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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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Dennehy R, Romano M, Ruggiero A, Mohamed YF, Dignam SL, Mujica Troncoso C, Callaghan M, Valvano MA, Berisio R, McClean S. The Burkholderia cenocepacia peptidoglycan-associated lipoprotein is involved in epithelial cell attachment and elicitation of inflammation. Cell Microbiol 2016; 19. [PMID: 27886433 DOI: 10.1111/cmi.12691] [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] [Received: 06/15/2016] [Revised: 10/18/2016] [Accepted: 11/03/2016] [Indexed: 12/26/2022]
Abstract
The Burkholderia cepacia complex (Bcc) is a group of Gram-negative opportunistic pathogens causing infections in people with cystic fibrosis (CF). Bcc is highly antibiotic resistant, making conventional antibiotic treatment problematic. The identification of novel targets for anti-virulence therapies should improve therapeutic options for infected CF patients. We previously identified that the peptidoglycan-associated lipoprotein (Pal) was immunogenic in Bcc infected CF patients; however, its role in Bcc pathogenesis is unknown. The virulence of a pal deletion mutant (Δpal) in Galleria mellonella was 88-fold reduced (p < .001) compared to wild type. The lipopolysaccharide profiles of wild type and Δpal were identical, indicating no involvement of Pal in O-antigen transport. However, Δpal was more susceptible to polymyxin B. Structural elucidation by X-ray crystallography and calorimetry demonstrated that Pal binds peptidoglycan fragments. Δpal showed a 1.5-fold reduced stimulation of IL-8 in CF epithelial cells relative to wild type (p < .001), demonstrating that Pal is a significant driver of inflammation. The Δpal mutant had reduced binding to CFBE41o- cells, but adhesion of Pal-expressing recombinant E. coli to CFBE41o- cells was enhanced compared to wild-type E. coli (p < .0001), confirming that Pal plays a direct role in host cell attachment. Overall, Bcc Pal mediates host cell attachment and stimulation of cytokine secretion, contributing to Bcc pathogenesis.
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Affiliation(s)
- Ruth Dennehy
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin, Ireland
| | - Maria Romano
- National Research Council, Institute of Biostructures and Bioimaging, Naples, Italy
| | - Alessia Ruggiero
- National Research Council, Institute of Biostructures and Bioimaging, Naples, Italy
| | - Yasmine F Mohamed
- Centre for Experimental Medicine, Queen's University, Belfast, Northern Ireland.,Faculty of Pharmacy, Department of Microbiology, Alexandria University, Alexandria, Egypt
| | - Simon L Dignam
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin, Ireland
| | | | - Máire Callaghan
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin, Ireland
| | - Miguel A Valvano
- Centre for Experimental Medicine, Queen's University, Belfast, Northern Ireland
| | - Rita Berisio
- National Research Council, Institute of Biostructures and Bioimaging, Naples, Italy
| | - Siobhán McClean
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin, Ireland
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Kim HY, Tsai S, Lo SC, Wear DJ, Izadjoo MJ. Production and characterization of chimeric monoclonal antibodies against Burkholderia pseudomallei and B. mallei using the DHFR expression system. PLoS One 2011; 6:e19867. [PMID: 21573027 PMCID: PMC3090420 DOI: 10.1371/journal.pone.0019867] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 04/13/2011] [Indexed: 01/30/2023] Open
Abstract
Burkholderia pseudomallei (BP) and B. mallei (BM) are closely related gram-negative, facultative anaerobic bacteria which cause life-threatening melioidosis in human and glanders in horse, respectively. Our laboratory has previously generated and characterized more than 100 mouse monoclonal antibodies (MAbs) against BP and BM, according to in vitro and in vivo assay. In this study, 3 MAbs (BP7 10B11, BP7 2C6, and BP1 7F7) were selected to develop into chimeric mouse-human monoclonal antibodies (cMAbs) against BP and/or BM. For the stable production of cMAbs, we constructed 4 major different vector systems with a dihydrofolate reductase (DHFR) amplification marker, and optimized transfection/selection conditions in mammalian host cells with the single-gene and/or double-gene expression system. These 3 cMAbs were stably produced by the DHFR double mutant Chinese hamster ovarian (CHO)-DG44 cells. By ELISA and Western blot analysis using whole bacterial antigens treated by heat (65°C/90 min), sodium periodate, and proteinase K, the cMAb BP7 10B11 (cMAb CK1) reacted with glycoproteins (34, 38, 48 kDa in BP; 28, 38, 48 kDa in BM). The cMAb BP7 2C6 (cMAb CK2) recognized surface-capsule antigens with molecular sizes of 38 to 52 kDa, and 200 kDa in BM. The cMAb CK2 was weakly reactive to 14∼28, 200 kDa antigens in BP. The cMAb BP1 7F7 (cMAb CK3) reacted with lipopolysaccharides (38∼52 kDa in BP; 38∼60 kDa in B. thailandensis). Western blot results with the outer surface antigens of the 3 Burkholderia species were consistent with results with the whole Burkholderia cell antigens, suggesting that these immunodominant antigens reacting with the 3 cMAbs were primarily present on the outer surface of the Burkholderia species. These 3 cMAbs would be useful for analyzing the role of the major outer surface antigens in Burkholderia infection.
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Affiliation(s)
- Hyung-Yong Kim
- Department of Environmental and Infectious Disease Sciences, Armed Forces Institute of Pathology and American Registry of Pathology, Washington, D. C., United States of America
| | - Shien Tsai
- Department of Environmental and Infectious Disease Sciences, Armed Forces Institute of Pathology and American Registry of Pathology, Washington, D. C., United States of America
| | - Shyh-Ching Lo
- Division of Cellular and Gene Therapies and Division of Human Tissues, Center for Biologics Evaluation and Research, U. S. Food and Drug Administration (FDA), Bethesda, Maryland, United States of America
| | - Douglas J. Wear
- Department of Environmental and Infectious Disease Sciences, Armed Forces Institute of Pathology and American Registry of Pathology, Washington, D. C., United States of America
| | - Mina J. Izadjoo
- Department of Environmental and Infectious Disease Sciences, Armed Forces Institute of Pathology and American Registry of Pathology, Washington, D. C., United States of America
- * E-mail:
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Induction of immune response to the 17 kDa OMPA Burkholderia cenocepacia polypeptide and protection against pulmonary infection in mice after nasal vaccination with an OMP nanoemulsion-based vaccine. Med Microbiol Immunol 2009; 199:81-92. [PMID: 19967396 DOI: 10.1007/s00430-009-0137-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Indexed: 10/20/2022]
Abstract
Burkholderia cepacia complex (Bcc) are opportunistic bacteria associated with life-threatening illness in persons with cystic fibrosis. Once Bcc colonization is established, these antimicrobial-resistant and biofilm-forming bacteria are difficult to eradicate and are associated with increased rates of morbidity and mortality. At present, no vaccines are available to prevent the Bcc infection. There is currently a paucity of published information regarding the development of vaccines designed to prevent Burkholderia colonization. This work expands on the recent studies published by Bertot et al. [Infect Immun 75(6):2740-2752, 2007], where successful protective immune responses were generated in mice using a B. multivorans OMP-based vaccine. Here, we evaluate an experimental mucosal vaccine against Bcc using a novel mucosal adjuvant (nanoemulsion) and a novel B. cenocepacia-based OMP antigen. The OMP antigen derived from B. cenocepacia was mixed with either nanoemulsion or with PBS and delivered intranasally to CD-1 mice. Serum analysis showed robust IgG and mucosal secretory IgA immune responses in vaccinated versus control mice. The antibodies had cross-neutralizing activity against both B. cenocepacia and B. multivorans species. We found that immunized mice were protected against pulmonary colonization with B. cenocepacia. We have also identified that a 17 kDa OmpA-like protein highly conserved between Burkholderia and Ralstonia species as a new immunodominant epitope in mucosal immunization.
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Mahenthiralingam E, Baldwin A, Dowson C. Burkholderia cepacia complex bacteria: opportunistic pathogens with important natural biology. J Appl Microbiol 2008; 104:1539-51. [DOI: 10.1111/j.1365-2672.2007.03706.x] [Citation(s) in RCA: 290] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Tabacchioni S, Ferri L, Manno G, Mentasti M, Cocchi P, Campana S, Ravenni N, Taccetti G, Dalmastri C, Chiarini L, Bevivino A, Fani R. Use of the gyrB gene to discriminate among species of the Burkholderia cepacia complex. FEMS Microbiol Lett 2008; 281:175-82. [PMID: 18312571 DOI: 10.1111/j.1574-6968.2008.01105.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Bacteria of the Burkholderia cepacia complex (Bcc) are opportunistic pathogens that can cause serious infections in lungs of cystic fibrosis patients. The Bcc comprises at least nine species that have been discriminated by a polyphasic taxonomic approach. In this study, we focused on the gyrB gene, universally distributed among bacteria, as a new target gene to discriminate among the Bcc species. New PCR primers were designed to amplify a gyrB DNA fragment of about 1900 bp from 76 strains representative of all Bcc species. Nucleotide sequences of PCR products were determined and showed more than 400 polymorphic sites with high sequence similarity values from most isolates of the same species. Phylogenetic tree analysis revealed that most of the 76 gyrB sequences grouped, forming clusters, each corresponding to a given Bcc species.
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Affiliation(s)
- Silvia Tabacchioni
- ENEA - CRE - CASACCIA -Department of Biotechnologies, Agroindustry, Protection of Health - Plant genetics and Genomics Section, S. Maria di Galeria, Rome, Italy
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Lavenir R, Jocktane D, Laurent F, Nazaret S, Cournoyer B. Improved reliability of Pseudomonas aeruginosa PCR detection by the use of the species-specific ecfX gene target. J Microbiol Methods 2007; 70:20-9. [PMID: 17490767 DOI: 10.1016/j.mimet.2007.03.008] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 03/14/2007] [Accepted: 03/20/2007] [Indexed: 10/23/2022]
Abstract
Reliability of the most widely used PCR screenings for the human opportunistic pathogen Pseudomonas aeruginosa was evaluated. Specificity analyses showed the gyrB, toxA, and 16S-23S rDNA internal transcribed spacer (ITS) but not the 16S rDNA, oprI, oprL, and fliC PCR screenings to discriminate P. aeruginosa cells from a collection of fifteen Pseudomonas species. Sensitivity analyses showed all these PCR except the toxA one to be reliable for 100% of the P. aeruginosa strains tested in this study. Specificity of the ITS and gyrB PCR screenings were further investigated on 9 soils and 29 freshwater DNA extracts of different origins, and on DNA extracted from 3 horse manures. The ITS PCR showed the highest efficacy on water and soil DNA extracts but only the gyrB one detected P. aeruginosa DNA in horse manure. DNA sequence analyses of ITS and gyrB PCR products revealed uncertainties and false positive results in these P. aeruginosa identification schemes. A novel PCR screening, targeting the ecfX gene, was thus developed. ecfX encodes an ECF (extracytoplasmic function) sigma factor which is restricted to P. aeruginosa, and might play a role in haem-uptake and virulence. Specificity and sensitivity analyses showed the ecfX PCR screening to be highly reliable, giving PCR products of the expected size for all P. aeruginosa strains tested and not amplifying DNA from any of the other Pseudomonas species tested. The ecfX PCR screening was validated on environmental DNA extracts. DNA sequence analyses of the ecfX PCR products confirmed their identity and allocation to P. aeruginosa. These investigations suggest a preferential colonization of water rather than soil environments by P. aeruginosa. Detection limits of P. aeruginosa in environmental samples were improved by the ecfX PCR screening.
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Affiliation(s)
- R Lavenir
- Research group on Bacterial Opportunistic Pathogens and Environment Université de Lyon, Lyon, F-69003, France
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Plesa M, Hernalsteens JP, Vandenbussche G, Ruysschaert JM, Cornelis P. The SlyB outer membrane lipoprotein of Burkholderia multivorans contributes to membrane integrity. Res Microbiol 2006; 157:582-92. [PMID: 16500084 DOI: 10.1016/j.resmic.2005.11.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Revised: 11/22/2005] [Accepted: 11/29/2005] [Indexed: 11/24/2022]
Abstract
SlyB is a small lipoprotein of 158 amino acids which is conserved in different Gram-negative bacteria. In contrast to other bacteria, where slyB is monocistronic, in Burkholderia multivorans and in B. cenocepacia, slyB is the last gene of an operon comprising three open reading frames encoding a putative thiol peroxidase, a putative sugar kinase and SlyB. B. multivorans slyB mutants produced elongated cells and filaments which were never observed in cultures of wild-type or slyB-complemented cells. The slyB mutant also showed increased sensitivity to EDTA and SDS, and decreased siderophore production. Proteome analysis of a fraction enriched for membrane proteins suggested that SlyB, like the peptidoglycan-associated protein OpcL, is a major protein of the outer membrane. Taken together, these phenotypes suggest that SlyB contributes to the integrity of the cell envelope. By PCR amplification we were also able to demonstrate the conservation of slyB in all B. cepacia complex species tested.
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Affiliation(s)
- Maria Plesa
- Flanders Interuniversity Institute of Biotechnology (VIB6), Laboratory of Microbial Interactions, Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Building E, room 6.6, Pleinlaan 2, B-1050 Brussels, Belgium
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Assaad W, Magalhães M, Plesa M, Hart CA, Cornelis P, Winstanley C. Identical Burkholderia cepacia complex strain types isolated from multiple patients attending a hospital in Brazil. J Med Microbiol 2006; 55:247-249. [PMID: 16434721 DOI: 10.1099/jmm.0.46321-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wail Assaad
- Division of Medical Microbiology and Genitourinary Medicine, University of Liverpool, Daulby Street, Liverpool L69 3GA, United Kingdom
| | - Marcelo Magalhães
- Department of Tropical Medicine, Federal University of Pernambuco, Recife, Brazil
| | - Maria Plesa
- Laboratory of Microbial Interactions, Department of Molecular and Cellular Interactions, Flanders Interuniversity Institute of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium
| | - C Anthony Hart
- Division of Medical Microbiology and Genitourinary Medicine, University of Liverpool, Daulby Street, Liverpool L69 3GA, United Kingdom
| | - Pierre Cornelis
- Laboratory of Microbial Interactions, Department of Molecular and Cellular Interactions, Flanders Interuniversity Institute of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Craig Winstanley
- Division of Medical Microbiology and Genitourinary Medicine, University of Liverpool, Daulby Street, Liverpool L69 3GA, United Kingdom
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