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Fan Y, Wang S, Song M, Zhou L, Liu C, Yang Y, Yu S, Yang M. Specific biomarker mining and rapid detection of Burkholderia cepacia complex by recombinase polymerase amplification. Front Microbiol 2023; 14:1270760. [PMID: 37779692 PMCID: PMC10539473 DOI: 10.3389/fmicb.2023.1270760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Objective To mine specific proteins and their protein-coding genes as suitable molecular biomarkers for the Burkholderia cepacia Complex (BCC) bacteria detection based on mega analysis of microbial proteomic and genomic data comparisons and to develop a real-time recombinase polymerase amplification (rt-RPA) assay for rapid isothermal screening for pharmaceutical and personal care products. Methods We constructed an automatic screening framework based on Python to compare the microbial proteomes of 78 BCC strains and 263 non-BCC strains to identify BCC-specific protein sequences. In addition, the specific protein-coding gene and its core DNA sequence were validated in silico with a self-built genome database containing 158 thousand bacteria. The appropriate methodology for BCC detection using rt-RPA was evaluated by 58 strains in pure culture and 33 batches of artificially contaminated pharmaceutical and personal care products. Results We identified the protein SecY and its protein-coding gene secY through the automatic comparison framework. The virtual evaluation of the conserved region of the secY gene showed more than 99.8% specificity from the genome database, and it can distinguish all known BCC species from other bacteria by phylogenetic analysis. Furthermore, the detection limit of the rt-RPA assay targeting the secY gene was 5.6 × 102 CFU of BCC bacteria in pure culture or 1.2 pg of BCC bacteria genomic DNA within 30 min. It was validated to detect <1 CFU/portion of BCC bacteria from artificially contaminated samples after a pre-enrichment process. The relative trueness and sensitivity of the rt-RPA assay were 100% in practice compared to the reference methods. Conclusion The automatic comparison framework for molecular biomarker mining is straightforward, universal, applicable, and efficient. Based on recognizing the BCC-specific protein SecY and its gene, we successfully established the rt-RPA assay for rapid detection in pharmaceutical and personal care products.
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Affiliation(s)
- Yiling Fan
- China State Institute of Pharmaceutical Industry, Shanghai, China
- National Medical Products Administration Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Shujuan Wang
- National Medical Products Administration Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Minghui Song
- National Medical Products Administration Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Liangliang Zhou
- College of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, Jiangxi, China
| | - Chengzhi Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou, China
| | - Yan Yang
- National Medical Products Administration Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Shuijing Yu
- College of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, Jiangxi, China
| | - Meicheng Yang
- China State Institute of Pharmaceutical Industry, Shanghai, China
- Shanghai Food and Drug Packaging Material Control Center, Shanghai, China
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2
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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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3
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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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Jin Y, Zhou J, Zhou J, Hu M, Zhang Q, Kong N, Ren H, Liang L, Yue J. Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status. Biol Direct 2020; 15:6. [PMID: 32131884 PMCID: PMC7057466 DOI: 10.1186/s13062-020-0258-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
Background Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed. Methods We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering. Results We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species. Conclusions This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species. Reviewer This article was reviewed by Dr. Xianwen Ren.
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Affiliation(s)
- Yuan Jin
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jianglin Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jing Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Mingda Hu
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Qi Zhang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Na Kong
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,Anhui University, Hefei, 230039, Anhui, China
| | - Hongguang Ren
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
| | - Long Liang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,Anhui University, Hefei, 230039, Anhui, China.
| | - Junjie Yue
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
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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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Gautam V, Sharma M, Singhal L, Kumar S, Kaur P, Tiwari R, Ray P. MALDI-TOF mass spectrometry: An emerging tool for unequivocal identification of non-fermenting Gram-negative bacilli. Indian J Med Res 2018; 145:665-672. [PMID: 28948958 PMCID: PMC5644302 DOI: 10.4103/ijmr.ijmr_1105_15] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND & OBJECTIVES Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has been instrumental in revolutionizing microbiological identification, especially in high-throughput laboratories. It has enabled the identification of organisms like non-fermenting Gram-negative bacilli (NFGNB), which has been a challenging task using conventional methods alone. In this study an attempt was made to validate MALDI-TOF MS for the identification of clinical isolates of each of the three most common NFGNB, other than Pseudomonas spp., taking molecular methods as the gold standard. METHODS One hundred and fifty clinical isolates of NFGNB, confirmed by molecular methods such as Acinetobacter baumannii[oxa-51 polymerase chain reaction (PCR)], Burkholderia cepacia complex (expanded multilocus sequence typing) and Stenotrophomonas maltophilia (species-specific PCR), were taken. Isolated colonies from fresh cultures of all 150 isolates were smeared onto ground steel plate, with and without formic acid extraction step. The identification was carried out using MALDI-TOF MS Biotyper database. RESULTS A concordance of 100 and 73.33 per cent was found between the molecular techniques and MALDI-TOF MS system in the identification of these isolates up to genus and species levels, respectively. Using a cut-off of 1.9 for reliable identification, rate of species identification rose to 82.66 per cent. Principal component analysis dendrogram and cluster analysis further increased discrimination of isolates. INTERPRETATION & CONCLUSIONS Our findings showed MALDI-TOF MS-based identification of NFGNB as a good, robust method for high-throughput laboratories.
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Affiliation(s)
- Vikas Gautam
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Megha Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Lipika Singhal
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Sunil Kumar
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Parvinder Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Rupinder Tiwari
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Pallab Ray
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
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Bach E, Sant'Anna FH, Magrich Dos Passos JF, Balsanelli E, de Baura VA, Pedrosa FDO, de Souza EM, Passaglia LMP. Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov. Pathog Dis 2018; 75:3934654. [PMID: 28859310 DOI: 10.1093/femspd/ftx076] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/04/2017] [Indexed: 12/31/2022] Open
Abstract
The correct identification of bacteria from the Burkholderia cepacia complex (Bcc) is crucial for epidemiological studies and treatment of cystic fibrosis infections. However, genome-based identification tools are revealing many controversial Bcc species assignments. The aim of this work is to re-examine the taxonomic position of the soil bacterium B. cepacia 89 through polyphasic and genomic approaches. recA and 16S rRNA gene sequence analysis positioned strain 89 inside the Bcc group. However, based on the divergence score of seven concatenated allele sequences, and values of average nucleotide identity, and digital DNA:DNA hybridization, our results suggest that strain 89 is different from other Bcc species formerly described. Thus, we propose to classify Burkholderia sp. 89 as the novel species Burkholderia catarinensis sp. nov. with strain 89T (=DSM 103188T = BR 10601T) as the type strain. Moreover, our results call the attention to some probable misidentifications of Bcc genomes at the National Center for Biotechnology Information database.
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Affiliation(s)
- Evelise Bach
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
| | - Fernando Hayashi Sant'Anna
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
| | | | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Luciane Maria Pereira Passaglia
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
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8
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Chien YC, Liao CH, Sheng WH, Chien JY, Huang YT, Yu CJ, Hsueh PR. Clinical characteristics of bacteraemia caused by Burkholderia cepacia complex species and antimicrobial susceptibility of the isolates in a medical centre in Taiwan. Int J Antimicrob Agents 2017; 51:357-364. [PMID: 28705667 DOI: 10.1016/j.ijantimicag.2017.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/21/2017] [Accepted: 07/01/2017] [Indexed: 01/02/2023]
Abstract
This study investigated the clinical characteristics and outcomes of bacteraemia due to Burkholderia cepacia complex (BCC) species among 54 patients without cystic fibrosis from January 2013 to February 2015. BCC isolates were identified to the species level by the Bruker Biotyper MALDI-TOF MS system and by sequencing analysis of the 16S rRNA and recA genes. Antimicrobial susceptibilities of the isolates were determined by the agar dilution method. Sequencing of the recA gene in the 54 blood isolates revealed 37 (68.5%) isolates of B. cenocepacia, 9 (16.7%) of B. cepacia, 4 (7.4%) of B. multivorans and one isolate each of B. arboris, B. pseudomultivorans, B. seminalis, and B. vietnamiensis. The overall performance of the Bruker Biotyper MALDI-TOF MS system for correctly identifying the 54 BCC isolates to the species level was 79.6%, which was better than that (16.7%) by 16S RNA sequencing analysis. Bacteraemic pneumonia (n = 23, 42.6%) and catheter-related bacteraemia (n = 21, 38.9%) were the most common types of infection. Higher rates of ceftazidime and meropenem resistance were found in B. cepacia isolates (33.3% and 22.2%, respectively) than in isolates of B. cenocepacia (21.6% and 10.8%, respectively) and other species (12.5% and 12.5%, respectively). Overall, the 30-day mortality rate was 38.9% (21/54). Bacteraemia caused by BCC species other than B. cenocepacia and B. cepacia (adjusted odds ratio [aOR] 20.005, P = 0.024) and high SOFA score (aOR 1.412, P = 0.003) were predictive of higher 30-day mortality. Different BCC species are associated with different outcomes of bacteraemia and exhibit different susceptibility patterns.
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Affiliation(s)
- Ying-Chun Chien
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Hsing Liao
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan; Department of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Wang-Huei Sheng
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jung-Yien Chien
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Tsung Huang
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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Edler C, Derschum H, Köhler M, Neubauer H, Frickmann H, Hagen RM. Comparison of Mast Burkholderia Cepacia, Ashdown + Gentamicin, and Burkholderia Pseudomallei Selective Agar for the Selective Growth of Burkholderia Spp. Eur J Microbiol Immunol (Bp) 2017; 7:15-36. [PMID: 28386468 PMCID: PMC5372478 DOI: 10.1556/1886.2016.00037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/05/2016] [Indexed: 01/16/2023] Open
Abstract
Reliable identification of pathogenic Burkholderia spp. like Burkholderia mallei and Burkholderia pseudomallei in clinical samples is desirable. Three different selective media were assessed for reliability and selectivity with various Burkholderia spp. and nontarget organisms. Mast Burkholderia cepacia agar, Ashdown + gentamicin agar, and B. pseudomallei selective agar were compared. A panel of 116 reference strains and well-characterized clinical isolates, comprising 30 B. pseudomallei, 20 B. mallei, 18 other Burkholderia spp., and 48 nontarget organisms, was used for this assessment. While all B. pseudomallei strains grew on all three tested selective agars, the other Burkholderia spp. showed a diverse growth pattern. Nontarget organisms, i.e., nonfermentative rod-shaped bacteria, other species, and yeasts, grew on all selective agars. Colony morphology did not allow unambiguous discrimination. While the assessed selective media reliably allowed the growth of a wide range of B. pseudomallei strains, growth of other Burkholderia spp. is only partially ensured. Growth of various nontarget organisms has to be considered. Therefore, the assessed media can only be used in combination with other confirmative tests in the diagnostic procedure for the screening for melioidosis or glanders.
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Affiliation(s)
- Carola Edler
- Department of Dermatology, German Armed Forces Hospital of Hamburg , Hamburg, Germany
| | - Henri Derschum
- CBRN Defence, Safety and Environmental Protection School, Science Division
| | | | - Heinrich Neubauer
- Friedrich Loeffler Institute, Federal Research Institute for Animal Health , Jena, Germany
| | - Hagen Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Hamburg, Germany; Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Ralf Matthias Hagen
- Department of Preventive Medicine, Bundeswehr Medical Academy , Munich, Germany
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10
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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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11
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Ostermann MF, Neubauer H, Frickmann H, Hagen RM. Correlation of rpsU Gene Sequence Clusters and Biochemical Properties, Gc-Ms Spectra and Resistance Profiles of Clinical Burkholderia Spp. Isolates. Eur J Microbiol Immunol (Bp) 2016; 6:25-39. [PMID: 27141312 PMCID: PMC4838983 DOI: 10.1556/1886.2016.00002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 02/02/2016] [Indexed: 01/23/2023] Open
Abstract
This study assessed the variation of phenotypic features of clinical isolates of Burkholderia spp. from common rpsU gene sequence clusters. A total of 41 clinical Burkholderia spp. isolates from German mucoviscidosis patients was subjected to rpsU gene sequencing. Biochemical assessment included the API systems 20 NE and 50 CHE as well as the Micronaut NF system. Fatty acid patterns were assessed using gas chromatography-mass spectrometry (GC-MS). Broth microdilution was used to identify minimum inhibitory concentrations. Five rpsU gene sequence clusters comprised more than one clinical isolate. Altogether, assignments to three species and seven clusters comprising more than one Burkholderia species were performed. Inhomogeneity of biochemical reactions within the clusters ranged from 0/28 to 45/50 reactions. The standard deviation for fatty acid distributions ranged from 0% to 11.5%. Minimum inhibitory concentrations within the clusters showed a wide variation but only minor differences between the clusters. Broad variations within identified rpsU gene sequence clusters regarding biochemical reactions, fatty acid patterns, and resistance patterns of clinical Burkholderia spp. isolates make the application of rpsU gene sequence analysis as a stand-alone procedure for discriminations within the Burkholderia cepacia complex unreliable.
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Affiliation(s)
| | | | - Hagen Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Germany; Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Germany
| | - Ralf Matthias Hagen
- Deployment Health Surveillance Capability, NATO Center of Excellence for Military Medicine , Munich, Germany
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12
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Melendrez MC, Becraft ED, Wood JM, Olsen MT, Bryant DA, Heidelberg JF, Rusch DB, Cohan FM, Ward DM. Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat. Front Microbiol 2016; 6:1540. [PMID: 26834710 PMCID: PMC4712262 DOI: 10.3389/fmicb.2015.01540] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/21/2015] [Indexed: 12/15/2022] Open
Abstract
Recent studies of bacterial speciation have claimed to support the biological species concept—that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which occurs among closest relatives. However, these previous studies did not attempt to determine whether the more-rapidly recombining close relatives within the clades studied may also have diversified ecologically, without benefit of sexual isolation. Here we have measured the impact of recombination on ecological diversification within and between two ecologically distinct clades (A and B') of Synechococcus in a hot spring microbial mat in Yellowstone National Park, using a cultivation-free, multi-locus approach. Bacterial artificial chromosome (BAC) libraries were constructed from mat samples collected at 60°C and 65°C. Analysis of multiple linked loci near Synechococcus 16S rRNA genes showed little evidence of recombination between the A and B' lineages, but a record of recombination was apparent within each lineage. Recombination and mutation rates within each lineage were of similar magnitude, but recombination had a somewhat greater impact on sequence diversity than mutation, as also seen in many other bacteria and archaea. Despite recombination within the A and B' lineages, there was evidence of ecological diversification within each lineage. The algorithm Ecotype Simulation identified sequence clusters consistent with ecologically distinct populations (ecotypes), and several hypothesized ecotypes were distinct in their habitat associations and in their adaptations to different microenvironments. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal diversification.
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Affiliation(s)
- Melanie C Melendrez
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Eric D Becraft
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Millie T Olsen
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, Pennsylvania State University University Park, PA, USA
| | - John F Heidelberg
- Department of Biological Sciences, College of Letters, Arts and Sciences, University of Southern California Los Angeles, CA, USA
| | - Douglas B Rusch
- Informatics Group, J. Craig Venter Institute Rockville, MD, USA
| | | | - David M Ward
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
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13
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Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Diverse Burkholderia Species Isolated from Soils in the Southern United States with No Evidence of B. pseudomallei. PLoS One 2015; 10:e0143254. [PMID: 26600238 PMCID: PMC4658082 DOI: 10.1371/journal.pone.0143254] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/02/2015] [Indexed: 01/28/2023] Open
Abstract
The global distribution of the soil-dwelling bacterium Burkholderia pseudomallei, causative agent of melioidosis, is poorly understood. We used established culturing methods developed for B. pseudomallei to isolate Burkholderia species from soil collected at 18 sampling sites in three states in the southern United States (Arizona (n = 4), Florida (n = 7), and Louisiana (n = 7)). Using multi-locus sequence typing (MLST) of seven genes, we identified 35 Burkholderia isolates from these soil samples. All species belonged to the B. cepacia complex (Bcc), including B. cenocepacia, B. cepacia, B. contaminans, B. diffusa, B. metallica, B. seminalis, B. vietnamiensis and two unnamed members of the Bcc. The MLST analysis provided a high level of resolution among and within these species. Despite previous clinical cases within the U.S. involving B. pseudomallei and its close phylogenetic relatives, we did not isolate any of these taxa. The Bcc contains a number of opportunistic pathogens that cause infections in cystic fibrosis patients. Interestingly, we found that B. vietnamiensis was present in soil from all three states, suggesting it may be a common component in southern U.S. soils. Most of the Burkholderia isolates collected in this study were from Florida (30/35; 86%), which may be due to the combination of relatively moist, sandy, and acidic soils found there compared to the other two states. We also investigated one MLST gene, recA, for its ability to identify species within Burkholderia. A 365bp fragment of recA recovered nearly the same species-level identification as MLST, thus demonstrating its cost effective utility when conducting environmental surveys for Burkholderia. Although we did not find B. pseudomallei, our findings document that other diverse Burkholderia species are present in soils in the southern United States.
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15
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Nannini EC, Ponessa A, Muratori R, Marchiaro P, Ballerini V, Flynn L, Limansky AS. Polyclonal outbreak of bacteremia caused by Burkholderia cepacia complex and the presumptive role of ultrasound gel. Braz J Infect Dis 2015; 19:543-5. [PMID: 26322722 PMCID: PMC9427536 DOI: 10.1016/j.bjid.2015.06.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/27/2015] [Accepted: 06/30/2015] [Indexed: 12/01/2022] Open
Abstract
A nosocomial polyclonal outbreak associated to bacteremia caused by different Burkholderia cepacia complex (BCC) species and clones is reported. Molecular characterization identified Burkholderia stabilis, Burkholderia contaminans, and Burkholderia ambifaria among BCC isolates obtained from patients in neonatal and adult intensive care units. BCC was also isolated from an intrinsically contaminated ultrasound gel, which constituted the presumptive BCC source. Prior BCC outbreak related to contaminated ultrasound gels have been described in the setting of transrectal prostate biopsy. Outbreak caused strains and/or clones of BCC have been reported, probably because BCC are commonly found in the natural environment; most BCC species are biofilm producers, and different species may contaminate an environmental source. The finding of multiple species or clones during the analysis of nosocomial BCC cases might not be enough to reject an outbreak from a common source.
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Affiliation(s)
- Esteban C Nannini
- Division of Infectious Diseases, Sanatorio Británico, Rosario, Argentina; Division of Infectious Diseases, School of Medicine, Universidad Nacional de Rosario, Rosario, Argentina.
| | - Adriana Ponessa
- Department of Microbiology, Sanatorio Británico, Rosario, Argentina
| | - Rosa Muratori
- Division of Infectious Diseases, Sanatorio Británico, Rosario, Argentina
| | - Patricia Marchiaro
- Instituto de Biología Molecular y Celular de Rosario - CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Viviana Ballerini
- Instituto de Biología Molecular y Celular de Rosario - CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luis Flynn
- Division of Infectious Diseases, Sanatorio Británico, Rosario, Argentina
| | - Adriana S Limansky
- Instituto de Biología Molecular y Celular de Rosario - CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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16
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Wang L, Wang M, Zhang J, Wu W, Lu Y, Fan Y. An outbreak of Burkholderia stabilis colonization in a nasal ward. Int J Infect Dis 2015; 33:71-4. [PMID: 25578264 DOI: 10.1016/j.ijid.2014.12.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 12/05/2014] [Accepted: 12/26/2014] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVE The aim of this study was to describe an outbreak of Burkholderia stabilis colonization among patients in a nasal ward. METHODS Multilocus sequence typing (MLST) was used for the molecular typing of B. stabilis isolates. Microbiological records were reviewed to delineate the colonization outbreak period. One hundred seventy-one cultures of environment and equipment samples from the nasal ward were performed to trace the source of contamination. Infection control measures were taken in order to end the outbreak. RESULTS All B. stabilis isolates were identified as a new MLST type, ST821. A total of 53 patients carried this B. stabilis in the nasal ward between March and September 2013, which was defined as the outbreak period. The source of the colonization was not determined because all environment cultures were negative for Burkholderia cepacia complex. No further B. stabilis carriers have been found in the ward since the implementation of interventions. CONCLUSIONS Attention must be paid to asymptomatic colonization in order to identify outbreaks early.
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Affiliation(s)
- Lijun Wang
- Department of Laboratory Medicine, Beijing Tsinghua Chang Gung Hospital, Medical Center, Tsinghua University, No. 168 Litang Road, Dongxiaokou Town, Changping District, Beijing 102218, China.
| | - Mei Wang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Junyi Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Department of Otolaryngology, Daqing Oilfield General Hospital, Daqing, Heilongjiang Province, China
| | - Wei Wu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yuan Lu
- Department of Laboratory Medicine, Xi'an No. 1 Hospital, Xi'an City, Shanxi Province, China
| | - Yanyan Fan
- Department of Laboratory Medicine, Beijing Tsinghua Chang Gung Hospital, Medical Center, Tsinghua University, No. 168 Litang Road, Dongxiaokou Town, Changping District, Beijing 102218, China
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18
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Frickmann H, Neubauer H, Loderstaedt U, Derschum H, Hagen RM. rpsU-based discrimination within the genus Burkholderia. Eur J Microbiol Immunol (Bp) 2014; 4:106-16. [PMID: 24883196 DOI: 10.1556/eujmi.4.2014.2.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 04/08/2014] [Indexed: 11/19/2022] Open
Abstract
Sequencing of the gene rpsU reliably delineates saprophytic Burkholderia (B.) thailandensis from highly pathogenic B. mallei and B. pseudomallei. We analyzed the suitability of this technique for the delineation of the B. pseudomallei complex from other Burkholderia species. Both newly recorded and previously deposited sequences of well-characterized or reference strains (n = 84) of Azoarcus spp., B. ambifaria, B. anthina, B. caledonica, B. caribensis, B. caryophylli, B. cenocepacia, B. cepacia, B. cocovenenans, B. dolosa, B. fungorum, B. gladioli, B. glathei, B. glumae, B. graminis, B. hospita, B. kururensis, B. mallei, B. multivorans, B. phenazinium, B. phenoliruptrix, B. phymatum, B. phytofirmans, B. plantarii, B. pseudomallei, B. pyrrocinia, B. stabilis, B. thailandensis, B. ubonensis, B. vietnamiensis, B. xenovorans, not further defined Burkholderia spp., and the outliers Cupriavidus metallidurans, Laribacter hongkongensis, Pandorea norimbergensis, and Ralstonia pickettii were included in a multiple sequence analysis. Multiple sequence alignments led to the delineation of four major clusters, rpsU-I to rpsU-IV, with a sequence homology >92%. The B. pseudomallei complex formed the complex rpsU-II. Several Burkholderia species showed 100% sequence homology. This procedure is useful for the molecular confirmation or exclusion of glanders or melioidosis from primary patient material. Further discrimination within the Burkholderia genus requires other molecular approaches.
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19
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Manji R, Bythrow M, Branda JA, Burnham CAD, Ferraro MJ, Garner OB, Jennemann R, Lewinski MA, Mochon AB, Procop GW, Richter SS, Rychert JA, Sercia L, Westblade LF, Ginocchio CC. Multi-center evaluation of the VITEK® MS system for mass spectrometric identification of non-Enterobacteriaceae Gram-negative bacilli. Eur J Clin Microbiol Infect Dis 2013; 33:337-46. [PMID: 24019163 DOI: 10.1007/s10096-013-1961-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/13/2013] [Indexed: 12/17/2022]
Abstract
Studies have demonstrated that matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid, accurate method for the identification of clinically relevant bacteria. The purpose of this study was to evaluate the performance of the VITEK MS v2.0 system (bioMérieux) for the identification of the non-Enterobacteriaceae Gram-negative bacilli (NEGNB). This multi-center study tested 558 unique NEGNB clinical isolates, representing 18 genera and 33 species. Results obtained with the VITEK MS v2.0 were compared with reference 16S rRNA gene sequencing and when indicated recA sequencing and phenotypic analysis. VITEK MS v2.0 provided an identification for 92.5 % of the NEGNB isolates (516 out of 558). VITEK MS v2.0 correctly identified 90.9 % of NEGNB (507 out of 558), 77.8 % to species level and 13.1 % to genus level with multiple species. There were four isolates (0.7 %) incorrectly identified to genus level and five isolates (0.9 %), with one incorrect identification to species level. The remaining 42 isolates (7.5 %) were either reported as no identification (5.0 %) or called "mixed genera" (2.5 %) since two or more different genera were identified as possible identifications for the test organism. These findings demonstrate that the VITEK MS v2.0 system provides accurate results for the identification of a challenging and diverse group of Gram-negative bacteria.
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Affiliation(s)
- R Manji
- Department of Pathology and Laboratory Medicine, North Shore-LIJ Health System Laboratories, 10 Nevada Drive, Lake Success, NY, 11042, USA
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Bevivino A, Costa B, Cantale C, Cesarini S, Chiarini L, Tabacchioni S, Caballero-Mellado J, Dalmastri C. Genetic relationships among Italian and Mexican maize-rhizosphere Burkholderia cepacia complex (BCC) populations belonging to Burkholderia cenocepacia IIIB and BCC6 group. BMC Microbiol 2011; 11:228. [PMID: 21995705 PMCID: PMC3377929 DOI: 10.1186/1471-2180-11-228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 10/13/2011] [Indexed: 11/25/2022] Open
Abstract
Background A close association between maize roots and Burkholderia cepacia complex (BCC) bacteria has been observed in different locations globally. In this study we investigated by MultiLocus Restriction Typing (MLRT) the genetic diversity and relationships among Burkholderia cenocepacia IIIB and BCC6 populations associated with roots of maize plants cultivated in geographically distant countries (Italy and Mexico), in order to provide new insights into their population structure, evolution and ecology. Results The 31 B. cenocepacia IIIB and 65 BCC6 isolates gave rise to 29 and 39 different restriction types (RTs), respectively. Two pairs of isolates of B. cenocepacia IIIB and BCC6, recovered from both Italian and Mexican maize rhizospheres, were found to share the same RT. The eBURST (Based Upon Related Sequence Types) analysis of MLRT data grouped all the B. cenocepacia IIIB isolates into four clonal complexes, with the RT-4-complex including the 42% of them, while the majority of the BCC6 isolates (94%) were grouped into the RT-104-complex. These two main clonal complexes included RTs shared by both Italian and Mexican maize rhizospheres and a clear relationship between grouping and maize variety was also found. Grouping established by eBURST correlated well with the assessment using unweighted-pair group method with arithmetic mean (UPGMA). The standardized index of association values obtained in both B. cenocepacia IIIB and BCC6 suggests an epidemic population structure in which occasional clones emerge and spread. Conclusions Taken together our data demonstrate a wide dispersal of certain B. cenocepacia IIIB and BCC6 isolates in Mexican and Italian maize rhizospheres. Despite the clear relationship found between the geographic origin of isolates and grouping, identical RTs and closely related isolates were observed in geographically distant regions. Ecological factors and selective pressure may preferably promote some genotypes within each local microbial population, favouring the spread of a single clone above the rest of the recombinant population.
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Affiliation(s)
- Annamaria Bevivino
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Development) Casaccia Research Center-Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Via Anguillarese 301, 00123 S, Maria di Galeria, Rome, Italy.
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Bittar F, Rolain JM. Detection and accurate identification of new or emerging bacteria in cystic fibrosis patients. Clin Microbiol Infect 2011; 16:809-20. [PMID: 20880410 DOI: 10.1111/j.1469-0691.2010.03236.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Respiratory infections remain a major threat to cystic fibrosis (CF) patients. The detection and correct identification of the bacteria implicated in these infections is critical for the therapeutic management of patients. The traditional methods of culture and phenotypic identification of bacteria lack both sensitivity and specificity because many bacteria can be missed and/or misidentified. Molecular analyses have recently emerged as useful means to resolve these problems, including molecular methods for accurate identification or detection of bacteria and molecular methods for evaluation of microbial diversity. These recent molecular technologies have increased the list of new and/or emerging pathogens and epidemic strains associated with CF patients. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of intact cells has also emerged recently as a powerful and rapid method for the routine identification of bacteria in clinical microbiology laboratories and will certainly represent the method of choice also for the routine identification of bacteria in the context of CF. Finally, recent data derived from molecular culture-independent analyses indicate the presence of a previously underestimated, complex microbial community in sputa from CF patients. Interestingly, full genome sequencing of some bacteria frequently recovered from CF patients has highlighted the fact that the lungs of CF patients are hotspots for lateral gene transfer and the adaptation of these ecosystems to a specific chronic condition.
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Affiliation(s)
- F Bittar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille Cedex 05, France
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Diversity of Burkholderia cepacia complex from the Moso bamboo (Phyllostachys edulis) rhizhosphere soil. Curr Microbiol 2010; 62:650-8. [PMID: 20882285 DOI: 10.1007/s00284-010-9758-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 09/02/2010] [Indexed: 01/08/2023]
Abstract
The purpose of this study was to determine the existence of Burkholderia cepacia complex (Bcc) at species level and the predominant species in the environment of moso bamboo plantations in Hangzhou, China. A total of 423 isolates were recovered from moso bamboo rhizhosphere soil samples of three sites on the selective medium during 2007-2008. Isolates were identified by Bcc-specific PCR assays, followed by recA-restriction fragment length polymorphism assays, species-specific PCR analysis, recA gene sequencing, multilocus sequence typing (MLST) scheme, and BOX-PCR fingerprinting for genomic diversity. Out of 423 isolates, 278 isolates were assigned to the following Bcc species, eight B. stabilis, 26 B. anthina, 193 B. pyrrocinia, and 51 B. arboris, which indicated B. pyrrocinia as the most dominant species followed by B. arboris. Moreover, false positives were observed in certain isolates of B. arboris while performing species-specific PCR test. Furthermore, the results of recA gene sequence similarity and MLST data demonstrated that nine isolates formed a single discrete cluster but were PCR negative to species-specific primers representing novel species may exist within the Bcc. In addition, BOX-PCR fingerprinting for all the Bcc isolates also showed the strain diversity. It is the first report of the existence of B. arboris and predominance of B. pyrrocinia in the moso bamboo environment.
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An outbreak of Burkholderia cenocepacia bacteremia in immunocompromised oncology patients. Infection 2010; 38:187-94. [DOI: 10.1007/s15010-010-0017-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 02/17/2010] [Indexed: 10/19/2022]
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Direct culture-independent Strain typing of Burkholderia cepacia complex in sputum samples from patients with cystic fibrosis. J Clin Microbiol 2010; 48:1888-91. [PMID: 20181898 DOI: 10.1128/jcm.02359-09] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined if multilocus sequence typing (MLST), a method for genotyping and species identification of Burkholderia cepacia complex bacteria, could be applied directly to cystic fibrosis sputum. The redesigned nested-PCR MLST format was successfully used to accurately identify strains in 23 sputum samples, of which 8 were culture negative.
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