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Maruri-Aransolo A, de Dios Caballero J, Michelena M, Medina-Pascual MJ, Carrasco G, Asensio O, Cols M, Cantón R. Evaluation of CHROMagar™ B. cepacia agar for the detection of Burkholderia cepacia complex species from sputum samples of patients with cystic fibrosis. Eur J Clin Microbiol Infect Dis 2024; 43:1349-1353. [PMID: 38780755 PMCID: PMC11271321 DOI: 10.1007/s10096-024-04845-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
INTRODUCTION Burkholderia cepacia complex (BCC) are non-fermenting Gram-negative bacteria that can chronically colonize the lungs of people with cystic fibrosis (pwCF), causing a severe and progressive respiratory failure, post-transplant complications and epidemic outbreaks. Therefore, rapid and accurate identification of these bacteria is relevant for pwCF, in order to facilitate early eradication and prevent chronic colonization. However, BCCs are often quite difficult to detect on culture media as they have a slow growth rate and can be hidden by other fast-growing microorganisms, including Pseudomonas aeruginosa and filamentous fungi. MATERIAL AND METHODS We evaluated the sensitivity of CHROMagar™ B. cepacia agar using 11 isolates from a well-characterized BCC collection, using BCA agar (Oxoid, UK) as a gold standard. We also studied 180 clinical sputum samples to calculate positive (PPV) and negative (NPV) predictive values. Furthermore, we used three of the well-characterized BCC isolates to determine the limit of detection (LOD). RESULTS Eleven isolates grew on CHROMagar™ B. cepacia at 37ºC after 48 h. The NPV and PPV of CHROMagar™ B. cepacia were 100% and 87.5%, respectively. The LOD of CHROMagar™ B. cepacia was around 1 × 103 CFU/ml, requiring a ten-fold dilution lower bacterial load than BCA for BCC detection. CONCLUSION CHROMagar™ B. cepacia agar proved to have a very good sensitivity and specificity for the detection of clinical BCCs. Moreover, the chromogenic nature of the medium allowed us to clearly differentiate BCC from other Gram-negative species, filamentous fungi and yeasts, thereby facilitating the identification of contaminants.
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Affiliation(s)
- Ainhize Maruri-Aransolo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Juan de Dios Caballero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.
- CIBER de Enfermedades Infecciosas CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
| | - Malkoa Michelena
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - María José Medina-Pascual
- Laboratorio de Referencia e Investigación en Taxonomía, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Gema Carrasco
- Laboratorio de Referencia e Investigación en Taxonomía, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Oscar Asensio
- Pediatric Pulmonology Unit, Consorci Corporació Sanitària Parc Taulí, Sabadell, Spain
| | - Maria Cols
- Pediatric Pulmonology Department and Cystic Fibrosis Unit, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
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Traglia GM, Betancor L, Yim L, Iriarte A, Chabalgoity JA. Genotypic and phenotypic analysis of Salmonella enterica serovar Derby, looking for clues explaining the impairment of egg isolates to cause human disease. Front Microbiol 2024; 15:1357881. [PMID: 38903793 PMCID: PMC11186997 DOI: 10.3389/fmicb.2024.1357881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/23/2024] [Indexed: 06/22/2024] Open
Abstract
Salmonella enterica serovar Derby causes foodborne disease (FBD) outbreaks worldwide, mainly from contaminated pork but also from chickens. During a major epidemic of FBD in Uruguay due to S. enteritidis from poultry, we conducted a large survey of commercially available eggs, where we isolated many S. enteritidis strains but surprisingly also a much larger number (ratio 5:1) of S. Derby strains. No single case of S. Derby infection was detected in that period, suggesting that the S. Derby egg strains were impaired for human infection. We sequenced fourteen of these egg isolates, as well as fifteen isolates from pork or human infection that were isolated in Uruguay before and after that period, and all sequenced strains had the same sequence type (ST40). Phylogenomic analysis was conducted using more than 3,500 genomes from the same sequence type (ST), revealing that Uruguayan isolates clustered into four distantly related lineages. Population structure analysis (BAPS) suggested the division of the analyzed genomes into nine different BAPS1 groups, with Uruguayan strains clustering within four of them. All egg isolates clustered together as a monophyletic group and showed differences in gene content with the strains in the other clusters. Differences included variations in the composition of mobile genetic elements, such as plasmids, insertion sequences, transposons, and phages, between egg isolates and human/pork isolates. Egg isolates showed an acid susceptibility phenotype, reduced ability to reach the intestine after oral inoculation of mice, and reduced induction of SPI-2 ssaG gene, compared to human isolates from other monophyletic groups. Mice challenge experiments showed that mice infected intraperitoneally with human/pork isolates died between 1-7 days p.i., while all animals infected with the egg strain survived the challenge. Altogether, our results suggest that loss of genes functions, the insertion of phages and the absence of plasmids in egg isolates may explain why these S. Derby were not capable of producing human infection despite being at that time, the main serovar recovered from eggs countrywide.
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Affiliation(s)
| | | | | | - Andrés Iriarte
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - José Alejandro Chabalgoity
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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Kim B, Han SR, Lee H, Oh TJ. Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus. Front Microbiol 2024; 14:1302236. [PMID: 38293557 PMCID: PMC10826400 DOI: 10.3389/fmicb.2023.1302236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
Burkholderia is a versatile strain that has expanded into several genera. It has been steadily reported that the genome features of Burkholderia exhibit activities ranging from plant growth promotion to pathogenicity across various isolation areas. The objective of this study was to investigate the secondary metabolite patterns of 366 Burkholderia species through comparative genomics. Samples were selected based on assembly quality assessment and similarity below 80% in average nucleotide identity. Duplicate samples were excluded. Samples were divided into two groups using FastANI analysis. Group A included B. pseudomallei complex. Group B included B. cepacia complex. The limitations of MLST were proposed. The detection of genes was performed, including environmental and virulence-related genes. In the pan-genome analysis, each complex possessed a similar pattern of cluster for orthologous groups. Group A (n = 185) had 14,066 cloud genes, 2,465 shell genes, 682 soft-core genes, and 2,553 strict-core genes. Group B (n = 181) had 39,867 cloud genes, 4,986 shell genes, 324 soft-core genes, 222 core genes, and 2,949 strict-core genes. AntiSMASH was employed to analyze the biosynthetic gene cluster (BGC). The results were then utilized for network analysis using BiG-SCAPE and CORASON. Principal component analysis was conducted and a table was constructed using the results obtained from antiSMASH. The results were divided into Group A and Group B. We expected the various species to show similar patterns of secondary metabolite gene clusters. For in-depth analysis, a network analysis of secondary metabolite gene clusters was conducted, exemplified by BiG-SCAPE analysis. Depending on the species and complex, Burkholderia possessed several kinds of siderophore. Among them, ornibactin was possessed in most Burkholderia and was clustered into 4,062 clans. There was a similar pattern of gene clusters depending on the species. NRPS_04014 belonged to siderophore BGCs including ornibactin and indigoidine. However, it was observed that each family included a similar species. This suggests that, besides siderophores being species-specific, the ornibactin gene cluster itself might also be species-specific. The results suggest that siderophores are associated with environmental adaptation, possessing a similar pattern of siderophore gene clusters among species, which could provide another perspective on species-specific environmental adaptation mechanisms.
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Affiliation(s)
- Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
| | - So-Ra Han
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
| | - Hyun Lee
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Division of Computer Science and Engineering, SunMoon University, Asan, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Republic of Korea
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Burkholderia species in human infections in Mexico: Identification of B. cepacia, B. contaminans, B. multivorans, B. vietnamiensis,B. pseudomallei and a new Burkholderia species. PLoS Negl Trop Dis 2021; 15:e0009541. [PMID: 34185783 PMCID: PMC8274841 DOI: 10.1371/journal.pntd.0009541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/12/2021] [Accepted: 06/06/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Burkholderia sensu stricto is comprised mainly of opportunistic pathogens. This group is widely distributed in the environment but is especially important in clinical settings. In Mexico, few species have been correctly identified among patients, most often B. cepacia is described. METHODOLOGY/PRINCIPAL FINDINGS In this study, approximately 90 strains identified as B. cepacia with the VITEK2 system were isolated from two medical centers in Mexico City and analyzed by MLSA, BOX-PCR and genome analysis. The initial identification of B. cepacia was confirmed for many strains, but B. contaminans, B. multivorans and B. vietnamiensis were also identified among clinical strains for the first time in hospitals in Mexico. Additionally, the presence of B. pseudomallei was confirmed, and a novel species within the B. cepacia complex was documented. Several strains misidentified as B. cepacia actually belong to the genera Pseudomonas, Stenotrophomonas and Providencia. CONCLUSIONS/SIGNIFICANCE The presence of different Burkholderia species in Mexico was confirmed. Correct identification of Burkholderia species is important to provide accurate treatment for immunosuppressed patients.
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Fiamanya S, Cipolla L, Prieto M, Stelling J. Exploring the value of MALDI-TOF MS for the detection of clonal outbreaks of Burkholderia contaminans. J Microbiol Methods 2020; 181:106130. [PMID: 33383044 DOI: 10.1016/j.mimet.2020.106130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Molecular genetics has risen in both output and affordability to become the gold standard in diagnosis, however it is not yet available for most routine clinical microbiology due to cost and the level of skill it requires. Matrix assisted laser desorption/ionisation - time of flight mass spectrometry (MALDI-TOF MS) approaches may be useful in bridging the gap between low-resolution phenotypic methods and bulky genotypic methods in the goal of epidemiological source-typing of microbes. Burkholderia has been shown to be identifiable at the subspecies level using MALDI-TOF MS. There have not yet been studies assessing the ability of MALDI-TOF MS to source-type Burkholderia contaminans isolates into epidemiologically relevant outbreak clusters. METHODS 55 well-characterised B. contaminans isolates were used to create a panel for analysis of MALDI-TOF MS biomarker peaks and their relation to outbreak strains, location, source, patient, diagnosis and isolate genetics. Unsupervised clustering was performed and classification models were generated using biostatistical analysis software. RESULTS B. contaminans spectra derived from MALDI-TOF MS were of sufficiently high resolution to identify 100% of isolates. Unsupervised clustering methods showed poor evidence of spectra clustering by all characteristics measured. Classification algorithms were discriminatory, with Genetic Algorithm models showing 100% recognition capability for all outbreaks, the pulsed-field gel electrophoresis (PFGE) typeability model, and 96.63% recognition for the location model. A consistent peak at m/z of approximately 6943 was identified in all non-typeable strains but in none of the typeable strains. CONCLUSIONS MALDI-TOF MS successfully discriminates B. contaminans isolates into clonal, epidemiological clusters, and can recognise isolates non-typeable by PFGE. Further work should investigate this capability, and include peptide studies and genomic sequencing to identify individual proteins or genes responsible for this non-typeablity, particularly at the peak weight identified.
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Affiliation(s)
- Selali Fiamanya
- Oxford University Clinical Academic Graduate School, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - Lucía Cipolla
- Servicio Bacteriología Especial, Instituto Nacional de Enfermedades Infecciosas 'Dr. C. G. Malbrán', Av Velez Sarsfield 563, 1281 Ciudad Autónoma de Buenos Aires, Argentina
| | - Mónica Prieto
- Servicio Bacteriología Especial, Instituto Nacional de Enfermedades Infecciosas 'Dr. C. G. Malbrán', Av Velez Sarsfield 563, 1281 Ciudad Autónoma de Buenos Aires, Argentina
| | - John Stelling
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School 25 Shattuck Street, Boston, MA 02115, USA
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Wong MY, Tseng YH, Huang TY, Lin BS, Tung CW, Chu C, Huang YK. Comparison of Microbiological Characteristics and Genetic Diversity between Burkholderia cepacia Complex Isolates from Vascular Access and Other Clinical Infections. Microorganisms 2020; 9:microorganisms9010051. [PMID: 33375496 PMCID: PMC7824166 DOI: 10.3390/microorganisms9010051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/19/2020] [Accepted: 12/23/2020] [Indexed: 11/24/2022] Open
Abstract
Burkholderia cepacia complex (BCC) is a group of closely related bacteria with widespread environmental distribution. BCC bacteria are opportunistic pathogens that cause nosocomial infections in patients, especially cystic fibrosis (CF). Multilocus sequence typing (MLST) is used nowadays to differentiate species within the BCC complex. This study collected 41 BCC isolates from vascular access infections (VAIs) and other clinical infections between 2014 and 2020. We preliminarily identified bacterial isolates using standard biochemical procedures and further conducted recA gene sequencing and MLST for species identification. We determined genetic diversity indices using bioinformatics software. We studied 14 isolates retrieved from patients with VAIs and observed that Burkholderia cepacia was the predominant bacterial species, and B. contaminans followed by B. cenocepacia were mainly retrieved from patients with other infections. According to MLST data, we identified that all B. contaminans isolates belonged to ST102, while a wide variety of sequence types (STs) were found in B. cenocepacia isolates. In summary, the high diversity and easy transmission of BCC increase BCC infections, which provides insights into their potential clinical effects in non-CF infections.
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Affiliation(s)
- Min Yi Wong
- Division of Thoracic and Cardiovascular Surgery, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan; (M.Y.W.); (Y.-H.T.)
- Microbiology Research and Treatment Center, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan;
- Institute of Imaging and Biomedical Photonics, National Chiao Tung University, Tainan 71150, Taiwan;
| | - Yuan-Hsi Tseng
- Division of Thoracic and Cardiovascular Surgery, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan; (M.Y.W.); (Y.-H.T.)
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan;
| | - Tsung-Yu Huang
- Microbiology Research and Treatment Center, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan;
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan;
- Division of Infectious Diseases, Department of Internal Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan
| | - Bor-Shyh Lin
- Institute of Imaging and Biomedical Photonics, National Chiao Tung University, Tainan 71150, Taiwan;
| | - Chun-Wu Tung
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan;
- Department of Nephrology, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan
| | - Chishih Chu
- Department of Microbiology, Immunology and Biopharmaceuticals, National Chiayi University, Chiayi City 60004, Taiwan;
| | - Yao-Kuang Huang
- Division of Thoracic and Cardiovascular Surgery, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan; (M.Y.W.); (Y.-H.T.)
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan;
- Division of Infectious Diseases, Department of Internal Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan
- Correspondence: ; Tel.: +886-975368209
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Depoorter E, De Canck E, Peeters C, Wieme AD, Cnockaert M, Zlosnik JEA, LiPuma JJ, Coenye T, Vandamme P. Burkholderia cepacia Complex Taxon K: Where to Split? Front Microbiol 2020; 11:1594. [PMID: 32760373 PMCID: PMC7372133 DOI: 10.3389/fmicb.2020.01594] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/18/2020] [Indexed: 01/08/2023] Open
Abstract
The objective of the present study was to provide an updated classification for Burkholderia cepacia complex (Bcc) taxon K isolates. A representative set of 39 taxon K isolates were analyzed through multilocus sequence typing (MLST) and phylogenomic analyses. MLST analysis revealed the presence of at least six clusters of sequence types (STs) within taxon K, two of which contain the type strains of Burkholderia contaminans (ST-102) and Burkholderia lata (ST-101), and four corresponding to the previously defined taxa Other Bcc groups C, G, H and M. This clustering was largely supported by a phylogenomic tree which revealed three main clades. Isolates of B. contaminans and of Other Bcc groups C, G, and H represented a first clade which generally shared average nucleotide identity (ANI) and average digital DNA-DNA hybridization (dDDH) values at or above the 95-96% ANI and 70% dDDH thresholds for species delineation. A second clade consisted of Other Bcc group M bacteria and of four B. lata isolates and was supported by average ANI and dDDH values of 97.2 and 76.1% within this clade and average ANI and dDDH values of 94.5 and 57.2% toward the remaining B. lata isolates (including the type strain), which represented a third clade. We therefore concluded that isolates known as Other Bcc groups C, G, and H should be classified as B. contaminans, and propose a novel species, Burkholderia aenigmatica sp. nov., to accommodate Other Bcc M and B. lata ST-98, ST-103, and ST-119 isolates. Optimized MALDI-TOF MS databases for the identification of clinical Burkholderia isolates may provide correct species-level identification for some of these bacteria but would identify most of them as B. cepacia complex. MLST facilitates species-level identification of many taxon K strains but some may require comparative genomics for accurate species-level assignment. Finally, the inclusion of Other Bcc groups C, G, and H into B. contaminans affects the phenotype of this species minimally and the proposal to classify Other Bcc group M and B. lata ST-98, ST-103, and ST-119 strains as a novel Burkholderia species is supported by a distinctive phenotype, i.e., growth at 42°C and lysine decarboxylase activity.
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Affiliation(s)
- Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Anneleen D Wieme
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium.,BCCM/LMG Bacteria Collection, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - James E A Zlosnik
- Division of Infectious Diseases, Department of Pediatrics, The University of British Columbia, Vancouver, BC, Canada
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium.,BCCM/LMG Bacteria Collection, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
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Rohit A, Rani MS, Anand NS, Chellappa C, Mohanapriya P, Karunasagar I, Karunasagar I, Deekshit VK. Burkholderia vietnamiensis causing a non-lactational breast abscess in a non-cystic fibrosis patient in Tamil Nadu, India. Indian J Med Microbiol 2020; 38:496-499. [PMID: 33154274 DOI: 10.4103/ijmm.ijmm_20_329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Burkholderia cepacia complex is a Gram-negative opportunistic pathogen usually found in people with an immunocompromised condition such as cystic fibrosis (CF). In a tropical country like India, this organism has been associated with a number of hospital-acquired infections including sepsis. We present here a report of a case of Burkholderia vietnamiensis causing a non-lactational breast abscess in a non-CF patient. The pathogen was identified as B. cepacia using Vitek system and matrix-assisted laser desorption ionisation-time of flight. This was confirmed by polymerase chain reaction (PCR) using recA genus-specific gene and sequencing of the PCR amplicons. recA-restriction fragment length polymorphism and recA gene sequencing revealed that the isolate is B. vietnamiensis. This is the first description of B. vietnamiensis isolated from a clinical case from India.
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Affiliation(s)
- Anusha Rohit
- Department of Microbiology, Madras Medical Mission, Chennai, Tamil Nadu, India
| | - M Shraddha Rani
- Division of Infectious Diseases, Nitte University Center for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangaluru, Karnataka, India
| | - N Suresh Anand
- Department of Breast Surgery, Madras Medical Mission, Chennai, Tamil Nadu, India
| | - Cynthia Chellappa
- Department of Breast Surgery, Madras Medical Mission, Chennai, Tamil Nadu, India
| | - P Mohanapriya
- Department of Microbiology, Madras Medical Mission, Chennai, Tamil Nadu, India
| | - Indrani Karunasagar
- Division of Infectious Diseases, Nitte University Center for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangaluru, Karnataka, India
| | - Iddya Karunasagar
- Division of Infectious Diseases, Nitte University Center for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangaluru, Karnataka, India
| | - Vijaya Kumar Deekshit
- Division of Infectious Diseases, Nitte University Center for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangaluru, Karnataka, India
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A Novel Inducible Prophage from Burkholderia Vietnamiensis G4 is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia. Viruses 2020; 12:v12060601. [PMID: 32486377 PMCID: PMC7354579 DOI: 10.3390/v12060601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/30/2022] Open
Abstract
Burkholderia species have environmental, industrial and medical significance, and are important opportunistic pathogens in individuals with cystic fibrosis (CF). Using a combination of existing and newly determined genome sequences, this study investigated prophage carriage across the species B. vietnamiensis, and also isolated spontaneously inducible prophages from a reference strain, G4. Eighty-one B. vietnamiensis genomes were bioinformatically screened for prophages using PHASTER (Phage Search Tool Enhanced Release) and prophage regions were found to comprise up to 3.4% of total genetic material. Overall, 115 intact prophages were identified and there was evidence of polylysogeny in 32 strains. A novel, inducible Mu-like phage (vB_BvM-G4P1) was isolated from B. vietnamiensis G4 that had lytic activity against strains of five Burkholderia species prevalent in CF infections, including the Boston epidemic B. dolosa strain SLC6. The cognate prophage to vB_BvM-G4P1 was identified in the lysogen genome and was almost identical (>93.5% tblastx identity) to prophages found in 13 other B. vietnamiensis strains (17% of the strain collection). Phylogenomic analysis determined that the G4P1-like prophages were widely distributed across the population structure of B. vietnamiensis. This study highlights how genomic characterization of Burkholderia prophages can lead to the discovery of novel bacteriophages with potential therapeutic or biotechnological applications.
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Savi D, Quattrucci S, Trancassini M, Dalmastri C, De Biase RV, Maggisano M, Palange P, Bevivino A. Impact of clonally-related Burkholderia contaminans strains in two patients attending an Italian cystic fibrosis centre: a case report. BMC Pulm Med 2019; 19:164. [PMID: 31464603 PMCID: PMC6714384 DOI: 10.1186/s12890-019-0923-6] [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: 04/13/2019] [Accepted: 08/19/2019] [Indexed: 11/11/2022] Open
Abstract
Background Burkholderia contaminans is one of the 20 closely related bacterial of the Burkholderia cepacia complex, a group of bacteria that are ubiquitous in the environment and capable of infecting people with cystic fibrosis (CF). This species is an emerging pathogen and it has been widely isolated from CF patients in Argentina, Spain, Portugal, Australia, Canada, USA with a low prevalence in Ireland, France, Russia, Switzerland, Czech Republic, and Italy. This is the first report of B. contaminans affecting two Italian CF patients attending the same CF Centre. We correlate B. contaminans colonisation with lung function decline and co-infection with other clinically relevant CF pathogens. Case presentation B. contaminans was identified by Multi Locus Sequence Typing in routine sputum analysis of two Caucasian CF women homozygous for Phe508del CFTR mutation. Sequence Type 102 was detected in both strains. It is known that B. contaminans ST102 was isolated both from CF and non-CF patients, with an intercontinental spread across the world. Random Amplified Polymorphic DNA analysis revealed the genetic relatedness between the two strains. We examined their susceptibility to antimicrobial agents, comparing the latter with that recorded for other B. contaminans isolated from different countries. We also described key virulence factors possibly linked with a clinical outcome. Specifically, we attempted to correlate colonization with the incidence of acute exacerbation of symptoms and lung function decline. Conclusions This case presentation suggests that acquisition of B. contaminans ST102 is not directly associated with a lung function decline. We retain that the presence of other CF pathogens (i.e. MRSA and Trichosporon) along with B. contaminans ST102 might have contributed to the worsening of clinical conditions in our CF patients. The circumstances leading to the establishment of B. contaminans ST102 infections are still unknown. We highlight the importance to proper detect and typing bacteria implicated in CF infection by using molecular techniques.
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Affiliation(s)
- Daniela Savi
- Department of Public Health and Infectious Diseases, Adult Cystic Fibrosis Centre, "Sapienza" University of Rome, V.le Universita' 37, 00185, Rome, Italy. .,Cystic Fibrosis Unit, Bambino Gesù Children's Hospital, Rome, Italy.
| | - Serena Quattrucci
- Dipartimento Materno Infantile e Scienze Urologiche, Sapienza University of Rome, Rome, Italy
| | - Maria Trancassini
- Department of Public Health and Infectious Diseases, Laboratory of Microbiology, Policlinico Umberto I Hospital, Rome, Italy
| | - Claudia Dalmastri
- Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA C.R Casaccia, 00123, Rome, Italy
| | | | - Marta Maggisano
- Sant'Andrea Hospital, Sapienza University of Rome, Rome, Italy
| | - Paolo Palange
- Department of Public Health and Infectious Diseases, Adult Cystic Fibrosis Centre, "Sapienza" University of Rome, V.le Universita' 37, 00185, Rome, Italy
| | - Annamaria Bevivino
- Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA C.R Casaccia, 00123, Rome, Italy
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11
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Hassan AA, Coutinho CP, Sá-Correia I. Burkholderia cepacia Complex Species Differ in the Frequency of Variation of the Lipopolysaccharide O-Antigen Expression During Cystic Fibrosis Chronic Respiratory Infection. Front Cell Infect Microbiol 2019; 9:273. [PMID: 31417878 PMCID: PMC6686744 DOI: 10.3389/fcimb.2019.00273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
Burkholderia cepacia complex (Bcc) bacteria can adapt to the lung environment of cystic fibrosis (CF) patients resulting in the emergence of a very difficult to eradicate heterogeneous population leading to chronic infections associated with rapid lung function loss and increased mortality. Among the important phenotypic modifications is the variation of the lipopolysaccharide (LPS) structure at level of the O-antigen (OAg) presence, influencing adherence, colonization and the ability to evade the host defense mechanisms. The present study was performed to understand whether the loss of OAg expression during CF infection can be considered a general phenomenon in different Bcc species favoring its chronicity. In fact, it is still not clear why different Bcc species/strains differ in their ability to persist in the CF lung and pathogenic potential. The systematic two-decade-retrospective-longitudinal-screening conducted covered 357 isolates retrieved from 19 chronically infected patients receiving care at a central hospital in Lisbon. The study involved 21 Bcc strains of six/seven Bcc species/lineages, frequently or rarely isolated from CF patients worldwide. Different strains/clonal variants obtained during infection gave rise to characteristic OAg-banding patterns. The two most prevalent and feared species, B. cenocepacia and B. multivorans, showed a tendency to lose the OAg along chronic infection. B. cenocepacia recA lineage IIIA strains known to lead to particularly destructive infections exhibit the most frequent OAg loss, compared with lineage IIIB. The switch frequency increased with the duration of infection and the level of lung function deterioration. For the first time, it is shown that the rarely found B. cepacia and B. contaminans, whose representation in the cohort of patients examined is abnormally high, keep the OAg even during 10- or 15-year infections. Data from co-infections with different Bcc species reinforced these conclusions. Concerning the two other rarely found species examined, B. stabilis exhibited a stable OAg expression phenotype over the infection period while for the single clone of the more distantly related B. dolosa species, the OAg-chain was absent from the beginning of the 5.5-year infection until the patient dead. This work reinforces the relevance attributed to the OAg-expression switch suggesting marked differences in the various Bcc species.
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Affiliation(s)
- A. Amir Hassan
- iBB - Institute for Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Carla P. Coutinho
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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12
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Leong LEX, Lagana D, Carter GP, Wang Q, Smith K, Stinear TP, Shaw D, Sintchenko V, Wesselingh SL, Bastian I, Rogers GB. Burkholderia lata Infections from Intrinsically Contaminated Chlorhexidine Mouthwash, Australia, 2016. Emerg Infect Dis 2019; 24:2109-2111. [PMID: 30334703 PMCID: PMC6199994 DOI: 10.3201/eid2411.171929] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Burkholderia lata was isolated from 8 intensive care patients at 2 tertiary hospitals in Australia. Whole-genome sequencing demonstrated that clinical and environmental isolates originated from a batch of contaminated commercial chlorhexidine mouthwash. Genomic analysis identified efflux pump-encoding genes as potential facilitators of bacterial persistence within this biocide.
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13
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Degrossi JJ, Merino C, Isasmendi AM, Ibarra LM, Collins C, Bo NE, Papalia M, Fernandez JS, Hernandez CM, Papp-Wallace KM, Bonomo RA, Vazquez MS, Power P, Ramirez MS. Whole Genome Sequence Analysis of Burkholderia contaminans FFH2055 Strain Reveals the Presence of Putative β-Lactamases. Curr Microbiol 2019; 76:485-494. [PMID: 30783798 DOI: 10.1007/s00284-019-01653-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/11/2019] [Indexed: 12/20/2022]
Abstract
Burkholderia contaminans is a member of the Burkholderia cepacia complex (Bcc), a pathogen with increasing prevalence among cystic fibrosis (CF) patients and the cause of numerous outbreaks due to the use of contaminated commercial products. The antibiotic resistance determinants, particularly β-lactamases, have been poorly studied in this species. In this work, we explored the whole genome sequence (WGS) of a B. contaminans isolate (FFH 2055) and detected four putative β-lactamase-encoding genes. In general, these genes have more than 93% identity with β-lactamase genes found in other Bcc species. Two β-lactamases, a class A (Pen-like, suggested name PenO) and a class D (OXA-like), were further analyzed and characterized. Amino acid sequence comparison showed that Pen-like has 82% and 67% identity with B. multivorans PenA and B. pseudomallei PenI, respectively, while OXA-like displayed strong homology with class D enzymes within the Bcc, but only 22-44% identity with available structures from the OXA family. PCR reactions designed to study the presence of these two genes revealed a heterogeneous distribution among clinical and industrial B. contaminans isolates. Lastly, blaPenO gene was cloned and expressed into E. coli to investigate the antibiotic resistance profile and confers an extended-spectrum β-lactamase (ESBL) phenotype. These results provide insight into the presence of β-lactamases in B. contaminans, suggesting they play a role in antibiotic resistance of these bacteria.
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Affiliation(s)
- José J Degrossi
- Cátedra de Salud Pública e Higiene Ambiental, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cindy Merino
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Adela M Isasmendi
- Servicio de Bacteriología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - Lorena M Ibarra
- Servicio de Bacteriología, Hospital de Niños Ricardo Gutierrez, Buenos Aires, Argentina
| | - Chelsea Collins
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Nicolás E Bo
- Cátedra de Salud Pública e Higiene Ambiental, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariana Papalia
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
- Cátedra de Microbiología, Laboratorio de Resistencia Bacteriana, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jennifer S Fernandez
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Claudia M Hernandez
- Servicio de Bacteriología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - Krisztina M Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, OH, 44106, USA
- Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, OH, 44106, USA
- Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
- Departments of Microbiology and Molecular Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Miryam S Vazquez
- Servicio de Bacteriología, Hospital de Niños Ricardo Gutierrez, Buenos Aires, Argentina
| | - Pablo Power
- Cátedra de Microbiología, Laboratorio de Resistencia Bacteriana, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María S Ramirez
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA.
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14
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[The controversial Burkholderia cepacia complex, a group of plant growth promoting species and plant, animals and human pathogens]. Rev Argent Microbiol 2018; 51:84-92. [PMID: 29691107 DOI: 10.1016/j.ram.2018.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 10/10/2017] [Accepted: 01/03/2018] [Indexed: 11/22/2022] Open
Abstract
The Burkholderia cepacia complex is a group of 22 species, which are known as opportunistic pathogens in immunocompromised people, especially those suffering from cystic fibrosis. It is also found in nosocomial infections and is difficult to eradicate due to intrinsic resistance to several antibiotics. The species have large genomes (up to 9 Mbp), distributed into 2-5 replicons. These features significantly contribute to genome plasticity, which makes them thrive in different environments like soil, water, plants or even producing nodules in legume plants. Some B. cepacia complex species are beneficial in bioremediation, biocontrol and plant-growth promotion. However, because the B. cepacia complex is involved in human infection, its use in agriculture is restricted. B. cepacia complex is being constantly studied due to the health problems that it causes and because of its agricultural potential. In this review, the history of B. cepacia complex and the most recently published information related to this complex are revised.
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15
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El-Halfawy OM, Naguib MM, Valvano MA. Novel antibiotic combinations proposed for treatment of Burkholderia cepacia complex infections. Antimicrob Resist Infect Control 2017; 6:120. [PMID: 29204272 PMCID: PMC5702217 DOI: 10.1186/s13756-017-0279-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/17/2017] [Indexed: 12/15/2022] Open
Abstract
Effective strategies to manage Burkholderia cepacia complex (Bcc) infections in cystic fibrosis (CF) patients are lacking. We tested combinations of clinically available antibiotics and show that moxifloxacin-ceftazidime could inhibit 16 Bcc clinical isolates at physiologically achievable concentrations. Adding low dose of colistin improved the efficacy of the combo, especially at conditions mimicking CF respiratory secretions.
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Affiliation(s)
- Omar M El-Halfawy
- Department of Microbiology and Immunology, University of Western Ontario, London, ON Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Marwa M Naguib
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7BL UK.,Department of Microbiology and Immunology, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Miguel A Valvano
- Department of Microbiology and Immunology, University of Western Ontario, London, ON Canada.,Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7BL UK
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16
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Prevalence of Burkholderia cepacia complex species in cystic fibrosis patients in Argentina during the period 2011-2015. Enferm Infecc Microbiol Clin 2017; 36:431-434. [PMID: 29055510 DOI: 10.1016/j.eimc.2017.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/29/2017] [Accepted: 09/05/2017] [Indexed: 11/23/2022]
Abstract
INTRODUCTION Burkholderia cepacia (B. cepacia) complex is composed of 20 phylogenetically closely related bacterial species. Some species have emerged as opportunistic pathogens in immunocompromised patients and are responsible for nosocomial outbreaks. The B. cepacia complex is a recognized respiratory pathogen in patients with cystic fibrosis. Burkholderia cenocepacia and Burkholderia multivorans (B. multivorans) are the most prevalent species in the world, according to the literature. However, research groups in Argentina have described a particular local epidemiology, with prevalence of Burkholderia contaminans (B. contaminans). METHODS A total of 68 isolates of B. cepacia complex recovered of 46 cystic fibrosis patients attended at 14 hospitals distributed in 9 provinces of the country were studied. Identification was carried out by conventional phenotypic methods and was confirmed by recA gene sequencing. Sequences were analysed using the BLASTN program and comparing with B. cepacia complex type strains sequences deposited in GenBank. Antibiotic susceptibility tests were performed on isolates of the most prevalent species according to CLSI M45 guidelines. RESULTS The prevalent specie was B. contaminans (49%, n = 33) followed by B. cenocepacia (25%; n = 17). The remaining species were Burkholderia seminalis (B. seminalis) (7%, n = 5), B. cepacia (7%, n = 5), B. multivorans (6%, n = 4), Burkholderia vietnamensis (5%, n=3) and Burkholderia pyrrocinia (1%; n = 1). The 46% of B. contaminans isolates were resistant to SXT and 76% sensitive to MIN, MEM and CAZ. The isolates of B. cenocepacia were 100% resistant to SXT and MIN and 47% to CAZ and MEM. B. seminalis showed high levels of resistance to TMS (80%), CAZ (60%) and MIN (60%), and 60% of the isolates showed intermediate sensitivity to MEM. CONCLUSION Previous reports have described the prevalence of B. contaminans isolation from cystic fibrosis patients in Argentina, Spain and Portugal, and a case of two patients with cystic fibrosis in Ireland has recently been reported. Due to the high frequency with which B. contaminans is isolated in our country, it is necessary to promote the investigation of possible sources of infection and to understand the factors and mechanisms involved in the apparent greater transmissibility of this species. Different antimicrobial resistance profiles were detected between the species.
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17
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Improved High-Quality Draft Genome Sequence and Annotation of Burkholderia contaminans LMG 23361 T. GENOME ANNOUNCEMENTS 2017; 5:5/16/e00245-17. [PMID: 28428315 PMCID: PMC5399274 DOI: 10.1128/genomea.00245-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Burkholderia contaminans LMG 23361 is the type strain of the species isolated from the milk of a dairy sheep with mastitis. Some pharmaceutical products contain disinfectants such as benzalkonium chloride (BZK) and previously we reported that B. contaminans LMG 23361T possesses the ability to inactivate BZK with high biodegradation rates. Here, we report an improved high-quality draft genome sequence of this strain.
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18
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Fila L, Dřevínek P. Burkholderia cepacia complex in cystic fibrosis in the post-epidemic period: multilocus sequence typing-based approach. Folia Microbiol (Praha) 2017; 62:509-514. [PMID: 28364392 DOI: 10.1007/s12223-017-0523-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 03/22/2017] [Indexed: 12/15/2022]
Abstract
Cystic fibrosis (CF) patients in the Czech Republic suffered in the late 1990s from an epidemic with ST32 strain of Burkholderia cepacia complex (Bcc). Cohort segregation of Bcc and of ST32 positive patients was introduced in 1999 and 2002, respectively. We performed a study to evaluate the molecular epidemiology of Bcc infection after implementation of these infection control measures. Patients attending the Prague CF adult Centre from 2000 to 2015 were included in the present study. Demographic data and microbial statuses were collected from patient records. All Bcc isolates were analyzed using multilocus sequence typing (MLST). The prevalences of epidemic strain ST32 and of other Bcc strains were calculated. Ninety out of 227 CF patients were infected with Bcc during the study period. The prevalence of ST32 cases significantly decreased from 46.5% in 2000-2001 to 10.4% in 2014-2015 (P < 0.001) due to occurrence of only one new case in 2003, as well as to the death of 72% of ST32-infected patients. Conversely, there was a significant increase in prevalence of other Bcc strains, which rose from 0 to 14.9% (P = 0.015) and of transient infections. A micro-epidemic of infection with ST630 strain was observed in 2014 in lung transplant patients hospitalized in intensive care unit. The prevalence of epidemic strain ST32 decreased, whereas that of non-clonal strains of Bcc increased. Routine use of MLST allowed early detection of new and potentially epidemic strains.
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Affiliation(s)
- Libor Fila
- Department of Pneumology, 2nd Faculty of Medicine, Charles University in Prague, and Motol University Hospital, V Úvalu 84, 150 06, Prague, Czech Republic.
| | - Pavel Dřevínek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague, and Motol University Hospital, V Úvalu 84, 150 06, Prague, Czech Republic
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19
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Guo FB, Xiong L, Zhang KY, Dong C, Zhang FZ, Woo PCY. Identification and analysis of genomic islands in Burkholderia cenocepacia AU 1054 with emphasis on pathogenicity islands. BMC Microbiol 2017; 17:73. [PMID: 28347342 PMCID: PMC5369199 DOI: 10.1186/s12866-017-0986-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 03/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic islands (GIs) are genomic regions that reveal evidence of horizontal DNA transfer. They can code for many functions and may augment a bacterium's adaptation to its host or environment. GIs have been identified in strain J2315 of Burkholderia cenocepacia, whereas in strain AU 1054 there has been no published works on such regions according to our text mining and keyword search in Medline. RESULTS In this study, we identified 21 GIs in AU 1054 by combining two computational tools. Feature analyses suggested that the predictions are highly reliable and hence illustrated the advantage of joint predictions by two independent methods. Based on putative virulence factors, four GIs were further identified as pathogenicity islands (PAIs). Through experiments of gene deletion mutants in live bacteria, two putative PAIs were confirmed, and the virulence factors involved were identified as lipA and copR. The importance of the genes lipA (from PAI 1) and copR (from PAI 2) for bacterial invasion and replication indicates that they are required for the invasive properties of B. cenocepacia and may function as virulence determinants for bacterial pathogenesis and host infection. CONCLUSIONS This approach of in silico prediction of GIs and subsequent identification of potential virulence factors in the putative island regions with final validation using wet experiments could be used as an effective strategy to rapidly discover novel virulence factors in other bacterial species and strains.
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Affiliation(s)
- Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Lifeng Xiong
- Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Kai-Yue Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Chuan Dong
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Fa-Zhan Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China.
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20
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Cunha BA, Gian J, Dieguez B, Santos-Cruz E, Matassa D, Gerson S, Daniels P, Rosales C, Silletti RP. Burkholderia contaminans Colonization from Contaminated Liquid Docusate (Colace) in a Immunocompetent Adult with Legionnaire's Disease: Infection Control Implications and the Potential Role of Candida pellucosa. J Clin Med 2016; 5:jcm5120110. [PMID: 27916878 PMCID: PMC5184783 DOI: 10.3390/jcm5120110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/14/2016] [Accepted: 11/18/2016] [Indexed: 11/16/2022] Open
Abstract
Objective:B. contaminans was cultured from respiratory secretions and liquid docusate (Colace) in a Neurosurgical Intensive Care Unit (NICU) patient with community-acquired Legionnaire’s disease but not from another bottle given to the patient. Unexpectedly, C. pelliculosa was cultured from two bottles, but not the B. contaminans bottle or respiratory secretions. Methods:B. cepacia, later identified as B. contaminans, was cultured from a bottle of liquid docusate (Colace) dispensed to a non-cystic fibrosis patient. His respiratory secretions were colonized with B. contaminans. Results: Eradication of B. contaminans colonization in the patient’s respiratory secretions was attempted. With levofloxacin, B. contaminans developed multidrug resistance (MDR). Subsequent TMP-SMX therapy did not result in further MDR. Nine other ICU patients were given docusate from the same lot, but there were no other B. contaminans isolates. Conclusion:B. contaminans colonization of respiratory secretion may be difficult to eliminate. The significance of C. pelliculosa cultured from liquid docusate (Colace) remains to be elucidated. In this case, it appeared that B. contaminans may have inhibited the growth of C. pelliculosa in the same bottle. Others should be alerted to the possibility that C. pelliculosa may be present in B. contaminans–contaminated lots of liquid docusate (Colace).
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Affiliation(s)
- Burke A Cunha
- Infectious Disease Division, Winthrop-University Hospital, Mineola, New York, NY 11501, USA.
- State University of New York, School of Medicine, Stony Brook, New York, NY 11501, USA.
| | - John Gian
- Infectious Disease Division, Winthrop-University Hospital, Mineola, New York, NY 11501, USA.
| | - Bertamaria Dieguez
- Infectious Disease Division, Winthrop-University Hospital, Mineola, New York, NY 11501, USA.
| | - Elsa Santos-Cruz
- Infection Control Department, Winthrop-University Hospital, Mineola, New York, NY 11501, USA.
| | - Daniela Matassa
- Infection Control Department, Winthrop-University Hospital, Mineola, New York, NY 11501, USA.
| | - Steve Gerson
- Pharmacy Department, Winthrop-University Hospital, Mineola, New York, NY 11501, USA.
| | - Pat Daniels
- Pharmacy Department, Winthrop-University Hospital, Mineola, New York, NY 11501, USA.
| | - Carlos Rosales
- Medical Microbiology Laboratory, Winthrop-University Hospital, 222 Station Plaza North, Mineola, New York, NY 11501, USA.
| | - Rodger P Silletti
- Medical Microbiology Laboratory, Winthrop-University Hospital, 222 Station Plaza North, Mineola, New York, NY 11501, USA.
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21
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Draft Genome Sequences of Burkholderia contaminans FFI-28, a Strain Isolated from a Contaminated Pharmaceutical Solution. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01177-16. [PMID: 27789640 PMCID: PMC5084864 DOI: 10.1128/genomea.01177-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Burkholderia contaminans is a species of the Burkholderia cepacia complex, a group of bacteria that can grow in pharmaceutical products and are capable of infecting the immunocompromised and people with cystic fibrosis. Here, we report draft genome sequences for Burkholderia contaminans FFI-28, a strain isolated from a contaminated pharmaceutical solution.
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22
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Nunvar J, Kalferstova L, Bloodworth RAM, Kolar M, Degrossi J, Lubovich S, Cardona ST, Drevinek P. Understanding the Pathogenicity of Burkholderia contaminans, an Emerging Pathogen in Cystic Fibrosis. PLoS One 2016; 11:e0160975. [PMID: 27512997 PMCID: PMC4981469 DOI: 10.1371/journal.pone.0160975] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/27/2016] [Indexed: 12/22/2022] Open
Abstract
Several bacterial species from the Burkholderia cepacia complex (Bcc) are feared opportunistic pathogens that lead to debilitating lung infections with a high risk of developing fatal septicemia in cystic fibrosis (CF) patients. However, the pathogenic potential of other Bcc species is yet unknown. To elucidate clinical relevance of Burkholderia contaminans, a species frequently isolated from CF respiratory samples in Ibero-American countries, we aimed to identify its key virulence factors possibly linked with an unfavorable clinical outcome. We performed a genome-wide comparative analysis of two isolates of B. contaminans ST872 from sputum and blood culture of a female CF patient in Argentina. RNA-seq data showed significant changes in expression for quorum sensing-regulated virulence factors and motility and chemotaxis. Furthermore, we detected expression changes in a recently described low-oxygen-activated (lxa) locus which encodes stress-related proteins, and for two clusters responsible for the biosynthesis of antifungal and hemolytic compounds pyrrolnitrin and occidiofungin. Based on phenotypic assays that confirmed changes in motility and in proteolytic, hemolytic and antifungal activities, we were able to distinguish two phenotypes of B. contaminans that coexisted in the host and entered her bloodstream. Whole genome sequencing revealed that the sputum and bloodstream isolates (each representing a distinct phenotype) differed by over 1,400 mutations as a result of a mismatch repair-deficient hypermutable state of the sputum isolate. The inferred lack of purifying selection against nonsynonymous mutations and the high rate of pseudogenization in the derived isolate indicated limited evolutionary pressure during evolution in the nutrient-rich, stable CF sputum environment. The present study is the first to examine the genomic and transcriptomic differences between longitudinal isolates of B. contaminans. Detected activity of a number of putative virulence factors implies a genuine pathogenic nature of this novel Bcc species.
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Affiliation(s)
- Jaroslav Nunvar
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Lucie Kalferstova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Ruhi A. M. Bloodworth
- Department of Medical Microbiology & Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Michal Kolar
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jose Degrossi
- School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
| | - Silvina Lubovich
- Centro Respiratorio Dr. A. Alvarez, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Silvia T. Cardona
- Department of Medical Microbiology & Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Pavel Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
- * E-mail:
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23
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Lewis ERG, Torres AG. The art of persistence-the secrets to Burkholderia chronic infections. Pathog Dis 2016; 74:ftw070. [PMID: 27440810 DOI: 10.1093/femspd/ftw070] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2016] [Indexed: 12/11/2022] Open
Abstract
The Gram-negative proteobacteria genus Burkholderia encompasses multiple bacterial species that are pathogenic to humans and other vertebrates. Two pathogenic species of interest within this genus are Burkholderia pseudomallei (Bpm) and the B. cepacia complex (Bcc); the former is the causative agent of melioidosis in humans and other mammals, and the latter is associated with pneumonia in immunocompromised patients. One understudied and shared characteristic of these two pathogenic groups is their ability to persist and establish chronic infection within the host. In this review, we will explore the depth of knowledge about chronic infections caused by persistent Bpm and Bcc. We examine the host risk factors and immune responses associated with more severe chronic infections. We also discuss host adaptation and phenotypes associated with persistent Burkholderia species. Lastly, we survey how other intracellular bacteria associated with chronic infections are combatted and explore possible future applications to target Burkholderia Our goal is to highlight understudied areas that should be addressed for a more thorough understanding of chronic Burkholderia infections and how to combat them.
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Affiliation(s)
- Eric R G Lewis
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1070, USA
| | - Alfredo G Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1070, USA Department of Pathology, Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX 7555-1070, USA
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24
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Power RF, Linnane B, Martin R, Power N, Harnett P, Casserly B, O'Connell NH, Dunne CP. The first reported case of Burkholderia contaminans in patients with cystic fibrosis in Ireland: from the Sargasso Sea to Irish Children. BMC Pulm Med 2016; 16:57. [PMID: 27103163 PMCID: PMC4840893 DOI: 10.1186/s12890-016-0219-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/12/2016] [Indexed: 12/26/2022] Open
Abstract
Background Burkholderia contaminans is an emerging pathogen in the cystic fibrosis (CF) setting. Included in the Burkholderia cepacia complex (Bcc), B. contaminans is a Gram negative, motile, obligate aerobe previously classified as a pseudomonad. Previous reports have described B. contaminans isolation from patients in Portugal, Switzerland, Spain, Argentina and the USA. This, however, is the first report relating to B. contaminans affecting Irish patients with CF, initially detected in a paediatric setting. Case presentation Burkholderia contaminans was identified in the routine analysis of sputum from a fourteen year old boy, at his annual review and subsequently from the sputum from his 19 year old brother. RecA gene sequencing and pulsed field gel electrophoresis (PFGE) were unable to distinguish between the isolates, which demonstrated with susceptibility to ciprofloxacin, cotrimoxazole, meropenem, pipercillin/tazobactam and ceftazidime. Both isolates were resistant to aztreonam, with reduced susceptibility to tobramycin. Following treatment with intravenous meropenem and ceftazidime, oral ciprofloxacin and nebulised tobramycin for 6 weeks, sputum specimens from both patients were negative for B. contaminans. No other member of the local CF cohort proved positive. Conclusions Bcc bacteria are associated with poor prognosis in CF and decreased life expectancy, specifically leading to a more rapid decline in lung function and, in some cases, to a fatal necrotizing pneumonia known as the “cepacia syndrome”. Some species exhibit innate resistance to multiple antimicrobial agents and their transmission rate can be high in susceptible patients. In that context, we describe the first incidence of CF-related B. contaminans in Ireland and its successful eradication from two patients, one paediatric, using an aggressive antimicrobial regimen.
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Affiliation(s)
- Rachel F Power
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.,University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Barry Linnane
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.,University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Ruth Martin
- University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Noelle Power
- University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Peig Harnett
- University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Brian Casserly
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.,University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Nuala H O'Connell
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.,University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Colum P Dunne
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.
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25
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SNaPBceBcon: a Practical Tool for Identification and Genotyping of Burkholderia cepacia and Burkholderia contaminans. J Clin Microbiol 2015; 54:483-8. [PMID: 26659211 DOI: 10.1128/jcm.02476-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/24/2015] [Indexed: 12/20/2022] Open
Abstract
We propose an optimized protocol for an extensive population analysis of Burkholderia cepacia and Burkholderia contaminans. Seven new polymorphisms were added to the recently proposed SNaPBcen assay, and a total of 18 markers ensured the clear identification and distinction of B. cepacia and B. contaminans isolates and high genotypic discrimination (Simpson index of 0.94) compared to those for multilocus sequence typing.
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26
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Bronchopulmonary infection-colonization patterns in Spanish cystic fibrosis patients: Results from a national multicenter study. J Cyst Fibros 2015; 15:357-65. [PMID: 26429520 DOI: 10.1016/j.jcf.2015.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 02/01/2023]
Abstract
BACKGROUND Clinical and demographical knowledge on Spanish cystic fibrosis (CF) patients is incomplete as no national registry exists. CF-microbiology has not been studied at national level. The results of the first Spanish multicenter study on CF microbiology are presented. METHODS 24 CF-Units for adult (n=12) and pediatric (n=12) patients from 17 hospitals provided sputa and clinical data from 15 consecutive patients. Cultures and susceptibility testing were performed. Colonization impact on pulmonary function was assessed. RESULTS 341 patients [mean (SD) age 21 (11) years, 180≥18years, mean (SD) FEV1=68 (25)%] were included. Pseudomonas aeruginosa was reported as chronic, intermittent or absent in 46%, 22% and 32% of patients, respectively. The annual prevalence was 62%. Positive P. aeruginosa and methicillin-resistant Staphylococcus aureus cultures were significantly associated with lower FEV1 (p<0.001 and p=0.003, respectively). CONCLUSIONS The representative subset of the Spanish CF-population which has been clinically, demographically and microbiologically characterized will serve as a reference for future CF studies in Spain.
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27
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Draft Genome Sequences of Burkholderia contaminans, a Burkholderia cepacia Complex Species That Is Increasingly Recovered from Cystic Fibrosis Patients. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00766-15. [PMID: 26251482 PMCID: PMC4541265 DOI: 10.1128/genomea.00766-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Burkholderia contaminans belongs to the Burkholderia cepacia complex (BCC), a group of bacteria that are ubiquitous in the environment and capable of infecting the immunocompromised and people with cystic fibrosis. We report here draft genome sequences for the B. contaminans type strain LMG 23361 and an Argentinian cystic fibrosis sputum isolate.
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28
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Coutinho CP, Barreto C, Pereira L, Lito L, Melo Cristino J, Sá-Correia I. Incidence of Burkholderia contaminans at a cystic fibrosis centre with an unusually high representation of Burkholderia cepacia during 15 years of epidemiological surveillance. J Med Microbiol 2015; 64:927-935. [DOI: 10.1099/jmm.0.000094] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Carla P. Coutinho
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Celeste Barreto
- Cystic Fibrosis Center, Department of Paediatrics, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Luísa Pereira
- Cystic Fibrosis Center, Department of Paediatrics, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Luís Lito
- Laboratório de Patologia Clínica, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - José Melo Cristino
- Laboratório de Patologia Clínica, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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