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Fadiji AE, Babalola OO. Metagenomics methods for the study of plant-associated microbial communities: A review. J Microbiol Methods 2020; 170:105860. [PMID: 32027927 DOI: 10.1016/j.mimet.2020.105860] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 12/20/2022]
Abstract
Plant microbiota have different effects on the plant which can be beneficial or pathogenic. In this study, we concentrated on beneficial microbes associated with plants using endophytic microbes as a case study. Detailed knowledge of the microbial diversity, abundance, composition, functional genes patterns, and metabolic pathways at genome level could assist in understanding the contributions of microbial community towards plant growth and health. Recently, the study of microbial community has improved greatly with the discovery of next-generation sequencing and bioinformatics technologies. Analysis of next generation sequencing data and a proper computational method plays a key role in examining microbial metagenome. This review presents the general metagenomics and computational methods used in processing plant associated metagenomes with concentration on endophytes. This includes 1) introduction of plant-associated microbiota and the factors driving their diversity. 2) plant metagenome focusing on DNA extraction, verification and quality control. 3) metagenomics methods used in community analysis of endophytes focusing on maize plant and, 4) computational methods used in the study of endophytic microbiomes. Limitations and future prospects of metagenomics and computational methods for the analysis of plant-associated metagenome (endophytic metagenome) were also discussed with the aim of fostering its development. We conclude that there is need to adopt advanced genomic features such as k-mers of random size, which do not depend on annotation and can represent other sequence alternatives.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa.
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Ondreičková K, Mihálik D, Ficek A, Hudcovicová M, Kraic J, Drahovská H. Impact of Genetically Modified Maize on the Genetic Diversity of Rhizosphere Bacteria: a Two-Year Study in Slovakia. POLISH JOURNAL OF ECOLOGY 2014. [DOI: 10.3161/104.062.0107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Damir K, Irena VS, Damir V, Emin T. Occurrence, characterization and antimicrobial susceptibility of Vibrio alginolyticus in the Eastern Adriatic Sea. MARINE POLLUTION BULLETIN 2013; 75:46-52. [PMID: 24012112 DOI: 10.1016/j.marpolbul.2013.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 06/02/2023]
Abstract
In 2007-2008, 162 samples (72 marine water samples, 90 swabs from the gills and skin) were collected from three European seabass fish farms in Eastern Adriatic. The aim of study was to determine the occurrence of Vibrio, to identify the isolated strains and to investigate their antimicrobial resistance. The comparison of the results obtained in spring and autumn periods indicated a higher Vibrio concentration in spring samplings. The greatest prevalence of Vibrio alginolyticus was on gills than on skin, whereas statistically significant differences were obtained between sampling periods with maximal prevalence in spring. Vibrio isolates from the marine water and from swabs of European seabass were analysed by DNA sequencing of partial 16S rDNA and gyrB genes and identified as V. alginolyticus. Isolates were highly susceptible to flumequine, chloramphenicol and oxytetracycline.
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Affiliation(s)
- Kapetanović Damir
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Aquaculture and Pathology of Aquatic Organisms, Zagreb, Croatia.
| | - Vardić Smrzlić Irena
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Aquaculture and Pathology of Aquatic Organisms, Zagreb, Croatia
| | - Valić Damir
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Aquaculture and Pathology of Aquatic Organisms, Zagreb, Croatia
| | - Teskeredžić Emin
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Aquaculture and Pathology of Aquatic Organisms, Zagreb, Croatia
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Ding T, Palmer MW, Melcher U. Community terminal restriction fragment length polymorphisms reveal insights into the diversity and dynamics of leaf endophytic bacteria. BMC Microbiol 2013; 13:1. [PMID: 23286760 PMCID: PMC3546043 DOI: 10.1186/1471-2180-13-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 12/20/2012] [Indexed: 12/02/2022] Open
Abstract
Background Plant endophytic bacteria play an important role benefiting plant growth or being pathogenic to plants or organisms that consume those plants. Multiple species of bacteria have been found co-inhabiting plants, both cultivated and wild, with viruses and fungi. For these reasons, a general understanding of plant endophytic microbial communities and their diversity is necessary. A key issue is how the distributions of these bacteria vary with location, with plant species, with individual plants and with plant growing season. Results Five common plant species were collected monthly for four months in the summer of 2010, with replicates from four different sampling sites in the Tallgrass Prairie Preserve in Osage County, Oklahoma, USA. Metagenomic DNA was extracted from ground, washed plant leaf samples, and fragments of the bacterial 16S rDNA genes were amplified for analysis of terminal restriction fragment length polymorphism (T-RFLP). We performed mono-digestion T-RFLP with restriction endonuclease DdeI, to reveal the structures of leaf endophytic bacterial communities, to identify the differences between plant-associated bacterial communities in different plant species or environments, and to explore factors affecting the bacterial distribution. We tested the impacts of three major factors on the leaf endophytic bacterial communities, including host plant species, sampling dates and sampling locations. Conclusions Results indicated that all of the three factors were significantly related (α = 0.05) to the distribution of leaf endophytic bacteria, with host species being the most important, followed by sampling dates and sampling locations.
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Affiliation(s)
- Tao Ding
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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Veselá AB, Pelantová H, Sulc M, Macková M, Lovecká P, Thimová M, Pasquarelli F, Pičmanová M, Pátek M, Bhalla TC, Martínková L. Biotransformation of benzonitrile herbicides via the nitrile hydratase-amidase pathway in rhodococci. J Ind Microbiol Biotechnol 2012; 39:1811-9. [PMID: 22922990 DOI: 10.1007/s10295-012-1184-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 07/31/2012] [Indexed: 10/28/2022]
Abstract
The aim of this work was to determine the ability of rhodococci to transform 3,5-dichloro-4-hydroxybenzonitrile (chloroxynil), 3,5-dibromo-4-hydroxybenzonitrile (bromoxynil), 3,5-diiodo-4-hydroxybenzonitrile (ioxynil) and 2,6-dichlorobenzonitrile (dichlobenil); to identify the products and determine their acute toxicities. Rhodococcus erythropolis A4 and Rhodococcus rhodochrous PA-34 converted benzonitrile herbicides into amides, but only the former strain was able to hydrolyze 2,6-dichlorobenzamide into 2,6-dichlorobenzoic acid, and produced also more of the carboxylic acids from the other herbicides compared to strain PA-34. Transformation of nitriles into amides decreased acute toxicities for chloroxynil and dichlobenil, but increased them for bromoxynil and ioxynil. The amides inhibited root growth in Lactuca sativa less than the nitriles but more than the acids. The conversion of the nitrile group may be the first step in the mineralization of benzonitrile herbicides but cannot be itself considered to be a detoxification.
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Affiliation(s)
- Alicja B Veselá
- Institute of Microbiology of the Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
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Elliott GN, Thomas N, Macrae M, Campbell CD, Ogden ID, Singh BK. Multiplex T-RFLP allows for increased target number and specificity: detection of Salmonella enterica and six species of Listeria in a single test. PLoS One 2012; 7:e43672. [PMID: 22937073 PMCID: PMC3427147 DOI: 10.1371/journal.pone.0043672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/24/2012] [Indexed: 01/14/2023] Open
Abstract
A multiplex T-RFLP test was developed to detect and identify Salmonella enterica and all six species of Listeria inoculated into milk at minimal levels. Extensive in silico analysis was used to design a fifteen-primer, six-amplimer methodology and in vitro application showed target organism DNA, when amplified individually, yielded the predicted terminal restriction fragments (TRFs) following digestion. Non-target organisms were either not-amplified or yielded TRFs which did not interfere with target identification. Multiple target DNA analysis gave over 86% detection of total TRFs predicted, and this was improved to over 90% detection of total TRFs predicted when only two target DNA extracts were combined analysed. Co-inoculation of milk with five strains each of the target species of S. enterica and L. monocytogenes, along with five strains of the non-target species E. coli was followed by enrichment in SEL medium for M-TRFLP analysis. This allowed for detection of both target species in all samples, with detection of one S. enterica and two Listeria TRFs in all cases, and detection of a second S. enterica TRF in 91% of cases. This was from an initial inoculum of <5 cfu per 25 ml milk with a background of competing E. coli present, and gave a result from sampling of under 20 hours. The ability to increase target species number without loss of sensitivity means that extensive screening can be performed at reduced cost due to a reduction in the number of tests required.
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Camarinha-Silva A, Wos-Oxley ML, Jáuregui R, Becker K, Pieper DH. Validating T-RFLP as a sensitive and high-throughput approach to assess bacterial diversity patterns in human anterior nares. FEMS Microbiol Ecol 2012; 79:98-108. [PMID: 22066869 DOI: 10.1111/j.1574-6941.2011.01197.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
While recent works aimed to thoroughly characterize the bacterial community of the human anterior nares of a few candidates, this work sought to analyse a greater cross-section by sampling 100 volunteers. After optimizing and validating the method of terminal restriction fragment length polymorphism against six previously pyrosequenced samples, abundant species could be discriminated and their relative abundances measured in a high-throughput manner. The 100 volunteers could be statistically clustered into 12 groups, where two-thirds of volunteers shared more than 40% similarity in respect to their bacterial community structure, while the remaining third clustered into smaller groups being dominated by Dolosigranulum pigrum, Moraxella spp. or Staphylococcus aureus. Moraxella spp. was present predominantly in women rather than in men. The use of network analysis charting bacterial ecological co-occurrences revealed new evidence of likely positive associations between some core human nasal species. So, in the age of post 'omics' and 'deep sequencing', there is still a place for these well-tried and well-tested methods that can offer a rapid, reproducible and economical alternative, whereby also yielding valuable new information.
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Affiliation(s)
- Amélia Camarinha-Silva
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Lactococcus lactis expressing food-grade β-galactosidase alleviates lactose intolerance symptoms in post-weaning Balb/c mice. Appl Microbiol Biotechnol 2012; 96:1499-506. [DOI: 10.1007/s00253-012-3977-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 01/26/2012] [Accepted: 02/15/2012] [Indexed: 11/24/2022]
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9
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Shoemaker CA, LaFrentz BR, Klesius PH. Vaccination of sex reversed hybrid tilapia (Oreochromis niloticus × O. aureus) with an inactivated Vibrio vulnificus vaccine. Biologicals 2011; 39:424-9. [DOI: 10.1016/j.biologicals.2011.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/18/2011] [Accepted: 08/11/2011] [Indexed: 12/20/2022] Open
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Montagner F, Gomes BP, Kumar PS. Molecular Fingerprinting Reveals the Presence of Unique Communities Associated with Paired Samples of Root Canals and Acute Apical Abscesses. J Endod 2010; 36:1475-9. [DOI: 10.1016/j.joen.2010.06.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 06/20/2010] [Accepted: 06/22/2010] [Indexed: 02/06/2023]
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Davidson SK, Powell RJ, Stahl DA. Transmission of a bacterial consortium in Eisenia fetida egg capsules. Environ Microbiol 2010; 12:2277-88. [PMID: 21966919 DOI: 10.1111/j.1462-2920.2010.02231.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The earthworm Eisenia fetida harbours Verminephrobacter eiseniae within their excretory nephridia. This symbiont is transferred from the parent into the egg capsules where the cells are acquired by the developing earthworm in a series of recruitment steps. Previous studies defined V. eiseniae as the most abundant cell type in the egg capsules, leaving approximately 30% of the bacteria unidentified and of unknown origin. The study presented here used terminal restriction fragment length polymorphism analysis together with cloning and sequencing of 16S rRNA genes to define the composition of the bacterial consortium in E. fetida egg capsules from early to late development. Newly formed capsules of E. fetida contained three bacterial types, a novel Microbacteriaceae member, a Flexibacteriaceae member and the previously described V. eiseniae. Fluorescent in situ hybridization (FISH) using specific and general rRNA probes demonstrated that the bacteria are abundant during early development, colonize the embryo and appear in the adult nephridia. As the capsules mature, Herbaspirillum spp. become abundant although they were not detected within the adult worm. These divergent taxa could serve distinct functions in both the adult earthworm and in the egg capsule to influence the competitive ability of earthworms within the soil community.
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Affiliation(s)
- Seana K Davidson
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195-5014, USA.
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Lord NS, Kaplan CW, Shank P, Kitts CL, Elrod SL. Assessment of fungal diversity using terminal restriction fragment (TRF) pattern analysis: comparison of 18S and ITS ribosomal regions. FEMS Microbiol Ecol 2009; 42:327-37. [PMID: 19709292 DOI: 10.1111/j.1574-6941.2002.tb01022.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Assessment of fungal diversity in environmental samples is currently a challenge. Several recently developed molecular methods offer new avenues for determining the presence and diversity of fungi in complex microbial communities. Terminal restriction fragment (TRF) pattern analysis was tested as a method for assessing the fungal molecular diversity of a terrestrial microbial community. Community DNA was isolated from sand samples taken from a pilot-scale petroleum-contaminated land treatment unit. PCR amplification was carried out using primers, one of which was fluorescently labeled, designed to hybridize to conserved sequences in the fungal ribosomal small subunit (18S) or the internal transcribed spacer ITS1-5.8S-ITS2 (ITS) ribosomal region. Amplicons were then digested separately with HpaII or HaeIII; fluorescently labeled TRFs were detected by capillary gel electrophoresis. ITS region TRF patterns were predicted and observed to generate a greater richness than 18S TRF patterns. Unique TRF patterns were also observed for each community examined. Finally, the ITS region showed a higher degree of specificity in matching observed TRF profiles to those generated from GenBank sequence data for species identification. These data suggest that ITS rDNA TRF pattern analysis has great potential as a rapid and specific method for fungal community analysis and species identification.
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Affiliation(s)
- N S Lord
- Environmental Biotechnology Institute, Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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Evans ML, Neff BD. Major histocompatibility complex heterozygote advantage and widespread bacterial infections in populations of Chinook salmon (Oncorhynchus tshawytscha). Mol Ecol 2009; 18:4716-29. [PMID: 19821902 DOI: 10.1111/j.1365-294x.2009.04374.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite growing evidence for parasite-mediated selection on the vertebrate major histocompatibility complex (MHC), little is known about variation in the bacterial parasite community within and among host populations or its influence on MHC evolution. In this study, we characterize variation in the parasitic bacterial community associated with Chinook salmon (Oncorhynchus tshawytscha) fry in five populations in British Columbia (BC), Canada across 2 years, and examine whether bacterial infections are a potential source of selection on the MHC. We found an unprecedented diversity of bacteria infecting fry with a total of 55 unique bacteria identified. Bacterial infection rates varied from 9% to 29% among populations and there was a significant isolation by distance relationship in bacterial community phylogenetic similarity across the populations. Spatial variation in the frequency of infections and in the phylogenetic similarity of bacterial communities may result in differential parasite-mediated selection at the MHC across populations. Across all populations, we found evidence of a heterozygote advantage at the MHC class II, which may be a source of balancing selection on this locus. Interestingly, a co-inertia analysis indicated only susceptibility associations between a few of the MHC class I and II alleles and specific bacterial parasites; there was no evidence that any of the alleles provided resistance to the bacteria. Our results reveal a complex bacterial community infecting populations of a fish and underscore the importance of considering the role of multiple pathogens in the evolution of host adaptations.
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Affiliation(s)
- Melissa L Evans
- Department of Biology, University of Western Ontario, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
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The use of polymerase chain reaction for the detection and speciation of bacterial bone and joint infection in children. J Pediatr Orthop 2009; 29:182-8. [PMID: 19352245 DOI: 10.1097/bpo.0b013e3181982533] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We evaluated 36 consecutive patients presenting with signs and symptoms of bacterial bone and joint infection and 10 control patients using bacterial cultures of blood and the presumed site of infection compared with polymerase chain reaction (PCR) techniques using a universal primer and restriction endonuclease digestion. Of the 28 patients with definitive clinical and/or laboratory evidence of bacterial infection, 16 patients had positive bacterial cultures and 12 were PCR-positive. Twenty of 28 patients were either PCR- or culture-positive. Nine of the 16 subjects who had culture-positive samples also had PCR-positive samples (8 positive for the same organism and 1 with 2 organisms identified by culture, but only a single organism by PCR. Six culture positive patients were PCR-negative. Of the 12 patients who were culture-negative, 4 had bacterial genomic material present indicating infection. We conclude that current PCR methods are not superior to standard bacterial culture methods when applied to children with presumed bone or joint infections, but that PCR may complement existing microbiologic cultures for detection of bone and joint infections in children.
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Santoro D, Prisco M, Ciaramella P. Cutaneous sterile granulomas/pyogranulomas, leishmaniasis and mycobacterial infections. J Small Anim Pract 2009; 49:552-61. [PMID: 19006488 DOI: 10.1111/j.1748-5827.2008.00638.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cutaneous "sterile" granulomas represent a group of uncommon skin disorders of unknown aetiopathogenesis. Many diseases are included in this group (for example, sterile granuloma/pyogranuloma syndrome and reactive histiocytosis). The definition of sterile is based on the exclusion of other possible aetiological agents (for example, microorganisms or foreign body). Many techniques are used to rule out a microbial aetiology including cytology, histology, immunohistochemistry and culture. However, some organisms are "fastidious" and difficult to culture or to identify with routine methods, and molecular studies are necessary. This is particularly true for mycobacteria (for example, canine leproid granuloma syndrome) and Leishmania. Recently, studies in human and veterinary medicine have proved the presence of microorganisms (mycobacteria and Leishmania) using a polymerase chain reaction technique in specimens previously diagnosed as sterile. Therefore, it is very important, with the development of new technologies, to use a multidisciplinary diagnostic approach to definitively rule out any microorganism before declaring a disease sterile.
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Affiliation(s)
- D Santoro
- Department of Veterinary Clinical Sciences, Section of Internal Medicine, University of Naples "Federico II", Via F. Delpino 1, 80137 Naples, Italy
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Meyers MS, Foran DR. Spatial and Temporal Influences on Bacterial Profiling of Forensic Soil Samples. J Forensic Sci 2008; 53:652-60. [DOI: 10.1111/j.1556-4029.2008.00728.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
A novel method called "multiplex-terminal restriction fragment length polymorphism (M-TRFLP)" has been recently developed which can be used for simultaneous analysis of the community composition of two or more microbial taxa (up to four). This method can also be used for microbial diagnostic purposes. For M-TRFLP analysis, primers specific to different target genes are used for multiplex-PCR, with one primer for each target being labeled with a unique fluorescent dye at its 5' end. Restriction digestion of the amplified products followed by fragment size analysis on a DNA sequencer produces profiles for targeted genes, which can be distinguished from each other by the color of the terminal fragments imparted by the unique fluorescent dye used for primer labeling. In contrast to current protocols, M-TRFLP allows multiple communities or multiple targets (genes) data to be obtained in just one reaction and therefore saves time, cost and labor. This protocol can be completed in 5-8 h.
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Martin A, Uwizeye C, Fissette K, De Rijk P, Palomino JC, Leao S, Portaels F. Application of the hsp65 PRA method for the rapid identification of mycobacteria isolated from clinical samples in Belgium. J Microbiol Methods 2007; 71:39-43. [PMID: 17719666 DOI: 10.1016/j.mimet.2007.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Revised: 06/20/2007] [Accepted: 07/23/2007] [Indexed: 11/16/2022]
Abstract
Biochemical identification of mycobacteria is slow and many times fail to produce correct results. We compared PCR-restriction fragment length polymorphism analysis (PRA) of hsp65 and biochemical methods for the identification of mycobacteria from human samples in Belgium. PRA was found useful in the identification of mycobacteria and simple to implement as a quick method in the laboratory.
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Affiliation(s)
- Anandi Martin
- Mycobacteriology Unit, Institute of Tropical Medicine, Nationalestraat, 155, Antwerp, B-2000-Belgium.
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Vickery MCL, Nilsson WB, Strom MS, Nordstrom JL, DePaola A. A real-time PCR assay for the rapid determination of 16S rRNA genotype in Vibrio vulnificus. J Microbiol Methods 2007; 68:376-84. [PMID: 17070612 DOI: 10.1016/j.mimet.2006.02.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 02/09/2006] [Indexed: 10/24/2022]
Abstract
In a terminal restriction fragment polymorphism (T-RFLP) study, we recently reported a significant association between the type B 16S rRNA gene and clinical strains of Vibrio vulnificus associated with the consumption of raw oysters. In the present study we describe a real-time PCR assay for the rapid determination of the 16S rRNA type of V. vulnificus isolates. This assay was used to reexamine the 16S rRNA gene type in the strains studied previously by T-RFLP and additional isolates from selected sources. Analyses revealed that 15 of the strains (10 environmental and 5 clinical) previously found to be 16S rRNA type A actually appear to possess both the type A and B genes. The presence of both alleles was confirmed by cloning and sequencing both gene types from one strain. To our knowledge, this is the first report of 16S rRNA sequence heterogeneity within individual strains of V. vulnificus. The findings confirm the T-RFLP data that 16S rRNA type may be a useful marker for determining the clinical significance of V. vulnificus in disease in humans and cultured eels. The real-time PCR assay is much more rapid and less resource-intensive than T-RFLP, and should facilitate further study of the occurrence and distribution of the 16S rRNA genotypes of V. vulnificus. These studies should provide more definitive estimates of the risks associated with this organism and may lead to a better understanding of its virulence mechanism(s).
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Affiliation(s)
- Michael C L Vickery
- Gulf Coast Seafood Laboratory, U. S. Food and Drug Administration, Dauphin Island, Alabama 36528, United States.
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Characterization of Fe(III)-reducing enrichment cultures and isolation of Fe(III)-reducing bacteria from the Savannah River site, South Carolina. Res Microbiol 2006; 157:772-83. [PMID: 16730954 DOI: 10.1016/j.resmic.2006.04.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 04/03/2006] [Accepted: 04/10/2006] [Indexed: 11/22/2022]
Abstract
The Savannah River site, South Carolina (SRS), has been subjected to heavy metal and radionuclide contamination. Dissimilatory Fe(III)-reducing bacteria, by reducing insoluble Fe(III) to soluble Fe(II), may enhance contaminant mobility through subsurface environments. In order to investigate populations of the indigenous iron-reducing microbes from the SRS, duplicate enrichment cultures were initiated using a 10% inoculum of 7 sediment/soil samples, and serial dilutions were made into Wolfe's minimal salts media amended with 50 mM Fe(III) floc, 10 mM acetate and 0.01% yeast extract. Terminal restriction fragment length polymorphism (T-RFLP) analysis was used to generate fingerprints of the cultures and track changes in the microbial communities through the dilutions. Cluster analysis determined the relatedness of individual fingerprints. Initial enrichment cultures exhibited complex fingerprints consisting of many individual T-RF peaks, and demonstrated low similarity between sites. After four serial dilutions the fingerprints were less complex and clustered at higher similarities. Several individual T-RF peaks became dominant in a majority of the fingerprints. Cloning and sequence analysis revealed the presence of microbes closely related to Clostridium and Bacillus species and to known iron reducers such as Geobacter species and Pantoea agglomerans. Several Fe(III)-reducing isolates related to Aeromonas, Bacillus and Clostridium species were obtained.
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Kuehl CJ, Wood HD, Marsh TL, Schmidt TM, Young VB. Colonization of the cecal mucosa by Helicobacter hepaticus impacts the diversity of the indigenous microbiota. Infect Immun 2005; 73:6952-61. [PMID: 16177375 PMCID: PMC1230902 DOI: 10.1128/iai.73.10.6852-6961.2005] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Establishment of mucosal and/or luminal colonization is the first step in the pathogenesis of many gastrointestinal bacterial pathogens. The pathogen must be able to establish itself in the face of competition from the complex microbial community that is already in place. We used culture-independent methods to monitor the colonization of the cecal mucosa of Helicobacter-free mice following experimental infection with the pathogen Helicobacter hepaticus. Two days after infection, H. hepaticus comprised a minor component of the mucosa-associated microbiota, but within 14 days, it became the dominant member of the community. Colonization of the mucosa by H. hepaticus was associated with a decrease in the overall diversity of the microbial community, in large part due to changes in evenness resulting from the relative dominance of H. hepaticus as a member of the community. Our results demonstrate that invasion of the complex gastrointestinal microbial community by a pathogenic microorganism causes reproducible and significant disturbances in the community structure. The use of non-culture-based methods to monitor these changes should lead to a greater understanding of the ecological principles that govern pathogen invasion and may lead to novel methods for the prevention and control of gastrointestinal pathogens.
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Affiliation(s)
- Carole J Kuehl
- Department of Microbiology and Molecular Genetics, National Food Safety and Toxicology Center, Michigan State University, East Lansing, 48824, USA
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22
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Countway PD, Gast RJ, Savai P, Caron DA. Protistan diversity estimates based on 18S rDNA from seawater incubations in the Western North Atlantic. J Eukaryot Microbiol 2005; 52:95-106. [PMID: 15817114 DOI: 10.1111/j.1550-7408.2005.05202006.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cloning/sequencing and fragment analysis of ribosomal RNA genes (rDNA) are becoming increasingly common methods for the identification of microbial taxa. Sequences of these genes provide many additional taxonomic characters for species that otherwise have few distinctive morphological features, or that require involved microscopy or laboratory culture and testing. These same approaches are now being applied with great success in ecological studies of natural communities of microorganisms. Extensive information on the composition of natural microbial assemblages is being amassed at a rapid pace through genetic analyses of environmental samples and comparison of the resulting genetic information with well-established (and rapidly growing) public databases. We examined microbial eukaryote diversity in a natural seawater sample from the coastal western North Atlantic Ocean using two molecular biological approaches: the cloning and sequencing of rRNA genes and by fragment analysis of these genes using the terminal restriction fragment length polymorphism (T-RFLP) method. A simple experiment was carried out to examine changes in the overall eukaryote (largely protistan) diversity and species composition (phylotype diversity) of a natural microbial assemblage when a seawater sample is placed in a container and incubated at ambient light and temperature for 72 h. Containment of the natural seawater sample resulted in relatively minor changes in the overall eukaryote diversity (species richness) obtained by either molecular method at three time points (time-zero, time-24 h, time-72 h). However, substantial changes in the dominance of particular eukaryote phylotypes took place between the three sampling times. Only 18% of the total number of phylotypes observed in the study were observed at all three time points, while 65% (108 of 165) phylotypes were observed only at a single time point (54 unique phylotypes initially, 37 more unique phylotypes at 24 h, and 17 more at 72 h). The results of this study indicate that a high diversity of protistan taxa existed in the original seawater sample at very low abundance, and thus were not observed in the initial characterization of community structure. Containment resulted in significant shifts in the dominance of these taxa, enabling the presence of previously unobserved phylotypes to be documented after 24 or 72 h of incubation.
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Affiliation(s)
- Peter D Countway
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0371, USA.
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23
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Smith CJ, Danilowicz BS, Clear AK, Costello FJ, Wilson B, Meijer WG. T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. FEMS Microbiol Ecol 2005; 54:375-80. [PMID: 16332335 DOI: 10.1016/j.femsec.2005.05.002] [Citation(s) in RCA: 203] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 04/25/2005] [Accepted: 05/01/2005] [Indexed: 11/22/2022] Open
Abstract
Terminal restriction fragment length polymorphism (tRFLP) is a potentially high-throughput method for the analysis of complex microbial communities. Comparison of multiple tRFLP profiles to identify shared and unique components of microbial communities however, is done manually, which is both time consuming and error prone. This paper describes a freely accessible web-based program, T-Align (http://inismor.ucd.ie/~talign/), which addresses this problem. Initially replicate profiles are compared and used to generate a single consensus profile containing only terminal restriction fragments that occur in all replicate profiles. Subsequently consensus profiles representing different communities are compared to produce a list showing whether a terminal restriction fragment (TRF) is present in a particular sample and its relative fluorescence intensity. The use of T-Align thus allows rapid comparison of numerous tRFLP profiles. T-Align is demonstrated by alignment of tRFLP profiles generated from bacterioplankton communities collected from the Irish and Celtic Seas in November 2000. Ubiquitous TRFs and site-specific TRFs were identified using T-Align.
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Affiliation(s)
- Cindy J Smith
- Department of Zoology, University College Dublin, Dublin 4, Ireland
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24
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Marsh TL. Culture-independent microbial community analysis with terminal restriction fragment length polymorphism. Methods Enzymol 2005; 397:308-29. [PMID: 16260299 DOI: 10.1016/s0076-6879(05)97018-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Terminal restriction fragment length polymorphism is a polymerase chain reaction (PCR)-based technique that has been used to effectively interrogate microbial communities to determine the diversity of both phylogenetic and functional markers. It requires the isolation of community DNA and knowledge of the target sequence. PCR amplification, performed with fluorescently labeled primers, is followed with restriction digestion and size selection on automated sequencing systems. The fluorescent tag identifies the terminal fragment, and the length polymorphism of the terminal fragments reveals a fraction of the phylogenetic diversity within the target sequence. Because the technique has high-throughput capabilities, it performs well in surveys where a large number of samples must be interrogated to ascertain spatial or temporal changes in community structure.
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Affiliation(s)
- Terence L Marsh
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing 48824, USA
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25
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Decostere A, Hermans K, Haesebrouck F. Piscine mycobacteriosis: a literature review covering the agent and the disease it causes in fish and humans. Vet Microbiol 2004; 99:159-66. [PMID: 15066718 DOI: 10.1016/j.vetmic.2003.07.011] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2003] [Revised: 07/23/2003] [Accepted: 07/23/2003] [Indexed: 10/26/2022]
Abstract
Mycobacterium marinum, M. fortuitum and M. chelonae are the etiological agents of fish mycobacteriosis. Fish mycobacteriosis is a disseminated infection reported in more than 150 fish species and is usually accompanied by emaciation and death over a period of months to years. Granulomas are formed both externally and scattered throughout the internal organs. Treatment is in most cases unsatisfactory and the overall recommendation is to destroy the diseased stock, particularly since these pathogens are capable of affecting man as well as fish. Especially fish handlers and aquarium hobbyists are infected and the disease is mostly confined to the superficial, cooler body tissues, most often the extremities. Dissemination is apparently rare but has been reported.
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Affiliation(s)
- A Decostere
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium.
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26
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Edwards IP, Cripliver JL, Gillespie AR, Johnsen KH, Scholler M, Turco RF. Nitrogen availability alters macrofungal basidiomycete community structure in optimally fertilized loblolly pine forests. THE NEW PHYTOLOGIST 2004; 162:755-770. [PMID: 33873755 DOI: 10.1111/j.1469-8137.2004.01074.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• We investigated the effect of an optimal nutrition strategy designed to maximize loblolly pine (Pinus taeda) growth on the rank abundance structure and diversity of associated basidiomycete communities. • We conducted both small- and large-scale below-ground surveys 10 years after the initiation of optimal nutrition, and used TRFLP of selectively PCR-amplified nrDNA ITS to determine the distribution and abundance of macrofungal basidiomycete species in c. 200 soil samples collected from optimally fertilized and unfertilized treatments at the SETRES loblolly pine experimental site, North Carolina, USA. • Our results indicated an increased relative abundance of Tylopilus and Thelephora spp. on optimally fertilized stands. Our results also suggested improved mycelial growth of several species, possibly caused by increased connectivity in the forest floor as a result of increased plant growth. • In addition, our results suggest a trend towards reduced basidiomycete diversity, and that large-scale application of optimal nutrition may need to be sensitive to increased nitrate availability.
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Affiliation(s)
- Ivan P Edwards
- Department of Agronomy, Purdue University, Lilly Hall of Life Sciences, 915 West State Street, West Lafayette, IN 47907-2054, USA
- Present address: Institute of Terrestrial Ecology, Swiss Federal Institute of Technology (ETH Zurich), Grabenstrasse 3, CH 8952, Schlieren, Switzerland
| | - Jennifer L Cripliver
- Department of Forestry & Natural Resources, Forestry Building, 195 Marsteller Street, West Lafayette, IN 47907-2033, USA
| | - Andrew R Gillespie
- Department of Forestry & Natural Resources, Forestry Building, 195 Marsteller Street, West Lafayette, IN 47907-2033, USA
| | - Kurt H Johnsen
- USDA Forest Service Southern Research Station, Forestry Sciences Laboratory, PO Box 12254, 3041 East Cornwallis Road, Research Triangle Park, NC 27709, USA
| | - M Scholler
- Staatliches Museum für Naturkunde, Erbprinzenstrasse 13, D- 76133, Karlsruhe, Germany
| | - Ronald F Turco
- Department of Agronomy, Purdue University, Lilly Hall of Life Sciences, 915 West State Street, West Lafayette, IN 47907-2054, USA
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27
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Abstract
Just as tuberculosis has persisted for many centuries as one of most serious and deadly infectious diseases in many parts of the world, so has the motivation to develop improved laboratory methods for characterizing M. tuberculosis isolates. Modern technology has lead to great improvements in mycobacteriology laboratory procedures, particularly in detection, identification, epidemiologic strain typing, and drug susceptibility testing. Although the usefulness of some of these newer methods is under evaluation, many already are showing potential as adjuncts to clinical diagnostic procedures.
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Affiliation(s)
- Robert C Cooksey
- Tuberculosis/Mycobacteriology Branch, Centers for Disease Control and Prevention, Mail Stop F08, 1600 Clifton Road, Atlanta, GA 30333, USA.
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28
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Kurabachew M, Enger Ø, Sandaa RA, Lemma E, Bjorvatn B. Amplified ribosomal DNA restriction analysis in the differentiation of related species of mycobacteria. J Microbiol Methods 2003; 55:83-90. [PMID: 14499998 DOI: 10.1016/s0167-7012(03)00119-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This study explores the potential of the amplified ribosomal DNA restriction analysis (ARDRA) for intra- and interspecies identification of the genus Mycobacteria. A set of primers was used to amplify part of the 16S and 23S rDNA as well as the 16S-23S rDNA spacer from 121 isolates belonging to 13 different mycobacterial species. Restriction analysis was carried out with five different restriction enzymes, namely CfoI, HaeIII, RsaI, MspI and TaqI. Restriction digestion of the PCR product using CfoI enabled differentiation between 9 of the 13 mycobacterial species, whereas the remaining four enzymes differentiated between 7 of these 13 species. None of the five enzymes distinguished between different isolates of Mycobacterium tuberculosis or between species within the M. tuberculosis complex i.e., M. tuberculosis, M. bovis, M. bovis BCG and M. africanum. Although ARDRA analysis of the 16S-23S rDNA does not seem to have a potential for intraspecies differentiation, it has proven to be a rapid and technically relatively simple method to recognise strains belonging to the M. tuberculosis complex as well as to identify mycobacterial species outside this complex.
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Affiliation(s)
- Mekonnen Kurabachew
- Centre for International Health, University of Bergen, Armauer Hansen Building, N-5021, Bergen, Norway.
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29
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Christensen JE, Stencil JA, Reed KD. Rapid identification of bacteria from positive blood cultures by terminal restriction fragment length polymorphism profile analysis of the 16S rRNA gene. J Clin Microbiol 2003; 41:3790-800. [PMID: 12904391 PMCID: PMC179800 DOI: 10.1128/jcm.41.8.3790-3800.2003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteremia results in significant morbidity and mortality, especially among patient populations that are immunocompromised. Broad-spectrum antibiotics are administered to patients suspected to have bloodstream infections that are awaiting diagnosis that depends on blood culture analysis. Significant delays in identification of pathogens can result, primarily due to the dependence on growth-based identification systems. To address these limitations, we took advantage of terminal restriction fragment (TRF) length polymorphisms (T-RFLP) due to 16S ribosomal DNA (rDNA) sequence diversity to rapidly identify bacterial pathogens directly from positive blood culture. TRF profiles for each organism were determined by sizing fragments from restriction digests of PCR products derived from two sets of 16S rDNA-specific fluorescent dye-labeled primers. In addition, we created a TRF profile database (TRFPD) with 5899 predicted TRF profiles from sequence information representing 2860 different bacterial species. TRF profiles were experimentally determined for 69 reference organisms and 32 clinical isolates and then compared against the predicted profiles in the TRFPD. The predictive value of the profiles was found to be accurate to the species level with most organisms tested. In addition, identification of 10 different genera was possible with profiles comprising two or three TRFs. Although it was possible to identify Enterobacteriaceae by using a profile of three TRFs, the similarity of the TRF profiles of these organisms makes differentiation of species less reliable with the current method. The ability to rapidly (i.e., within approximately 8 h) identify bacteria from blood cultures has potential for reducing unnecessary use of broad-spectrum antibiotics and promoting more timely prescription of appropriate antibiotics.
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Affiliation(s)
- Jeffrey E Christensen
- Clinical Research Center, Marshfield Clinic Research Foundation, Marshfield, Wisconsin 54449, USA
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30
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Brunello F, Ligozzi M, Cristelli E, Bonora S, Tortoli E, Fontana R. Identification of 54 mycobacterial species by PCR-restriction fragment length polymorphism analysis of the hsp65 gene. J Clin Microbiol 2001; 39:2799-806. [PMID: 11473995 PMCID: PMC88242 DOI: 10.1128/jcm.39.8.2799-2806.2001] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 121 reference and clinical strains of both slowly and rapidly growing mycobacteria belonging to 54 species were studied for restriction fragment length polymorphism of a PCR-amplified 439-bp segment of the gene encoding the 65-kDa heat shock protein. Restriction digests were separated by 10% polyacrylamide gel electrophoresis (PAGE). By including a size standard in each sample, the restriction fragment profile was calculated using a computer-aided comparison program. An algorithm describing these 54 species (including 22 species not previously described) is proposed. We found that this assay based on 10% PAGE provided a more precise estimate than that based on agarose gel electrophoresis of the real size of restriction fragments as deduced from the sequence analysis and allowed identification of mycobacteria whose PCR-restriction fragment length polymorphism analysis patterns were unequivocally identified by fragments shorter than 60 bp.
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Affiliation(s)
- F Brunello
- Dipartimento di Patologia, Sezione di Microbiologia, Università di Verona, Italy
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31
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Lünsdorf H, Strömpl C, Osborn AM, Bennasar A, Moore ER, Abraham WR, Timmis KN. Approach to analyze interactions of microorganisms, hydrophobic substrates, and soil colloids leading to formation of composite biofilms, and to study initial events in microbiogeological processes. Methods Enzymol 2001; 336:317-31. [PMID: 11398409 DOI: 10.1016/s0076-6879(01)36598-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
MESH Headings
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacterial Physiological Phenomena
- Base Sequence
- Biofilms/growth & development
- Chromatography, Gas
- Colloids
- DNA Fingerprinting
- DNA Primers/genetics
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- Microscopy, Electron
- Microscopy, Electron, Scanning
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Soil Microbiology
- Spectrum Analysis
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Affiliation(s)
- H Lünsdorf
- Division of Microbiology, GBF, German Research Centre for Biotechnology, D-38124 Braunschweig, Germany
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32
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Kaplan CW, Astaire JC, Sanders ME, Reddy BS, Kitts CL. 16S ribosomal DNA terminal restriction fragment pattern analysis of bacterial communities in feces of rats fed Lactobacillus acidophilus NCFM. Appl Environ Microbiol 2001; 67:1935-9. [PMID: 11282651 PMCID: PMC92815 DOI: 10.1128/aem.67.4.1935-1939.2001] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
16S ribosomal DNA terminal restriction fragment patterns from rat fecal samples were analyzed to track the dynamics of Lactobacillus acidophilus NCFM and discern bacterial populations that changed during feeding with NCFM. Lactobacillus johnsonii and Ruminococcus flavefaciens were tentatively identified as such bacterial populations. The presence of L. johnsonii was confirmed by isolation from feces.
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Affiliation(s)
- C W Kaplan
- Environmental Biotechnology Institute, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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33
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Hongmanee P, Stender H, Rasmussen OF. Evaluation of a fluorescence in situ hybridization assay for differentiation between tuberculous and nontuberculous Mycobacterium species in smears of Lowenstein-Jensen and Mycobacteria Growth Indicator Tube cultures using peptide nucleic acid probes. J Clin Microbiol 2001; 39:1032-5. [PMID: 11230423 PMCID: PMC87869 DOI: 10.1128/jcm.39.3.1032-1035.2001] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new fluorescence in situ hybridization assay based on peptide nucleic acid probes (MTB and NTM probes targeting tuberculous and nontuberculous species, respectively) for the identification of Mycobacterium tuberculosis complex and differentiation between tuberculous and nontuberculous mycobacteria (NTM) was evaluated using Lowenstein-Jensen (LJ) solid cultures from 100 consecutive sputum samples and 50 acid-fast bacillus (AFB)-positive sputum samples as well as Mycobacteria Growth Indicator Tube (MGIT) liquid cultures from 80 AFB-positive sputum samples. Mycobacterium species could be identified from a total of 53 LJ cultures and 77 MGIT cultures. The diagnostic specificities of the MTB and NTM probes were 100% for both cultures. The diagnostic sensitivities of the MTB probe for the LJ and MGIT cultures were 98 and 99%, respectively, whereas the sensitivities of the NTM probe were 57 and 100%, respectively. The relatively low sensitivity of the NTM probe was due to a high proportion of M. fortuitum, which is not identified by the probe.
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Affiliation(s)
- P Hongmanee
- Department of Pathology, Ramathibodi Hospital, 10400 Bangkok, Thailand
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34
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Vaneechoutte M, Heyndrickx M. Application and Analysis of ARDRA Patterns in Bacterial Identification, Taxonomy and Phylogeny. NEW APPROACHES FOR THE GENERATION AND ANALYSIS OF MICROBIAL TYPING DATA 2001:211-247. [DOI: 10.1016/b978-044450740-2/50010-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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35
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Lee H, Park HJ, Cho SN, Bai GH, Kim SJ. Species identification of mycobacteria by PCR-restriction fragment length polymorphism of the rpoB gene. J Clin Microbiol 2000; 38:2966-71. [PMID: 10921960 PMCID: PMC87161 DOI: 10.1128/jcm.38.8.2966-2971.2000] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PCR-restriction fragment length polymorphism analysis (PRA) using the novel region of the rpoB gene was developed for rapid and precise identification of mycobacteria to the species level. A total of 50 mycobacterial reference strains and 3 related bacterial strains were used to amplify the 360-bp region of rpoB, and the amplified DNAs were subsequently digested with restriction enzymes such as MspI and HaeIII. The results from this study clearly show that most of the mycobacterial species were easily differentiated at the species level by this PRA method. In addition, species with several subtypes, such as Mycobacterium gordonae, M. kansasii, M. celatum, and M. fortuitum, were also differentiated by this PRA method. Subsequently, an algorithm was constructed based on the results, and a blinded test was carried out with more than 260 clinical isolates that had been identified on the basis of conventional tests. Comparison of these two sets of results clearly indicates that this new PRA method based on the rpoB gene is more simple, more rapid, and more accurate than conventional procedures for differentiating mycobacterial species.
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Affiliation(s)
- H Lee
- Department of Microbiology, Korean Institute of Tuberculosis, The Korean National Tuberculosis Association, Seocho-gu, Seoul 137-140, Korea
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36
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Scala DJ, Kerkhof LJ. Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis. Appl Environ Microbiol 2000; 66:1980-6. [PMID: 10788370 PMCID: PMC101443 DOI: 10.1128/aem.66.5.1980-1986.2000] [Citation(s) in RCA: 131] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although it is widely believed that horizontal patchiness exists in microbial sediment communities, determining the extent of variability or the particular members of the bacterial community which account for the observed differences among sites at various scales has not been routinely demonstrated. In this study, horizontal heterogeneity was examined in time and space for denitrifying bacteria in continental shelf sediments off Tuckerton, N.J., at the Rutgers University Long-Term Ecosystem Observatory (LEO-15). Characterization of the denitrifying community was done using PCR amplification of the nitrous oxide reductase (nosZ) gene combined with terminal restriction fragment length polymorphism analysis. Spatial scales from centimeters to kilometers were examined, while temporal variation was assayed over the course of 1995 to 1996. Sorenson's indices (pairwise similarity values) were calculated to permit comparison between samples. The similarities of benthic denitrifiers ranged from 0.80 to 0.85 for centimeter scale comparisons, from 0.52 to 0.79 for meter level comparisons, and from 0.23 to 0.53 for kilometer scale comparisons. Sorenson's indices for temporal comparisons varied from 0.12 to 0.74. A cluster analysis of the similarity values indicated that the composition of the denitrifier assemblages varied most significantly at the kilometer scale and between seasons at individual stations. Specific nosZ genes were identified which varied at centimeter, meter, or kilometer scales and may be associated with variability in meio- or macrofaunal abundance (centimeter scale), bottom topography (meter scale), or sediment characteristics (kilometer scale).
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Affiliation(s)
- D J Scala
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey 08854, USA
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37
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Osborn AM, Moore ER, Timmis KN. An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2000; 2:39-50. [PMID: 11243261 DOI: 10.1046/j.1462-2920.2000.00081.x] [Citation(s) in RCA: 616] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A systematic evaluation of the value and potential of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure has been undertaken. The reproducibility and robustness of the method has been assessed using environmental DNA samples isolated directly from PCB-polluted or pristine soil, and subsequent polymerase chain reaction (PCR) amplification of total community 16S rDNA. An initial investigation to assess the variability both within and between different polyacrylamide gel electrophoresis (PAGE) runs showed that almost identical community profiles were consistently produced from the same sample. Similarly, very little variability was observed as a result of variation between replicate restriction digestions, PCR amplifications or between replicate DNA isolations. Decreasing concentrations of template DNA produced a decline in both the complexity and the intensity of fragments present in the community profile, with no additional fragments detected in the higher dilutions that were not already present when more original template DNA was used. Reducing the number of cycles of PCR produced similar results. The greatest variation between profiles generated from the same DNA sample was produced using different Taq DNA polymerases, while lower levels of variability were found between PCR products that had been produced using different annealing temperatures. Incomplete digestion by the restriction enzyme may, as a result of the generation of partially digested fragments, lead to an overestimation of the overall diversity within a community. The results obtained indicate that, once standardized, T-RFLP analysis is a highly reproducible and robust technique that yields high-quality fingerprints consisting of fragments of precise sizes, which, in principle, could be phylogenetically assigned, once an appropriate database is constructed.
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Affiliation(s)
- A M Osborn
- Department of Environmental Microbiology, GBF-National Research Centre for Biotechnology, Braunschweig, Germany
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38
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Häggblom MM, Knight VK, Kerkhof LJ. Anaerobic decomposition of halogenated aromatic compounds. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2000; 107:199-207. [PMID: 15092996 DOI: 10.1016/s0269-7491(99)00138-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/1998] [Accepted: 05/22/1999] [Indexed: 05/24/2023]
Abstract
Halogenated compounds constitute one of the largest groups of environmental pollutants, partly as a result of their widespread use as biocides, solvents and other industrial chemicals. A critical step in degradation of organohalides is the cleavage of the carbon?halogen bond. Reductive dehalogenation is generally the initial step in metabolism under methanogenic conditions, which requires a source of reducing equivalents, with the halogenated compound serving as an electron acceptor. Dehalogenation is greatly influenced by alternate electron acceptors; e.g. sulfate frequently inhibits reductive dehalogenation. On the other hand, a number of halogenated aromatic compounds can be degraded under different electron-accepting conditions and their complete oxidation to CO(2) can be coupled to processes such as denitrification, iron(III)-reduction, sulfate reduction and methanogenesis. Reductive dehalogenation was the initial step in degradation not only under methanogenic, but also under sulfate- and iron(III)-reducing conditions. Dehalogenation rates were in general slower under sulfidogenic and iron-reducing conditions, suggesting that dehalogenation was affected by the electron acceptor. The capacity for dehalogenation appears to be widely distributed in anoxic environments; however, the different substrate specificities and activities observed for the halogenated aromatic compounds suggest that distinct dehalogenating microbial populations are enriched under the different reducing conditions. Characterization of the microbial community structure using a combination of biomolecular techniques, such as cellular fatty acid profiling, and 16 S rRNA fingerprinting/sequence analysis, was used to discern the distinct populations enriched with each substrate and under each electron-accepting condition. These combined techniques will aid in identifying the organisms responsible for dehalogenation and degradation of halogenated aromatic compounds.
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Affiliation(s)
- M M Häggblom
- Biotechnology Center for Agriculture and the Environment, and Department of Biochemistry Microbiology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA.
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Hernandez SM, Morlock GP, Butler WR, Crawford JT, Cooksey RC. Identification of Mycobacterium species by PCR-restriction fragment length polymorphism analyses using fluorescence capillary electrophoresis. J Clin Microbiol 1999; 37:3688-92. [PMID: 10523575 PMCID: PMC85725 DOI: 10.1128/jcm.37.11.3688-3692.1999] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed a scheme for the rapid identification of Mycobacterium species based upon PCR amplification of polymorphic genetic regions with fluorescent primers followed by restriction and analysis by fluorescence capillary electrophoresis. Mycobacterium species were identified by restriction enzyme analysis of a 439-bp segment of the 65-kDa heat shock protein gene (labeled [both strands] at the 5' end with 4,7,2',7'-tetrachloro-6-carboxyfluorescein) using HaeIII and BstEII and of a 475-bp hypervariable region of the 16S rRNA gene (labeled [both strands] at the 5' end with 6-carboxyfluorescein) using HaeIII and CfoI. Samples were analyzed on an automated fluorescence capillary electrophoresis instrument, and labeled fragments were sized by comparison with an internal standard. DNA templates were prepared with pure cultures of type strains. In all, we analyzed 180 strains, representing 22 Mycobacterium species, and obtained distinctive restriction fragment length polymorphism (RFLP) patterns for 19 species. Three members of the Mycobacterium tuberculosis complex had a common RFLP pattern. A computerized algorithm which eliminates subjectivity from pattern interpretation and which is capable of identifying the species within a sample was developed. The convenience and short preparatory time of this assay make it comparable to conventional methodologies such as high-performance liquid chromatography and hybridization assays for identification of mycobacteria.
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Affiliation(s)
- S M Hernandez
- Division of AIDS, Sexually Transmitted Diseases, and Tuberculosis Laboratory Research, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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Ivnitski D, Abdel-Hamid I, Atanasov P, Wilkins E. Biosensors for detection of pathogenic bacteria. Biosens Bioelectron 1999. [DOI: 10.1016/s0956-5663(99)00039-1] [Citation(s) in RCA: 420] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Marsh TL. Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr Opin Microbiol 1999; 2:323-7. [PMID: 10383864 DOI: 10.1016/s1369-5274(99)80056-3] [Citation(s) in RCA: 300] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Terminal restriction fragment length polymorphism is a recent molecular approach that can assess subtle genetic differences between strains as well as provide insight into the structure and function of microbial communities. The technique has both high sensitivity and throughput making it ideal for comparative analyses.
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Affiliation(s)
- T L Marsh
- Center for Microbial Ecology, Department of Microbiology, Michigan State University, East Lansing, MI 48824, USA.
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42
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Posteraro B, Sanguinetti M, Garcovich A, Ardito F, Zampetti A, Masucci L, Sbordoni G, Cerimele D, Fadda G. Polymerase chain reaction-reverse cross-blot hybridization assay in the diagnosis of sporotrichoid Mycobacterium marinum infection. Br J Dermatol 1998; 139:872-6. [PMID: 9892957 DOI: 10.1046/j.1365-2133.1998.02516.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this paper, we report a patient in whom Mycobacterium marinum sporotrichoid infection was diagnosed using polymerase chain reaction (PCR) amplification of the 16S rRNA gene and subsequent analysis of the amplified product in a reverse cross-blot hybridization assay with mycobacterial species-specific probes. This molecular method allowed us rapidly to detect and identify this organism directly in the patient's lesional skin biopsy rather than in cultures in conventional media. The identification provided by PCR-reverse cross-blot hybridization assay was confirmed by examination of the morphological and biochemical features and by high-performance liquid chromatography analysis of mycolic acid from the clinical isolate, suggesting the validity of our molecular approach.
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Affiliation(s)
- B Posteraro
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome,Italy
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Sansila A, Hongmanee P, Chuchottaworn C, Rienthong S, Rienthong D, Palittapongarnpim P. Differentiation between Mycobacterium tuberculosis and Mycobacterium avium by amplification of the 16S-23S ribosomal DNA spacer. J Clin Microbiol 1998; 36:2399-403. [PMID: 9705362 PMCID: PMC105132 DOI: 10.1128/jcm.36.9.2399-2403.1998] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Differentiation between Mycobacterium tuberculosis and M. avium is helpful for the treatment of disseminated mycobacterial infection in AIDS patients. This can traditionally be done by time-consuming biochemical tests or with Accuprobe. Previously, PCR restriction enzyme analysis (PCR-REA) of the 16S-23S rRNA gene spacer was shown to be able to identify a limited number of strains of Mycobacterium. In this study the method was improved by using more specific primers and was tested with 50 clinical isolates of M. tuberculosis and 65 clinical isolates of M. avium complex. Probes specific to the spacers of M. tuberculosis and M. avium were also tested. Both M. tuberculosis and M. avium could be reliably identified either by PCR-REA or by PCR-hybridization, with the results completely agreeing with those obtained by biochemical tests and with the Accuprobe, respectively. The method may therefore be useful as an alternative in-house method for identification of the bacteria.
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Affiliation(s)
- A Sansila
- Department of Pathology, Faculty of Veterinary Medicine, Khonkaen University, Bangkok, Thailand
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44
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Sanguinetti M, Posteraro B, Ardito F, Zanetti S, Cingolani A, Sechi L, De Luca A, Ortona L, Fadda G. Routine use of PCR-reverse cross-blot hybridization assay for rapid identification of Mycobacterium species growing in liquid media. J Clin Microbiol 1998; 36:1530-3. [PMID: 9620371 PMCID: PMC104871 DOI: 10.1128/jcm.36.6.1530-1533.1998] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A PCR-reverse cross-blot hybridization assay procedure that is able to rapidly identify 13 species of clinically relevant mycobacteria was evaluated for routine use in the identification of acid-fast isolates growing in BACTEC 460 TB (12B and 13A) and BACTEC 9000 MB (Myco/F) liquid media. Eight of the probes used were already described by Kox et al. (L. F. F. Kox et al., J. Clin. Microbiol. 33:3225-3233, 1995). In addition, we used six other probes specific for M. chelonae, M. malmoense or M. szulgai, M. genavense, M. gordonae, M. terrae, and M. marinum/M. ulcerans that we designed ourselves. This procedure allowed us to identify 459 mycobacterial species directly from broth cultures of 5,466 clinical samples collected over 1 year and processed with the radiometric or nonradiometric BACTEC system. Our results were in agreement with those obtained by conventional identification methods and also with those obtained by mycolic acid analysis by high-performance liquid chromatography. This assay seems to be a reliable procedure for the routine identification of mycobacteria, providing an accurate identification of mycobacterial isolates more rapidly than conventional tests, with remarkable implications for an efficacious specific antimycobacterial therapy.
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Affiliation(s)
- M Sanguinetti
- Istituto di Microbiologia, Universitá Cattolica del Sacro Cuore, Rome, Italy.
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Clement BG, Kehl LE, DeBord KL, Kitts CL. Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J Microbiol Methods 1998. [DOI: 10.1016/s0167-7012(97)00105-x] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Liu WT, Marsh TL, Cheng H, Forney LJ. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 1997; 63:4516-22. [PMID: 9361437 PMCID: PMC168770 DOI: 10.1128/aem.63.11.4516-4522.1997] [Citation(s) in RCA: 1122] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A quantitative molecular technique was developed for rapid analysis of microbial community diversity in various environments. The technique employed PCR in which one of the two primers used was fluorescently labeled at the 5' end and was used to amplify a selected region of bacterial genes encoding 16S rRNA from total community DNA. The PCR product was digested with restriction enzymes, and the fluorescently labeled terminal restriction fragment was precisely measured by using an automated DNA sequencer. Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragment lengths or "ribotypes." Using T-RFLP, we were able to distinguish all bacterial strains in a model bacterial community, and the pattern was consistent with the predicted outcome. Analysis of complex bacterial communities with T-RFLP revealed high species diversity in activated sludge, bioreactor sludge, aquifer sand, and termite guts; as many as 72 unique ribotypes were found in these communities, with 36 ribotypes observed in the termite guts. The community T-RFLP patterns were numerically analyzed and hierarchically clustered. The pattern derived from termite guts was found to be distinctly different from the patterns derived from the other three communities. Overall, our results demonstrated that T-RFLP is a powerful tool for assessing the diversity of complex bacterial communities and for rapidly comparing the community structure and diversity of different ecosystems.
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Affiliation(s)
- W T Liu
- Department of Microbiology, Michigan State University, East Lansing 48824, USA
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Devallois A, Goh KS, Rastogi N. Rapid identification of mycobacteria to species level by PCR-restriction fragment length polymorphism analysis of the hsp65 gene and proposition of an algorithm to differentiate 34 mycobacterial species. J Clin Microbiol 1997; 35:2969-73. [PMID: 9350770 PMCID: PMC230098 DOI: 10.1128/jcm.35.11.2969-2973.1997] [Citation(s) in RCA: 160] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
PCR-restriction fragment length polymorphism analysis (PRA) of the hsp65 gene (A. Telenti, F. Marchesi, M. Balz, F. Bally, E. C. Böttger, and T. Bodmer, J. Clin. Microbiol. 31:175-178, 1993) was applied to 108 mycobacterial isolates representing 34 species to evaluate its potential as a rapid reference method. A total of 49 distinct patterns were obtained; 25 species were characterized by a single PRA pattern, while 9 species gave more than one specific pattern. An algorithm describing these 34 species (which includes five additional species and new subgroups of Mycobacterium kansasii, M. abscessus, and M. peregrinum) is proposed. A relatively simple and inexpensive method, PRA may be particularly helpful in routine clinical microbiology laboratories.
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Affiliation(s)
- A Devallois
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur, Point à Pitre, Guadeloupe, French West Indies
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49
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Steingrube VA, Wilson RW, Brown BA, Jost KC, Blacklock Z, Gibson JL, Wallace RJ. Rapid identification of clinically significant species and taxa of aerobic actinomycetes, including Actinomadura, Gordona, Nocardia, Rhodococcus, Streptomyces, and Tsukamurella isolates, by DNA amplification and restriction endonuclease analysis. J Clin Microbiol 1997; 35:817-22. [PMID: 9157134 PMCID: PMC229682 DOI: 10.1128/jcm.35.4.817-822.1997] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A previously described PCR-restriction fragment length polymorphism (RFLP) identification schema for Nocardia that used an amplified 439-bp segment (amplicon) of the 65-kDa heat shock protein gene was evaluated for potential use with isolates of all clinically significant aerobic actinomycetes. The study included 28 reference (American Type Culture Collection) strains and 198 clinical isolates belonging to 20 taxonomic groups. Of these 198 isolates, 188 could be differentiated by this PCR-RFLP method. Amplicons from all aerobic actinomycete isolates lacked BstEII recognition sites, thereby distinguishing them from those of mycobacteria that contain one or more such sites. Of 29 restriction endonucleases, MspI plus HinfI produced RFLP patterns that differentiated 16 of the 20 taxa. A single RFLP pattern was observed for 15 of 20 taxa that included 65% of phenotypically clustered isolates. Multiple patterns were seen with Gordona bronchialis, Nocardia asteroides complex type VI, Nocardia otitidiscaviarum, Nocardia transvalensis, and Streptomyces spp. Streptomyces RFLP patterns were the most heterogeneous (five patterns among 19 isolates), but exhibited a unique HinfI fragment of > 320 bp. RFLP patterns that matched those from type strains of Streptomyces albus, Streptomyces griseus, or Streptomyces somaliensis were obtained from 14 of 19 Streptomyces isolates. Only 10 of 28 isolates of N. otitidiscaviarum failed to yield satisfactory amplicons, while only 6 of 188 (3.2%) clinical isolates exhibited patterns that failed to match one of the 21 defined RFLP patterns. These studies extended the feasibility of using PCR-RFLP analysis as a rapid method for the identification of all clinically significant species and taxa of aerobic actinomycetes.
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Affiliation(s)
- V A Steingrube
- Department of Microbiology University of Texas Health Center at Tyler 75710-2003, USA
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50
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Brunk CF, Avaniss-Aghajani E, Brunk CA. A computer analysis of primer and probe hybridization potential with bacterial small-subunit rRNA sequences. Appl Environ Microbiol 1996; 62:872-9. [PMID: 8975616 PMCID: PMC167853 DOI: 10.1128/aem.62.3.872-879.1996] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Analysis of restriction fragment length polymorphism of bacterial small-subunit (SSU) rRNA sequences represents a potential means for characterizing complex bacterial populations such as those found in natural environments. In order to estimate the resolution potential of this approach, we have examined the SSU rRNA sequences in the Ribosomal Database Project bank using a computer algorithm which simulates hybridization between DNA sequences. Simulated hybridizations between a primer or probe sequence and an SSU rRNA sequence yield a value for each potential hybridization. This algorithm has been used to evaluate sites for PCR primers and hybridization probes used for classifying SSU rRNA sequences. Our analysis indicates that length variation in terminal restriction fragments of PCR products from the SSU rRNA sequences can identify a wide spectrum of bacteria. We also observe that the majority of restriction fragment length variation is the result of insertions and deletions rather than restriction site polymorphisms. This approach is also used to evaluate the relative efficiency and specificity of a number of published hybridization probes.
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Affiliation(s)
- C F Brunk
- Biology Department, University of California, Los Angeles 90024-1606, USA
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