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PubMed1997

Plasmids isolated from marine sediment microbial communities contain replication and incompatibility regions unrelated to those of known plasmid groups.

Two hundred ninety-seven bacteria carrying plasmids that range in size from 5 to 250 kb were identified from more than 1,000 aerobic heterotrophic bacteria isolated from coastal California marine sediments. While some isolates contained numerous (three to five) small (5- to 10-kb) plasmids, the majority of the natural isolates typically contained one large (40- to 100-kb) plasmid. By the method of plasmid isolation used in this study, the frequency of plasmid incidence ranged from 24 to 28% depending on the samples examined. Diversity of the plasmids occurring in the marine sediment bacterial populations was examined at the molecular level by hybridization with 14 different DNA probes specific for the incompatibility and replication (inc/rep) regions of a number of well-characterized plasmid incompatibility groups (repB/O, FIA, FII, FIB, HI1, HI2, I1, L/M, X, N, P, Q, W, and U). Interestingly, we found no DNA homology between the plasmids isolated from the culturable bacterial population of marine sediments and the replicon probes specific for numerous incompatibility groups developed by Couturier et al. (M. F. Couturier, F. Bex, P. L. Bergquist, and W. K. Maas, Microbiol. Rev. 52:375-395, 1988). Our findings suggest that plasmids in marine sediment microbial communities contain novel, as-yet-uncharacterized, incompatibility and replication regions and that the present replicon typing system, based primarily on plasmids derived from clinical isolates, may not be representative of the plasmid diversity occurring in some marine environments. Since the vast majority of marine bacteria are not culturable under laboratory conditions, we also screened microbial community DNA for the presence of broad- and narrow-host-range plasmid replication sequences. Although the replication origin of the conjugally promiscuous broad-host-range plasmid RK2 (incP) was not detectable in any of the plasmid-containing culturable marine isolates, DNA extracted from the microbial community and amplified by PCR yielded a positive signal for RK2 oriV replication sequences. The strength of the signal suggests the presence of a low level of the incP replicon within the marine microbial community. In contrast, replication sequences specific for the narrow-host-range plasmid F were not detectable in DNA extracted from marine sediment microbial communities. With the possible exception of mercuric chloride, phenotypic analysis of the 297 plasmid-bearing isolates did not demonstrate a correlation between plasmid content and antibiotic or heavy metal resistance traits.

Basidiomycota↗

PubMed2005

Evaluation of a real-time quantitative polymerase chain reaction assay for detection and quantitation of virulent Rhodococcus equi.

OBJECTIVE: To evaluate a real-time quantitative polymerase chain reaction (QPCR) assay in the detection and quantitation of virulent Rhodococcus equi. SAMPLE POPULATION: 1 virulent, 2 intermediately virulent, and 2 avirulent strains of R. equi and 16 isolates of bacteria genetically related to R. equi. PROCEDURE: The QPCR assay was evaluated for detection and quantitation of the virulence-associated gene (vapA) of R. equi in pure culture and in samples of tracheobronchial fluid, which were inoculated with known numbers of virulent R. equi. Results were compared with those derived via quantitative microbial culture and standard polymerase chain reaction methods. RESULTS: The QPCR assay detected the vapA gene in pure culture of R. equi and in tracheobronchial fluid samples that contained as few as 20 CFUs of virulent R. equi/mL and accurately quantitated virulent R. equi to 10(3) CFUs/mL of fluid. The assay was highly specific for detection of the vapA gene of virulent R. equi and was more sensitive than standard polymerase chain reaction for detection of R. equi in tracheobronchial fluid. CONCLUSIONS AND CLINICAL RELEVANCE: The QPCR assay appears to be a rapid and reliable method for detecting and quantitating virulent R. equi. The accuracy of the QPCR assay is comparable to that of quantitative microbial culture. The increased sensitivity of the QPCR method in detection of virulent R. equi should facilitate rapid and accurate diagnosis of R. equi pneumonia in foals.

Actinomycetales Infections↗

PubMed2006

F+ RNA coliphage typing for microbial source tracking in surface waters.

AIMS: The utility of coliphages to detect and track faecal pollution was evaluated using South Carolina surface waters that exceeded State faecal coliform standards. METHODS AND RESULTS: Coliphages were isolated from 117 surface water samples by single agar layer (SAL) and enrichment presence/absence (EP/A) methods. Confirmed F+ RNA coliphages were typed for microbial source tracking using a library-independent approach. Concentrations of somatic coliphages using 37 and 44.5 degrees C incubation temperatures were found to be significantly different and the higher temperature may be more specific for faecal contamination. The EP/A technique detected coliphages infecting Escherichia coli Famp in 38 (66%) of the 58 surface water samples negative for F+ coliphages by the SAL method. However, coliphages isolated by EP/A were found to be less representative of coliphage diversity within a sample. Among the 2939 coliphage isolates tested from surface water and known source samples, 813 (28%) were found to be F+ RNA. The majority (94%) of surface water F+ RNA coliphage isolates typed as group I. Group II and/or III viruses were identified from 14 surface water stations, the majority of which were downstream of wastewater discharges. These sites were likely contaminated by human-source faecal pollution. CONCLUSIONS: The results suggest that faecal contamination in surface waters can be detected and source identifications aided by coliphage analyses. SIGNIFICANCE AND IMPACT OF THE STUDY: This study supports the premise that coliphage typing can provide useful, but not absolute, information to distinguish human from animal sources of faecal pollution. Furthermore, the comparison of coliphage isolation methods detailed in this study should provide valuable information to those wishing to incorporate coliphage detection into water quality assessments.

Animals↗

PubMed1990

Solution hybridization assay for detecting genetically engineered microorganisms in environmental samples.

A solution hybridization method was developed for detecting genetically engineered microorganisms in environmental samples. The detection method involves recovery of DNA from the microbial community of an environmental sample followed by hybridization in solution with a radiolabeled RNA gene probe. After nuclease digestion of non-hybridized probe RNA, the DNA-RNA hybrids formed in the solution hybridization reaction are separated by sephadex or hydroxyapatite column chromatography and detected by liquid scintillation counting. Using solution hybridization-gene probe detection, as few as 100-1000 target cells per gram sediment sample of a 2,4,5-T-degrading genetically engineered microorganisms could be detected.

Chromatography, Gel↗

PubMed2006

Rapid quantitative profiling of complex microbial populations.

Diverse and complex microbial ecosystems are found in virtually every environment on earth, yet we know very little about their composition and ecology. Comprehensive identification and quantification of the constituents of these microbial communities--a 'census'--is an essential foundation for understanding their biology. To address this problem, we developed, tested and optimized a DNA oligonucleotide microarray composed of 10,462 small subunit (SSU) ribosomal DNA (rDNA) probes (7167 unique sequences) selected to provide quantitative information on the taxonomic composition of diverse microbial populations. Using our optimized experimental approach, this microarray enabled detection and quantification of individual bacterial species present at fractional abundances of <0.1% in complex synthetic mixtures. The estimates of bacterial species abundance obtained using this microarray are similar to those obtained by phylogenetic analysis of SSU rDNA sequences from the same samples--the current 'gold standard' method for profiling microbial communities. Furthermore, probes designed to represent higher order taxonomic groups of bacterial species reliably detected microbes for which there were no species-specific probes. This simple, rapid microarray procedure can be used to explore and systematically characterize complex microbial communities, such as those found within the human body.

Adult↗

PubMed2001

Endogenous isolation of replicon probes for assessing plasmid ecology of marine sediment microbial communities.

Six functional replication origins (repGA14, repGA33, repGA70, repSD41, repSD164 and repSD172), obtained from endogenously isolated, broad-host-range (BHR) marine plasmids ranging in size from 5 to 60 kb, were used to determine plasmid occurrence in three coastal marine sediment sites (in California, Georgia and South Carolina, USA). The plasmid-specific replicons were isolated from plasmid-bearing marine sediment bacteria belonging to the alpha and gamma subclasses of the Proteobacteria. The plasmid sources of the endogenous replicons were considered to be cryptic due to a lack of identifiable phenotypic traits. The putative Rep proteins from a number of these replicons showed similarity to replicons of two recognized families: RCR group III (repSD164) and the FIA family of theta group A (repSD41, repSD121, repGA33 and repGA14). Plasmids isolated from marine bacteria belonging to the genera Pseudoalteromonas, Shewanella and Vibrio cultivated from geographically different coastal sites exhibited homology to two of the marine plasmid replicons, repSD41 and repGA70, obtained from a Vibrio sp. The repGA33 plasmid origin, obtained from a Shewanella sp. isolated from coastal Georgia, was detected in 7% of the Georgia marine sediment Shewanella sp. isolates. Microbial community DNA extracted from marine sediments was also screened for the presence of the plasmid replication sequences. Community DNA samples amplified by PCR yielded a positive signal for the repSD172 and repGA14 replication sequences. The replication origin of BHR plasmid RK2 (IncP) was also detected in marine Vibrio sp. and microbial community DNA extracted from the three coastal sites. These findings provide molecular evidence that marine sediment bacteria harbour an untapped population of BHR plasmids.

Alphaproteobacteria↗

PubMed1976

Counterimmunoelectrophoresis in the detection of antibodies against Coccidioides immitis.

In recent years counterimmunoelectrophoresis has been increasingly used in the diagnosis of microbial diseases, and our study was undertaken to evaluate its possible use in the rapid detection of antibodies against Coccidioides immitis. One hundred twelve specimens from 50 patients were studied. The study population comprised the following: Group I, 34 patients with an active coccidioidomycosis infection; Group II, five patients with a positive coccidioidin skin test; Group III, five patients with a negative coccidioidin skin test; and Group IV, six patients with other fungal infections. Counterimmunoelectrophoresis was positive in 93 of 96 specimens in Group I and negative in the other groups. The results obtained by counterimmunoelectrophoresis correlated well with complement fixation and double immunodiffusion and indicate that it is an excellent tool for the diagnosis of patients with coccidioidomycosis.

Acute Disease↗

PubMed2002

Enumeration of 16S rDNA of Desulfotomaculum lineage 1 in rice field soil by real-time PCR with SybrGreen detection.

Real-time PCR is a new and highly sensitive method for the quantification of microbial organisms in environmental samples. This work was conducted to evaluate real-time PCR with SybrGreen (SG) detection as quantification method for Desulfotomaculum lineage 1 organisms in samples of rice field soil. The method was optimized in several parameters like SG concentration. These allowed quantitative PCR with different primer combinations yielding PCR products with lengths up to 1066 bp and with sensitivities of 10(2) targets for all assays. The detection limit in environmental DNA extracts (rice bulk soil and rice roots) was 10(6) targets per gram dry weight according to the dilution of the DNA extracts necessary to overcome PCR inhibition of humic substances. A verification, that the fluorescence increase was due to specific PCR products, was done by agarose gel electrophoresis since melting curve analysis of the PCR products did not show a distinct peak in the first derivative, when the environmental DNA extracts were used in PCR. Amplification with a primer combination specific for Desulfotomaculum lineage 1 organisms showed an abundance of this group of approximately 2% and 0.5% of the eubacterial 16S rDNA targets in rice bulk soil and rice root samples, respectively. Approximately half of this number was obtained in both habitats with a PCR assay specific for a Desulfotomaculum sequence cluster obtained previously from rice field soil.

Benzothiazoles↗

PubMed1983

Rapid and economical identification and antimicrobial susceptibility test methodology for urinary tract pathogens.

To decrease the time and cost of processing urine cultures, we devised a critical pathway to identify and perform antibiotic susceptibility tests on commonly isolated microbial pathogens within 6 h of growth detection. The strategy was based on eliminating expensive kits and automated procedures when not required. A pathway utilizing a statistical matrix and three rapid biochemical tests required to identify the most common pathogen, Escherichia coli, was developed. This species, which represented 82% of urinary isolates, was identified in 1 h for less than 10% the cost of a commercial kit. The specificity of the 1-h E. coli identification battery was greater than or equal to 99.9% with a sensitivity of 93%. In addition, this critical pathway, adapting published methods, permitted the identification of other enteric pathogens, the group D streptococci, and Pseudomonas aeruginosa within 4 to 6 h. Furthermore, it accounted for other microbes that required longer periods of incubation. The pathway also included a rapid disk diffusion sensitivity test. Utilizing the critical pathway strategy, 76% (E. coli frequency of 0.82 X E. coli sensitivity of 0.93) of all urinary pathogens were identified within 1 h, and 98% were identified within 4 h with an antibiotic sensitivity test available within 6 h after the observation of growth. Costs were reduced from 2.5 to 5.0 times. This methodology is applicable to other specimen types.

Anti-Bacterial Agents↗

PubMed2002

A putative iron-regulated TonB-dependent receptor of Mannheimia (Pasteurella) haemolytica A1: possible mechanism for phase variation.

A recombinant plasmid that codes for a novel iron receptor protein (Irp) of Mannheimia (Pasteurella) haemolytica A1 was isolated by the partial complementation of an Escherichia coli fur mutant. The deduced amino acid sequence of Irp exhibited characteristics typical of TonB-dependent receptors. These include: a TonB-box at the N-terminal; a 50 amino acid region homologous to the "plug" domain of the E. coli FhuA and FepA receptors; and a C-terminal TonB-dependent signature which likely functions as an outer membrane anchoring domain. Previously uncharacterized Irp homologues were detected by BLAST analysis of available databases and incomplete microbial genomes. When the irp homologues from Neisseria gonorrhoeae and N. meningitidis were cloned by PCR and expressed in E. coli, novel proteins of the predicted size (84kDa) were detected in cell lysates, demonstrating that these are functional genes. The M. haemolytica A1 irp gene undergoes phase variation at a nucleotide region which contain the sequence AAAAAAATTAAAA (7A-2T-4A) flanked by a short inverted repeat. Site-specific mutagenesis of the 7A-2T-4A sequence as well as replacement of the inverted repeats resulted in a stable construct that expressed the Irp protein without phase variation. The expression of irp in M. haemolytica A1 was regulated by iron concentrations and most likely a Fur homologue, consistent with the proposed function of Irp in iron metabolism. The irp genes may represent contingency loci that play a role in iron acquisition during infection.

Amino Acid Sequence↗

PubMed2002

Metabolic shifts in hypersaline microbial mats upon addition of organic substrates.

The responses of hypersaline microbial mats to the addition of acetate, glycolate or glucose were investigated using oxygen, pH and sulphide microsensors. Changes in community structure were investigated with molecular techniques. Acetate addition inhibited respiration in the photic zone, stimulated respiration in the aphotic zone and had no effect on gross photosynthesis. Glycolate addition strongly increased both respiration and gross photosynthesis in the photic zone. Thus, glycolate and acetate were probably consumed in those regions of the mat where these substrates are usually formed. Moreover, photosynthesis was only stimulated by increased respiration and concomitant CO2 production in the photic zone which indicates that the photosynthetic and respiratory populations must be present in close proximity to each other. Glucose addition had an unexpected negative effect on the microbial population, strongly inhibiting both respiration and gross photosynthesis within hours. After four days, oxygen profiles in the light were equal to those measured in the dark. After replacing the water phase with unamended water, photosynthesis and respiration recovered within a week. None of the physiological changes were accompanied by detectable shifts in the cyanobacterial or the overall microbial community. The mechanism of inhibition of photosynthesis by glucose requires further investigation.

Acetates↗

PubMed2006

A review of current and future molecular diagnostic tests for use in the microbiology laboratory.

Nucleic acid-based diagnostics gradually are replacing or complementing culture-based, biochemical, and immunological assays in routine microbiology laboratories. Similar to conventional tests, the first-generation deoxyribonucleic acid assays determined only a single analyte. Recent improvements in detection technologies have paved the way for the development of multiparameter assays using macroarrays or micro-arrays, while the introduction of closed-tube real-time polymerase chain reaction systems has resulted in the development of rapid microbial diagnostics with a reduced contamination risk. The use of these new molecular technologies is not restricted to detection and identification of microbial pathogens but also can be used for genotyping, allowing one to determine antibiotic resistance or to perform microbial fingerprinting.

Bacteria↗

PubMed2005

Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases.

Phylogenetics is a powerful tool for microbial epidemiology, but it is a tool that is often misused and misinterpreted by the field. Microbial epidemiologists are cautioned that in order to draw any inferences about the order of descent from a common ancestor it is necessary to correctly root a phylogenetic tree. Epidemiological samples of microbial populations typically include both ancestors and their descendants. In order to illustrate the relationships of those isolates, the phylogenetic method used must be able to detect zero-length branches. Unweighted Pair-Group Method (UPGMA) is the phylogenetic method that is most widely used in microbial epidemiology. Because UPGMA cannot detect zero length branches, and because it places the root of the tree based on a usually-false assumption, UPGMA is the worst possible choice among the several phylogenetic methods available. Because microbial epidemiology deals with relationships among strains within a species, rather than with relationships among species, recombination within those species can render phylogenetic trees meaningless and positively misleading. When there is evidence of significant recombination within the species of interest phylogenetic trees should not be used at all. Instead, alternative tools such as eBURST should be used to understand relationships among isolates.

Base Sequence↗

PubMed2005

Community-level analysis: genes encoding methanopterin-dependent enzymes.

This chapter describes a set of novel tools for the environmental detection of C1 transfer functions linked to the cofactor methanopterin. These tools include degenerate environmental primers targeting four of the most conserved genes in the methanopterin-linked C1 transfer pathway in bacteria, fae, mtdB, mch, and fhcD, and extensive databases of the respective genes. The tools described are suitable for detecting methanopterin-linked formaldehyde-oxidizing capacity in natural microbial communities and for determining the phylogenetic affiliations of major phyla involved in single-carbon cycling in the environment. The range of detection includes a variety of methano- and methylotrophic groups, other proteobacterial species capable of methanopterin-mediated reactions, and a variety of planctomycetes, as well as groups of microbes with currently unknown phylogenetic affiliations.

Bacterial Proteins↗

PubMed1983

Colorimetric determination of catechol siderophores in microbial cultures.

A highly sensitive spectrophotometric method for the selective detection of catechol compounds such as catechol siderophores (e.g., enterobactin) is described. The basis of the method involves the ability of the vicinal aromatic hydroxyl groups under acidic conditions to bring about a reduction of Fe3+ (from ferric ammonium citrate) to Fe2+. Detection of Fe2+ in the presence of Fe3+ is made with 1,10-phenanthroline under previously established conditions. The assay mixture is heated at 60 degrees C for 1 h to accelerate the development of color which is subsequently measured at 510 nm. The Beer-Lambert law is obeyed over the range of 0.16 to 60 microM 2,3-dihydroxybenzoic acid. Compared to the Arnow nitration method, the assay is more responsive, is approximately seven times more sensitive, and is effective with catechols substituted at positions 3 and 4. The method gives positive results with catechols such as DL-DOPA, L-dopamine, (+/-)-epinephrine, and DL-norepinephrine. Very rapid color development is obtained with ascorbic acid and p-diols, while m-diols are poorly detected. Low degrees of reactivity are shown by hydroxylamino and hydroxamate compounds. Phenolic, sulfydryl, indolyl, and quinonyl derivatives do not interfere with the reaction. The method has been adapted to determine catechol compounds in the culture medium of bacterial cells grown at different iron concentrations.

Catechols↗

PubMed1981

Microbial surface interactions: reduction of the haemagglutination activity of the oral bacterium Fusobacterium nucleatum by absorption with Streptococcus and Bacteroides.

Oral strains of Fusobacterium nucleatum showed haemagglutination (HA) of sheep red blood cells and attachment of HA-active F. nucleatum fragments to other microorganisms allowed a means of studying microbial surface interactions. HA-active sonicated fragments (SF) prepared from F. nucleatum were mixed with whole cell suspensions of 48 bacterial strains and, after incubation, the whole cells were separated from the non-absorbed fragments by differential centrifugation. Attachment of F. nucleatum fragments to the cells was indicated by a reduction in the HA activity of the SF in the supernatant fluid remaining after absorption with whole cells. HA activity of the microbial cells used for absorption and the detection of F. nucleatum fragments on these cells by an indirect fluorescent antibody technique provided further evidence of attachment. Of the 48 strains tested, 10 absorbed F. nucleatum HA-active fragments. They included Bacteroides gingivalis, Bacteroides fragilis subsp. distasonis, Bacteroides corrodens, Streptococcus morbillorum, Streptococcus sanguis (Blackburn and JC 74) and Streptococcus mutans AHT, BHT, 10449 and 6715. Chelators revealed that F. nucleatum attached to the microorganisms via a Ca2+-dependent interaction. Sugar inhibition demonstrated that F. nucleatum attached to the microorganisms via a D-galactose-containing moiety on their surface. A reduction in the absorption of F. nucleatum HA-active fragments by Strep. mutans grown in a higher concentration of sucrose was observed.

Absorption↗

PubMed1982

Attachment of cell fragments of Fusobacterium nucleatum to oral epithelial cells, gingival fibroblasts and white blood cells.

The characteristic haemagglutination (HA) caused by Fusobacterium nucleatum strains was used for measuring their attachment to oral epithelial, gingival fibroblast and white blood cells. Whole cells and sonicated preparations of oral F. nucleatum strains VPI No. 4355, 10197 and ATCC No. 10953 haemagglutinated human and sheep red blood cells. Sonicated preparations of the organisms were tested for HA activity before and after absorption with human cells. Buccal epithelial, gingival fibroblast and white blood cells bound the HA-active fragments, as observed by: (1) decrease in the HA activity of the sonicated preparation after absorption, (2) increase in HA activity of the cells used for absorption, (3) presence of microbial fragments on the cells after absorption detected by fluorescent antibody. The HA-active fragments were released from the cells by EDTA; furthermore, galactose but not glucose inhibited the attachment of F. nucleatum to human cells. The role of cell binding in colonization by the organisms and in immune-stimulated damage to host cells is important.

Absorption↗

PubMed1996

Biogenic amines: their importance in foods.

Biogenic amines are important nitrogen compounds of biological importance in vegetable, microbial and animal cells. They can be detected in both raw and processed foods. In food microbiology they have sometimes been related to spoilage and fermentation processes. Some toxicological characteristics and outbreaks of food poisoning are associated with histamine and tyramine. Secondary amines may undergo nitrosation and form nitrosamines. A better knowledge of the factors controlling their formation is necessary in order to improve the quality and safety of food.

Bacteria↗