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Volpato FCZ, Lovison OVA, de Lima-Morales D, Martins AF, Maróstica PJC, Barth AL. Can the data of microbiome be used to predict the presence of Burkholderia spp in pulmonary microbiota of cystic fibrosis patients? Braz J Infect Dis 2023; 27:102777. [PMID: 37150211 DOI: 10.1016/j.bjid.2023.102777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/22/2023] [Indexed: 05/09/2023] Open
Affiliation(s)
- Fabiana Caroline Zempulski Volpato
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil; Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, RS, Brazil.
| | - Otávio von Ameln Lovison
- Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Farmacêuticas, Porto Alegre, RS, Brazil; Hospital de Clínicas de Porto Alegre, Bioinformatics Core, Porto Alegre, RS, Brazil
| | - Daiana de Lima-Morales
- Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, RS, Brazil
| | - Andreza Francisco Martins
- Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Farmacêuticas, Porto Alegre, RS, Brazil; Hospital de Clínicas de Porto Alegre, Bioinformatics Core, Porto Alegre, RS, Brazil
| | - Paulo José Cauduro Maróstica
- Universidade Federal do Rio Grande do Sul, Programa de Pós-graduação em Saúde da Criança e do Adolescente, Porto Alegre, RS, Brazil
| | - Afonso Luís Barth
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil; Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Farmacêuticas, Porto Alegre, RS, Brazil
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Epidemiology of Burkholderia Infections in People with Cystic Fibrosis in Canada between 2000 and 2017. Ann Am Thorac Soc 2021; 17:1549-1557. [PMID: 32946281 DOI: 10.1513/annalsats.201906-443oc] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Rationale: Infections by Burkholderia species bacteria in cystic fibrosis (CF) may be transmissible, necessitating infection control measures, and remain a serious cause of morbidity and mortality. The last major study of Burkholderia epidemiology in Canada included cases up until July 2000 and was marked by the dominance of a limited number of epidemic clones of Burkholderia cenocepacia.Objectives: Describe the nationwide epidemiology of Burkholderia species infections in people with cystic fibrosis in Canada over the 17-year period since 2000.Methods: Isolates were collected from across Canada between August 2000 and July 2017 and identified to the species and, for isolates between 2015 and 2017, strain level.Results: We analyzed 1,362 Burkholderia isolates from at least 396 people with CF. Forty-nine percent (n = 666) of all isolates and 47% (n = 179) of new incident infections were identified as B. multivorans. The incidence of Burkholderia infection in the Canadian CF population did not change between 2000 and 2017 at 6 cases per 1,000 annually. Multilocus sequence typing analysis suggested minimal sharing of clones in Canada.Conclusions: The epidemiology of Burkholderia in CF in Canada has shifted from limited numbers of epidemic strains of B. cenocepacia to largely nonclonal isolates of B. multivorans, B. cenocepacia, and other species. Despite widespread infection control, however, Burkholderia species bacteria continue to be acquired by people with CF at an unchanged rate, posing a continued hazard.
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Presence of the Hmq System and Production of 4-Hydroxy-3-Methyl-2-Alkylquinolines Are Heterogeneously Distributed between Burkholderia cepacia Complex Species and More Prevalent among Environmental than Clinical Isolates. Microbiol Spectr 2021; 9:e0012721. [PMID: 34132614 PMCID: PMC8552760 DOI: 10.1128/spectrum.00127-21] [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] [Indexed: 12/23/2022] Open
Abstract
The Burkholderia cepacia complex (Bcc) comprises several species of closely related, versatile bacteria. Some Bcc strains produce 4-hydroxy-3-methyl-2-alkylquinolines (HMAQs), analogous to the 4-hydroxy-2-alkylquinolines of Pseudomonas aeruginosa. Using in silico analyses, we previously estimated that the hmqABCDEFG operon, which encodes enzymes involved in the biosynthesis of HMAQs, is carried by about one-third of Bcc strains, with considerable inter- and intraspecies variability. In the present study, we investigated by PCR, using consensus primers, the distribution of hmqABCDEFG in a collection of 312 Bcc strains (222 of clinical and 90 of environmental origins) belonging to 18 Bcc species. We confirmed that this operon is not distributed evenly among Bcc species. Among the 30% of strains bearing the hmqABCDEFG operon, we found that 92% of environmental isolates and 82% of clinically isolated Bcc strains produce levels of HMAQs detectable by liquid chromatography-mass spectrometry in at least one of the tested culture conditions. Among the hmqABCDEFG-positive but HMAQ-negative strains, none expressed the hmqA gene under the specified culture conditions. Interestingly, the hmqABCDEFG operon is more prevalent among plant root environment species (e.g., Burkholderia ambifaria and Burkholderia cepacia) and absent in species commonly found in chronically colonized individuals with cystic fibrosis (e.g., Burkholderia cenocepacia and Burkholderia multivorans), suggesting a role for the Hmq system in niche adaptation. We investigated the impact of the Hmq system on plant growth promotion and found that Pisum sativum root development by B. ambifaria required a functional HMAQ system. IMPORTANCE Environmental bacteria belonging to the various closely related species forming the Burkholderia cepacia complex (Bcc) can infect plants and animals, including humans. Their pathogenicity is regulated by intercellular communication, or quorum sensing, allowing them to collaborate instead of acting individually. Bcc organisms generally exploit interacting quorum sensing systems based on N-acyl-homoserine lactones as signaling molecules. Several Bcc strains also carry an hmqABCDEFG operon responsible for the biosynthesis of 4-hydroxy-3-methyl-2-alkylquinolines (HMAQs), molecules analogous to the Pseudomonas quinolone signal (PQS) system of P. aeruginosa. Our finding that the prevalences of the Hmq system and HMAQ production are very different between various Bcc species suggests a key role in niche adaptation or pathogenicity. This is supported by a significant reduction in plant growth promotion in the absence of HMAQ production for a beneficial Bcc strain.
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De Volder AL, Teves S, Isasmendi A, Pinheiro JL, Ibarra L, Breglia N, Herrera T, Vazquez M, Hernandez C, Degrossi J. Distribution of Burkholderia cepacia complex species isolated from industrial processes and contaminated products in Argentina. Int Microbiol 2020; 24:157-167. [PMID: 33184776 DOI: 10.1007/s10123-020-00151-z] [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: 04/21/2020] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 01/03/2023]
Abstract
Burkholderia cepacia complex (Bcc) members have clinical relevance as opportunistic pathogens in patients with cystic fibrosis and are responsible of numerous nosocomial infections. These closely related bacteria are also reported as frequent contaminants of industrial products. In this retrospective study, we use PCR and recA gene sequence analysis to identify at species level Bcc isolates recovered from massive consumption products and industrial processes in Argentina during the last 25 years. The sequences obtained were also compared with recA sequences from clinical Bcc isolates deposited in GenBank database. We detected Bcc in purified water and preserved products from pharmaceutics, cosmetics, household cleaning articles, and beverages industries. B. contaminans (which is prevalent among people with cystic fibrosis in Argentina) was the most frequent Bcc species identified (42% of the Bcc isolates studied). B. cepacia (10%), B. cenocepacia (5%), B. vietnamiensis (16%), B. arboris (3%), and the recently defined B. aenigmatica (24%) were also detected. Rec A sequences from all B. cepacia and most B. contaminans industrial isolates obtained in this study displayed 100% identity with recA sequences from isolates infecting Argentinean patients. This information brings evidence for considering industrial massive consumption products as a potential source of Bcc infections. In addition, identification at species level in industrial microbiological laboratories is necessary for a better epidemiological surveillance. Particularly in Argentina, more studies are required in order to reveal the role of these products in the acquisition of B. contaminans infections.
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Affiliation(s)
- A López De Volder
- Cátedra de Microbiología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - S Teves
- Cátedra de Microbiología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - A Isasmendi
- Servicio de Microbiología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - J L Pinheiro
- Servicio de Microbiología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - L Ibarra
- Servicio de Bacteriología Clínica, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - N Breglia
- Cátedra de Microbiología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - T Herrera
- Facultad de Ciencias Exactas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M Vazquez
- Servicio de Bacteriología Clínica, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - C Hernandez
- Servicio de Microbiología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - José Degrossi
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina. .,Cátedra de Salud Pública e Higiene Ambiental, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4° Floor, Ciudad Autónoma de Buenos Aires, Argentina.
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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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Burkholderia cepacia complex: 11 years of surveillance in patients with Cystic Fibrosis in Posadas, Argentina. Rev Argent Microbiol 2020; 52:176-182. [DOI: 10.1016/j.ram.2019.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/20/2019] [Accepted: 08/27/2019] [Indexed: 11/23/2022] Open
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Cipolla L, Rocca F, Armitano RI, Martinez C, Almuzara M, Faccone D, Vay C, Prieto M. [Development and evaluation of an in-house database for quick identification of Burkholderia contaminans by MALDI-TOF MS]. Rev Argent Microbiol 2018; 51:255-258. [PMID: 30558855 DOI: 10.1016/j.ram.2018.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/24/2018] [Accepted: 09/29/2018] [Indexed: 12/30/2022] Open
Abstract
MALDI-TOF (matrix assisted laser desorption ionization-time of flight) mass spectrometry (MS) proved to be a robust tool for the identification of numerous taxonomic groups. However, it has limitations. A key advantage of this technique is the flexibility for the incorporation of protein profiles of microorganisms not included in the commercial database. Due to the prevalence of Burkholderia contaminans in fibrocystic patients in Argentina and the fact that rapid and reliable microbiological diagnosis is crucial in them, MALDI-TOF MS emerges as a strategic tool. The aim of this work was to develop an additional database with peptide spectra of reference isolates of B. contaminans. This database demonstrated to be successful for the identification of 97% of the isolates analyzed. Therefore, MALDI-TOF MS with the extended database was a useful tool for the identification and differentiation of other related species to B. contaminans.
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Affiliation(s)
- Lucía Cipolla
- Servicio de Bacteriología Especial, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina.
| | - Florencia Rocca
- Servicio de Bacteriología Especial, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
| | - Rita I Armitano
- Servicio de Bacteriología Especial, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
| | - Claudia Martinez
- Servicio de Bacteriología Especial, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
| | - Marisa Almuzara
- Laboratorio de Bacteriología, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Diego Faccone
- Servicio de Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
| | - Carlos Vay
- Laboratorio de Bacteriología, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mónica Prieto
- Servicio de Bacteriología Especial, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
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de los Santos-Villalobos S, Kremer JM, Parra-Cota FI, Hayano-Kanashiro AC, García-Ortega LF, Gunturu SK, Tiedje JM, He SY, Peña-Cabriales JJ. Draft genome of the fungicidal biological control agent Burkholderia anthina strain XXVI. Arch Microbiol 2018; 200:803-810. [DOI: 10.1007/s00203-018-1490-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 01/12/2023]
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