technique (total counts) and plate count method (viable counts). The findings from this study revealed that in addition to P. aeruginosa, among the emerging pathogens evaluated, A. xylosoxidans showed an increased propensity for adherence to both CL materials and S. maltophilia showed lower viability. ATS influenced the viable counts more than the total counts on CLs.
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Affiliation(s)
- Jaya Dantam
- Centre for Ocular Research & Education, School of Optometry & Vision Science, University of Waterloo, Waterloo, Canada
| | - Lakshman N Subbaraman
- Centre for Ocular Research & Education, School of Optometry & Vision Science, University of Waterloo, Waterloo, Canada
| | - Lyndon Jones
- Centre for Ocular Research & Education, School of Optometry & Vision Science, University of Waterloo, Waterloo, Canada
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22
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Coward A, Kenna DTD, Woodford N, Turton JF. Structured surveillance of Achromobacter, Pandoraea and Ralstonia species from patients in England with cystic fibrosis. J Cyst Fibros 2019; 19:388-393. [PMID: 31862307 DOI: 10.1016/j.jcf.2019.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/16/2019] [Accepted: 11/11/2019] [Indexed: 11/17/2022]
Abstract
A structured survey of the cystic fibrosis pathogens Achromobacter, Pandoraea and Ralstonia species from thirteen sentinel hospitals throughout England was undertaken by Public Health England. One isolate per patient of these genera collected from CF patients during the seven-month survey period in 2015 was requested from participating hospitals. Species-level identification was performed using nrdA/gyrB sequence cluster analysis, and genotyping by pulsed-field gel electrophoresis. In total, 176 isolates were included in the survey; 138 Achromobacter spp. (78.4%), 29 Pandoraea spp. (16.5%) and 9 Ralstonia spp. (5.1%). Novel Achromobacter and Pandoraea clusters were identified. High levels of antimicrobial resistance were found, particularly among Pandoraea isolates. Genotyping analysis revealed considerable diversity, however one geographically-widespread cluster of A. xylosoxidans isolates from six hospitals was found, in addition to two other clusters, both comprising isolates from two hospitals, either derived from the same region (A. xylosoxidans), or from hospitals within the same city (P. apista).
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Affiliation(s)
- Amy Coward
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Dervla T D Kenna
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, United Kingdom..
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Jane F Turton
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, United Kingdom
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23
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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: 14] [Impact Index Per Article: 2.8] [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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24
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Vaneechoutte M, Guschin A, Van Simaey L, Gansemans Y, Van Nieuwerburgh F, Cools P. Emended description of Gardnerella vaginalis and description of Gardnerella leopoldii sp. nov., Gardnerella piotii sp. nov. and Gardnerella swidsinskii sp. nov., with delineation of 13 genomic species within the genus Gardnerella. Int J Syst Evol Microbiol 2019; 69:679-687. [PMID: 30648938 DOI: 10.1099/ijsem.0.003200] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Whole genome sequence analysis (digital DNA-DNA hybridization and average nucleotide identity) was carried out for 81 sequenced full genomes of the genus Gardnerella, including ten determined in this study, and indicated the existence of 13 genomic species, of which five consist of only one strain and of which only five contain more than four sequenced genomes. Furthermore, a collection of ten Gardnerella strains, representing the emended species G. vaginalis and the newly described species Gardnerella leopoldii, Gardnerella piotii and Gardnerella swidsinskii, was studied. Matrix-assisted laser desorption ionization time-of-flight MS analysis of the protein signatures identified specific peaks that can be used to differentiate these four species. Only strains of G. vaginalis produce β-galactosidase. We emend the description of G. vaginalis (type strain ATCC 14018T=LMG 7832T=CCUG 3717T) and describe the novel species Gardnerella leopoldii sp. nov. (UGent 06.41T=LMG 30814T=CCUG 72425T), Gardnerella piotii sp. nov. (UGent 18.01T=LMG 30818T=CCUG 72427T) and Gardnerella swidsinskii sp. nov. (GS 9838-1T=LMG 30812T=CCUG 72429T).
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Affiliation(s)
- Mario Vaneechoutte
- 1Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine & Health Sciences, Ghent University, Flanders, Belgium
| | - Alexander Guschin
- 2Laboratory of Molecular Diagnostics and Epidemiology of Central Research Institute of Epidemiology, Moscow, Russia
| | - Leen Van Simaey
- 1Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine & Health Sciences, Ghent University, Flanders, Belgium
| | - Yannick Gansemans
- 3Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | - Piet Cools
- 4Laboratory of Parasitology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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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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26
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Furlan JPR, Sanchez DG, Gallo IFL, Stehling EG. Replicon typing of plasmids in environmental Achromobacter sp. producing quinolone-resistant determinants. APMIS 2018; 126:864-869. [PMID: 30357960 DOI: 10.1111/apm.12896] [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: 07/05/2018] [Accepted: 09/21/2018] [Indexed: 12/24/2022]
Abstract
This study aimed to investigate the antimicrobial resistance profile to quinolones, the presence of quinolone-resistant determinants and the plasmid replicon typing in environmental Achromobacter sp. isolated from Brazil. Soil and water samples were used for bacterial isolation. The antimicrobial susceptibility testing was performed by minimum inhibitory concentration method. The detection of mutations in the quinolone resistance-determining regions (QRDR) genes, the presence of plasmid-mediated quinolone resistance (PMQR) genes, and plasmid replicons were performed by PCR. A total of 16 isolates was obtained from different cultures, cities, and states of Brazil. All isolates were non-susceptible to ciprofloxacin, norfloxacin, and levofloxacin. Some mutations in QRDR genes were found, including Gln-83-Leu and Asp-87-Asn in the gyrA and Gln-80-Ile and Asp-84-Ala in the parC. Different PMQR genes were detected, such as qnrA, qnrB, qnrS, oqxA, and oqxB. Three different plasmid families were detected, being most presented the ColE-like, followed by IncFIB and IncA/C. The presence of different PMQR genes and plasmids in the isolates of the present study shows that environmental bacteria can act as reservoir of important genes of resistance to fluoroquinolones, which is of great concern, due to the potential of horizontal dissemination of these genes. Besides that, there are no studies reporting these results in Achromobacter sp. isolates.
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Affiliation(s)
- João Pedro Rueda Furlan
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Danilo Garcia Sanchez
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Inara Fernanda Lage Gallo
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Eliana Guedes Stehling
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
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27
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Furlan JPR, Stehling EG. High-level of resistance to β-lactam and presence of β-lactamases encoding genes in Ochrobactrum sp. and Achromobacter sp. isolated from soil. J Glob Antimicrob Resist 2017; 11:133-137. [PMID: 29111479 DOI: 10.1016/j.jgar.2017.10.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/04/2017] [Accepted: 10/13/2017] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Bacteria belonging to the genera Ochrobactrum and Achromobacter are bacteria considered opportunistic, causing infections mainly in immunocompromised patients. β-lactamases are the main cause of resistance to β-lactam antibiotics. This study aimed to investigate the antimicrobial resistance profile and the presence of β-lactamases encoding genes in Ochrobactrum sp. and Achromobacter sp. isolated from Brazilian soils. METHODS Soil samples from the five regions of Brazil were collected for the isolation of bacteria, which were identified molecularly and then, the minimum inhibitory concentration and detection of β-lactamases encoding genes were performed. RESULTS High-level of resistance to β-lactam antibiotics and different β-lactamases encoding genes were found (blaCTX-M-Gp1, blaSHV, blaOXA-1-like and blaKPC), including the first report of the presence of blaKPC in bacteria belonging to the genera Ochrobactrum and Achromobacter. CONCLUSION The results showed that the bacteria from this study, belonging to genera Ochrobactrum and Achromobacter isolated from soil, harbor different β-lactamases encoding genes and can act as a reservoir of these genes.
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Affiliation(s)
- João Pedro Rueda Furlan
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Eliana Guedes Stehling
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil.
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28
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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: 53] [Impact Index Per Article: 7.6] [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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Jeukens J, Freschi L, Vincent AT, Emond-Rheault JG, Kukavica-Ibrulj I, Charette SJ, Levesque RC. A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter. Genome Biol Evol 2017; 9:1030-1046. [PMID: 28383665 PMCID: PMC5405338 DOI: 10.1093/gbe/evx061] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2017] [Indexed: 12/13/2022] Open
Abstract
Over the past decade, there has been a rising interest in Achromobacter sp., an emerging opportunistic pathogen responsible for nosocomial and cystic fibrosis lung infections. Species of this genus are ubiquitous in the environment, can outcompete resident microbiota, and are resistant to commonly used disinfectants as well as antibiotics. Nevertheless, the Achromobacter genus suffers from difficulties in diagnosis, unresolved taxonomy and limited understanding of how it adapts to the cystic fibrosis lung, not to mention other host environments. The goals of this first genus-wide comparative genomics study were to clarify the taxonomy of this genus and identify genomic features associated with pathogenicity and host adaptation. This was done with a widely applicable approach based on pan-genome analysis. First, using all publicly available genomes, a combination of phylogenetic analysis based on 1,780 conserved genes with average nucleotide identity and accessory genome composition allowed the identification of a largely clinical lineage composed of Achromobacter xylosoxidans, Achromobacter insuavis, Achromobacter dolens, and Achromobacter ruhlandii. Within this lineage, we identified 35 positively selected genes involved in metabolism, regulation and efflux-mediated antibiotic resistance. Second, resistome analysis showed that this clinical lineage carried additional antibiotic resistance genes compared with other isolates. Finally, we identified putative mobile elements that contribute 53% of the genus's resistome and support horizontal gene transfer between Achromobacter and other ecologically similar genera. This study provides strong phylogenetic and pan-genomic bases to motivate further research on Achromobacter, and contributes to the understanding of opportunistic pathogen evolution.
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Affiliation(s)
- Julie Jeukens
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Luca Freschi
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), Quebec City, Quebec, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Quebec City, Quebec, Canada
| | | | - Irena Kukavica-Ibrulj
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), Quebec City, Quebec, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Quebec City, Quebec, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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30
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Li P, Niu Q, Wei Q, Zhang Y, Ma X, Kim SW, Lin M, Huang R. Microbial shifts in the porcine distal gut in response to diets supplemented with Enterococcus Faecalis as alternatives to antibiotics. Sci Rep 2017; 7:41395. [PMID: 28165001 PMCID: PMC5292720 DOI: 10.1038/srep41395] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/19/2016] [Indexed: 01/04/2023] Open
Abstract
Gut microbiota plays an important role in host health and nutrient digestion of animals. Probiotics have become one of effective alternatives to antibiotics enhancing animal health and performance through modulating gut microbiota. Previously, our research demonstrated that dietary Enterococcus Faecalis UC-100 substituting antibiotics enhanced growth and health of weaned pigs. To investigate the alterations of microbiota in the distal gut of pigs fed E. faecalis UC-100 substituting antibiotics, this study assessed fecal microbiota in pigs from different dietary treatments: the basal diet group, the E. faecalis group, and the antibiotic group on d 0, 14, and 28 of feeding through 16 S rRNA sequencing. Twenty-one phyla and 137 genera were shared by all pigs, whereas 12 genera were uniquely identified in the E. faecalis group on d 14 and 28. Bacterial abundance and diversity in the E. faecalis group, bacterial diversity in the antibiotic group, especially abundances of Fibrobacteres phylum and 12 genera in the E. faecalis group and antibiotics group were lower than that in the basal diet group on d 28. These results showed that microbial shifts in the porcine gut in response to diets containing E. faecalis were similar to the response to which containing antibiotics.
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Affiliation(s)
- Pinghua Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.,Huaian Academy of Nanjing Agricultural University, Huaian, 223005, China
| | - Qing Niu
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.,Huaian Academy of Nanjing Agricultural University, Huaian, 223005, China
| | - Qingtian Wei
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.,Huaian Academy of Nanjing Agricultural University, Huaian, 223005, China
| | - Yeqiu Zhang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.,Huaian Academy of Nanjing Agricultural University, Huaian, 223005, China
| | - Xiang Ma
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.,Huaian Academy of Nanjing Agricultural University, Huaian, 223005, China
| | - Sung Woo Kim
- Department of Animal Science, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Mingxin Lin
- Changxing Ecoagriculture Co. Limited, Yixing, 214246, China
| | - Ruihua Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China.,Huaian Academy of Nanjing Agricultural University, Huaian, 223005, China
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31
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Impact of High Diversity of Achromobacter Populations within Cystic Fibrosis Sputum Samples on Antimicrobial Susceptibility Testing. J Clin Microbiol 2016; 55:206-215. [PMID: 27807149 DOI: 10.1128/jcm.01843-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 10/25/2016] [Indexed: 01/31/2023] Open
Abstract
Chronic colonization by opportunistic environmental bacteria is frequent in the airways of cystic fibrosis (CF) patients. Studies of Pseudomonas aeruginosa evolution during persistence have highlighted the emergence of pathoadaptive genotypes and phenotypes, leading to complex and diversified inpatient colonizing populations also observed at the intraspecimen level. Such diversity, including heterogeneity in resistance profiles, has been considered an adaptive strategy devoted to host persistence. Longitudinal genomic diversity has been shown for the emergent opportunistic pathogen Achromobacter, but phenotypic and genomic diversity has not yet been studied within a simple CF sputum sample. Here, we studied the genomic diversity and antimicrobial resistance heterogeneity of 132 Achromobacter species strains (8 to 27 strains of identical or distinct colonial morphotypes per specimen) recovered from the sputum samples of 9 chronically colonized CF patients. We highlighted the high within-sample and within-morphotype diversity of antimicrobial resistance (disk diffusion) and genomic (pulsed-field gel electrophoresis) profiles. No sputum sample included strains with identical pulsotypes or antibiotic susceptibility patterns. Differences in clinical categorization were observed for the 9 patients and concerned 3 to 11 antibiotics, including antibiotics recommended for use against Achromobacter Within-sample antimicrobial resistance heterogeneity, not predictable from colonial morphology, suggested that it may represent a selective advantage against antibiotics in an Achromobacter persisting population and potentially compromise the antibiotic management of CF airway infections.
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Raclavsky V, Stromerova N, Safarova D, Bardon J, Zatloukal J, Zapalka M, Jakubec P, Navratilova L, Novotny R. McRAPD unlike MALDI-TOF MS is a suitable candidate for routine discrimination of new Haemophilus influenzae strain acquisition in chronic obstructive pulmonary disease (COPD) and cystic fibrosis. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2016; 160:503-511. [PMID: 27752148 DOI: 10.5507/bp.2016.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 09/21/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND AND AIMS Haemophilus influenzae new strain acquisition has been demonstrated to increase the relative risk of acute exacerbation fourfold in contrast to colonisation or chronic infection by the same strain in chronic obstructive pulmonary disease (COPD). Unfortunately, molecular typing techniques are not suitable for routine use due to cost, labour-intensity and need for special expertise. We tested two techniques potentially useful for routine typing, namely the newly available MALDI-TOF MS and the modified McRAPD compared to MLST as the gold standard. METHODS In 10 patients (10.8%) suffering from COPD or cystic fibrosis, H. influenzae isolates were recovered repeatedly at different timepoints from the same patient during the study period. This allowed for thirteen pairwise comparisons of typing results in isolates recovered consecutively from the same patient to test the ability of the techniques to uncover new strain acquisition. RESULTS MLST detected 9 cases of new strain acquisition among the 13 pairwise comparisons. However, MALDI-TOF MS reported all 13 pairs as different and thus new. In contrast, McRAPD was able to differentiate all the new strain acquisitions from pre-existing ones, both by visual inspection of melting profiles and by Relative Significant Difference values. CONCLUSIONS Unlike MALDI-TOF MS, McRAPD appears to be a suitable candidate for routine discrimination of new strain acquisitions because of its accuracy and, rapid, easy and economic performance.
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Affiliation(s)
- Vladislav Raclavsky
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic.,Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | | | - Dana Safarova
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University Olomouc, Czech Republic
| | - Jan Bardon
- State Veterinary Institute Olomouc, Czech Republic
| | - Jaromir Zatloukal
- Department of Respiratory Medicine, University Hospital Olomouc, Czech Republic
| | - Martin Zapalka
- Department of Pediatrics, University Hospital Olomouc, Czech Republic
| | - Petr Jakubec
- Department of Respiratory Medicine, University Hospital Olomouc, Czech Republic
| | - Lucie Navratilova
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Radko Novotny
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
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