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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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Methodological tools to study species of the genus Burkholderia. Appl Microbiol Biotechnol 2021; 105:9019-9034. [PMID: 34755214 PMCID: PMC8578011 DOI: 10.1007/s00253-021-11667-3] [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: 09/13/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022]
Abstract
Bacteria belonging to the Burkholderia genus are extremely versatile and diverse. They can be environmental isolates, opportunistic pathogens in cystic fibrosis, immunocompromised or chronic granulomatous disease patients, or cause disease in healthy people (e.g., Burkholderia pseudomallei) or animals (as in the case of Burkholderia mallei). Since the genus was separated from the Pseudomonas one in the 1990s, the methodological tools to study and characterize these bacteria are evolving fast. Here we reviewed the techniques used in the last few years to update the taxonomy of the genus, to study gene functions and regulations, to deepen the knowledge on the drug resistance which characterizes these bacteria, and to elucidate their mechanisms to establish infections. The availability of these tools significantly impacts the quality of research on Burkholderia and the choice of the most appropriated is fundamental for a precise characterization of the species of interest. Key points • Updated techniques to study the genus Burkholderia were reviewed. • Taxonomy, genomics, assays, and animal models were described. • A comprehensive overview on recent advances in Burkholderia studies was made.
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Su X, Shi Y, Li R, Lu ZN, Zou X, Wu JX, Han ZG. Application of qPCR assays based on haloacids transporter gene dehp2 for discrimination of Burkholderia and Paraburkholderia. BMC Microbiol 2019; 19:36. [PMID: 30744555 PMCID: PMC6371555 DOI: 10.1186/s12866-019-1411-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/31/2019] [Indexed: 12/05/2022] Open
Abstract
Background A major facilitator superfamily transporter Dehp2 was recently shown to be playing an important role in transport and biodegradation of haloacids in Paraburkholderia caribensis MBA4, and Dehp2 is phylogenetically conserved in Burkholderia sensu lato. Results We designed both Burkholderia sensu stricto-specific and Paraburkholderia-specific qPCR assays based on dehp2 and 16S rRNA, and validated the qPCR assays in 12 bacterial strains. The qPCR assays could detect single species of Burkholderia sensu stricto or Paraburkholderia with high sensitivity and discriminate them in mixtures with high specificity over a wide dynamic range of relative concentrations. At relatively lower cost compared with sequencing-based approach, the qPCR assays will facilitate discrimination of Burkholderia sensu stricto and Paraburkholderia in a large number of samples. Conclusions For the first time, we report the utilization of a haloacids transporter gene for discriminative purpose in Burkholderia sensu lato. This enables not only quick decision on proper handling of putative pathogenic samples in Burkholderia sensu stricto group but also future exploitation of relevant species in Paraburkholderia group for haloacids biodegradation purposes. Electronic supplementary material The online version of this article (10.1186/s12866-019-1411-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianbin Su
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ruihong Li
- Shanghai Quality Safety Centre of Agricultural Products, Shanghai, China
| | - Zhao-Ning Lu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiao-Xiang Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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Devanga Ragupathi NK, Veeraraghavan B. Accurate identification and epidemiological characterization of Burkholderia cepacia complex: an update. Ann Clin Microbiol Antimicrob 2019; 18:7. [PMID: 30717798 PMCID: PMC6360774 DOI: 10.1186/s12941-019-0306-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 01/25/2019] [Indexed: 12/16/2022] Open
Abstract
Bacteria belonging to the Burkholderia cepacia complex (Bcc) are among the most important pathogens isolated from cystic fibrosis (CF) patients and in hospital acquired infections (HAI). Accurate identification of Bcc is questionable by conventional biochemical methods. Clonal typing of Burkholderia is also limited due to the problem with identification. Phenotypic identification methods such as VITEK2, protein signature identification methods like VITEK MS, Bruker Biotyper, and molecular targets such as 16S rRNA, recA, hisA and rpsU were reported with varying level of discrimination to identify Bcc. rpsU and/or 16S rRNA sequencing, VITEK2, VITEK MS and Bruker Biotyper could discriminate between Burkholderia spp. and non-Burkholderia spp. Whereas, Bcc complex level identification can be given by VITEK MS, Bruker Biotyper, and 16S rRNA/rpsU/recA/hisA sequencing. For species level identification within Bcc hisA or recA sequencing are reliable. Identification of Bcc is indispensable in CF patients and HAI to ensure appropriate antimicrobial therapy.
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Affiliation(s)
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, 632004, India.
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De Gregorio PR, Michavila G, Ricciardi Muller L, de Souza Borges C, Pomares MF, Saccol de Sá EL, Pereira C, Vincent PA. Beneficial rhizobacteria immobilized in nanofibers for potential application as soybean seed bioinoculants. PLoS One 2017; 12:e0176930. [PMID: 28472087 PMCID: PMC5417607 DOI: 10.1371/journal.pone.0176930] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/19/2017] [Indexed: 11/18/2022] Open
Abstract
Seed inoculation with plant growth promoting rhizobacteria (PGPR) is an ideal tool to supply the soil with a high density of beneficial microorganisms. However, maintaining viable microorganisms is a major problem during seed treatment and storage. In this work, an evaluation was made of the effect of bacterial immobilization in nanofibers on the stability (viability and maintenance of beneficial properties) of two potential PGPR, Pantoea agglomerans ISIB55 and Burkholderia caribensis ISIB40. Moreover, the impact of soybean seed coating with nanofiber-immobilized rhizobacteria on bacterial survival during seed storage and on germination and plant growth parameters was determined. Bacterial nanoimmobilization and subsequent seed coating with nanofiber-immobilized rhizobacteria were carried out by electrospinning. The results demonstrate that this technique successfully immobilized P. agglomerans ISIB55 and B. caribensis ISIB40 because it did not affect the viability or beneficial properties of either rhizobacteria. Seed coating with nanofiber-immobilized rhizobacteria improved P. agglomerans ISIB55 and B. caribensis ISIB40 survival on seeds stored for 30 days and contributed to the successful colonization of both bacteria on the plant root. Moreover, seed coating with P. agglomerans ISIB55 increased germination, length and dry weight of the root. Furthermore, seed coating with B. caribensis ISIB40 increased leaf number and dry weight of the shoot. Therefore, the technique applied in the present work to coat seeds with nanofiber-immobilized PGPR could be considered a promising eco-friendly approach to improve soybean production using a microbial inoculant.
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Affiliation(s)
- Priscilla Romina De Gregorio
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, San Miguel de Tucumán, Tucumán, Argentina
| | - Gabriela Michavila
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, San Miguel de Tucumán, Tucumán, Argentina
| | | | - Clarissa de Souza Borges
- Departamento de Solos, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 7712, Porto Alegre, RS, Brazil
| | - María Fernanda Pomares
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, San Miguel de Tucumán, Tucumán, Argentina
| | - Enilson Luiz Saccol de Sá
- Departamento de Solos, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 7712, Porto Alegre, RS, Brazil
| | - Claudio Pereira
- Tecnano Produtos e Serviços Ltda, Rua Washington Luiz, 675, Porto Alegre, RS, Brazil
| | - Paula Andrea Vincent
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, San Miguel de Tucumán, Tucumán, Argentina
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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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Obersteller S, Neubauer H, Hagen RM, Frickmann H. Comparison of Five Commercial Nucleic Acid Extraction Kits for the PCR-based Detection of Burkholderia Pseudomallei DNA in Formalin-Fixed, Paraffin-Embedded Tissues. Eur J Microbiol Immunol (Bp) 2016; 6:244-252. [PMID: 27766174 PMCID: PMC5063018 DOI: 10.1556/1886.2016.00028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/26/2016] [Indexed: 01/20/2023] Open
Abstract
The extraction and further processing of nucleic acids (NA) from formalin-fixed paraffin-embedded (FFPE) tissues for microbiological diagnostic polymerase chain reaction (PCR) approaches is challenging. Here, we assessed the effects of five different commercially available nucleic acid extraction kits on the results of real-time PCR. FFPE samples from organs of Burkholderia pseudomallei-infected Swiss mice were subjected to processing with five different extraction kits from QIAGEN (FFPE DNA Tissue Kit, EZ1 DNA Tissue Kit, DNA Mini Kit, DNA Blood Mini Kit, and FlexiGene DNA Kit) in combination with three different real-time PCRs targeting B. pseudomallei-specific sequences of varying length after 16 years of storage. The EZ1 DNA Tissue Kit and the DNA Mini Kit scored best regarding the numbers of successful PCR reactions. In case of positive PCR, differences regarding the cycle-threshold (Ct) values were marginal. The impact of the applied extraction kits on the reliability of PCR from FFPE material seems to be low. Interfering factors like the quality of the dewaxing procedure or the sample age appear more important than the selection of specialized FFPE kits.
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Affiliation(s)
| | - Heinrich Neubauer
- Friedrich Loeffler Institute, Federal Research Institute for Animal Health , Jena, Germany
| | - Ralf Matthias Hagen
- NATO Center of Excellence for Military Medicine (MilMedCOE), Deployment Health Surveillance Capability (DHSC) , Munich, Germany
| | - Hagen Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Hamburg, Germany; Institut for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
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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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