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At least 19 recordsLinked to original sources
PubMed2025

kSanity: A k-mer based application for precision bacterial strain detection and quantification.

MOTIVATION: Accurate detection and quantification of bacterial strains in clinical samples is necessary to measure their colonization and persistence. Past methods to achieve this relied either on strain-specific qPCR assays, or shotgun metagenomic read mapping approaches. The resident microbial community is a major source of interference in both assays because it can contain conspecific strains bearing similarity to the focal strain(s). RESULTS: We present kSanity, a k-mer based application for the detection and quantification of targeted bacterial strains in shotgun metagenomic data. Because kSanity uses exact string matches between the reads and reference, it is less sensitive to interference by conspecific strains. We test the performance of kSanity using a combination of in silico spike-in experiments, and in vivo observational data. Our results demonstrate that kSanity provides precise and accurate quantification of targeted bacterial strains, even when they are present at low sequence coverage in the metagenome. AVAILABILITY AND IMPLEMENTATION: kSanity is available at: https://github.com/ravel-lab/kSanity.

bacterial strain detection↗
PubMed1987

A bacterial strain for detecting agents that produce free radical-mediated DNA strand breaks.

In an E. coli strain carrying two mutations, one in the dnaC gene involved in initiation of DNA replication and another in the uvrB gene which affects the excision-repair system, it has been shown that the SOS response cannot be induced by UV. This is probably due to the absence of any inducing signal (Salles and Defais, 1984). The capacity to induce the SOS network was followed using RecA protein amplification as a probe. When breaks were produced in DNA, RecA protein induction was restored. We describe here a strain in which both RecA protein and beta-galactosidase from a sfiA::lacZ fusion can be measured simultaneously in the same bacterial extract. In conditions in which no replication proceeds, this strain can be used to detect the ability of chemicals to produce free radical-mediated DNA breaks in vivo.

Bleomycin↗
PubMedDate not supplied

[Obtaining bioluminescent bacterial strains for detection of thallium ions].

The possibility of Alcaligenes eutrophus T1 luxphenotype creation by temperature induced mutagenesis has been shown. These mutants are able to emit light after induction by thallium ions. This biological method of thallium detection possesses high specificity and sensitivity (0.5 microM of metal). Such microbial cells can be used to quantify bioavailability of thallium part in the environment.

Biological Availability↗
PubMed2006

Detection of bacterial strains producing sulbactam- or tazobactam-sensitive beta-lactamases by the use of disks containing the inhibitors alone instead of combining them with antibiotics.

The author demonstrated that disks containing beta-lactamase inhibitors sulbactam or tazobactam combined with ampicillin (SAM) and piperacillin (TZP) are not suitable for performing the double-disk synergy test (DDST) with the aim of determining the sensitivity of beta-lactamases to these inhibitors. The presence of antibiotics (especially of piperacillin) is so disturbing that the results of testing are not specific. In contrast, the use of disks containing sulbactam or tazobactam alone yields very specific results. The author suggested to the firms producing sensi-disks that they make these commercially available to laboratory workers.

Ampicillin↗
PubMed2006

[Isolation and characterization of 4 benzene/toluene-degrading bacterial strains and detection of related degradation genes].

Four bacteria with the ability of benzene or toluene degradation were isolated from the active sludge of a life sewage treatment farm, two of which degraded benzene, and named B1 and B2; and other two degraded toluene, and named J2 and J6, respectively. Sequence analysis of 16S rDNA showed that strain B1 and J2 belonged to Pseudomonas, and B2, J6 belonged to Acinetobacter. They all well adapted to the circumstances from 18 degrees C to 37 degrees C, 0% to 3% NaCl, and pH 7-10. The isolate J2 showed a high tolerance to organic solvent as it could grow well in the medium containing 70% (V/V) toluene, and degraded 92.4% of 0.1% (V/V) toluene within 72 hrs in a medium with toluene as the sole carbon source; while J6 presented 84.8% degradation under the same conditions to toluene. In the case of B1 and B2, they degraded 67.7% and 94.2% of 0.1% (V/V) benzene within 72 hours, respectively. Moreover, all strains were detected harboring the same benzene dioxygenase gene. In addition, J2 and J6 also had toluene dioxygenase genes which share 86.5% homology from each other. These bacteria are of potential in bio-treatment of benzene and toluene pollutants.

Acinetobacter↗
PubMed2003

Quantitative detection of probiotic Bifidobacterium strains in bacterial mixtures by using real-time PCR.

Strain-specific rRNA-targeted primers were designed for the quantitative detection of Bifidobacterium infantis Y1, B. breve Y8 and B. longum Y10 used in a pharmaceutical probiotic product (VSL-3). PCR and real-time PCR techniques with the selected primers were employed for the direct enumeration of the bifidobacteria in the probiotic preparation and for studying their kinetic characteristics in batch cultures. These analysis revealed that B. infantis Y1 was the predominant strain in the probiotic product and that its growth rate was the highest. Since B. infantis Y1, B. breve Y8 and B. longum Y10 are co-cultured during the industrial production of VSL-3, the kinetic characteristics of these strains can explain their different concentrations in the probiotic preparation. A validation of the PCR quantification method was performed by identifying a representative number of isolates from the bacterial mixtures with automated ribotyping. The methodology described represents a useful tool for the specific quantitative detection of bacterial strains and species in complex mixtures such as pharmaceutical preparations, dairy starter cultures, faecal samples and biopsies.

Bacterial Typing Techniques↗
PubMed2004

Genetic characterization and specific detection of beer-spoilage Lactobacillus sp. LA2 and related strains.

AIMS: Lactobacillus sp. LA2 (DSM15502) and related strains (LA2 group) possess strong beer-spoilage ability. The 16S rDNA sequence of LA2 strain is virtually indistinguishable from that of L. collinoides, generally considered to be nonbeer-spoilage bacteria. The aim of this study was to identify the genetic marker to distinguish between Lactobacillus sp. LA2 group and L. collinoides and to provide a rapid means of identifying beer-spoilage strains belonging to Lactobacillus sp. LA2 group. METHODS AND RESULTS: The 16-23S rDNA intergenic spacer (ITS) regions of Lactobacillus sp. LA2 and L. collinoides JCM1123T were sequenced to identify a genetic marker to distinguish between the two groups. As a result, 300 and 500 bp ITS regions of Lactobacillus sp. LA2 were found to be almost identical with those of L. collinoides JCM1123T. Sequence comparison analysis between Lactobacillus sp. LA2 and L. collinoides JCM1123T revealed that the two contiguously located nucleotides are absent in both ITS regions of Lactobacillus sp. LA2. Based on the sequence difference, we have designed specific PCR primers with a minor modification to the primer sequence that can differentiate between beer-spoilage Lactobacillus sp. LA2 group and nonbeer-spoilage L. collinoides. CONCLUSIONS: The PCR-based method has been developed to identify Lactobacillus sp. LA2 group, providing a rapid and sensitive means of determining the beer-spoilage ability of detected bacterial strains. SIGNIFICANCE AND IMPACT OF THE STUDY: The substitution of one nucleotide, located at the third position to the 3'-end in the primer sequence, enhanced the specificity of the PCR method while retaining sufficient sensitivity. The nucleotide gap identified in this study appeared to serve as a useful genetic marker that can differentiate 12 beer-spoilage Lactobacillus sp. LA2 group strains from its close relatives that exhibit no beer-spoilage ability.

Bacterial Typing Techniques↗
PubMed1995

Salmonella strains and mammalian cells genetically engineered for expression of sulfotransferases.

Rat and human sulfotransferases (STs) were expressed in his- S. typhimurium strains. These new bacterial strains detected various mutagens which are difficult to recognize in traditional test systems, including benzylic alcohols derived from polycyclic aromatic hydrocarbons, hycanthone and 1'-hydroxysafrole. STs were also stably expressed in V79 Chinese hamster cells, which do not express endogenous ST and are suitable for the detection of genotoxic effects. Positive responses in these test systems were observed with various benzylic alcohols, including benzo[a]pyrene-7,8,9,10-tetrols. We demonstrate that a few reactive sulfuric acid conjugates are efficiently detected as genotoxicants only when generated directly within the indicator cell.

Animals↗
PubMed1998

Urinary and serum mutagenicity studies with rats implanted with depleted uranium or tantalum pellets.

During the 1991 Persian Gulf War several US military personnel were wounded by shrapnel fragments consisting of depleted uranium. These fragments were treated as conventional shrapnel and were not surgically removed to spare excessive tissue damage. Uranium bioassays conducted over a year after the initial uranium injury indicated a significant increase in urine uranium levels above natural background levels. The potential mutagenic effects of depleted uranium are unknown. To assess the potential mutagenic effects of long-term exposure to internalized depleted uranium, Sprague-Dawley rats were implanted with depleted uranium and their urine and serum were evaluated for mutagenic potential at various times after pellet implantation using the Ames Salmonella reversion assay. Tantalum, an inert metal widely used in prosthetic devices was used for comparison. Enhancement of mutagenic activity in Salmonella typhimurium strain TA98 and the Ames II mixed strains (TA7001-7006) was observed in urine samples from animals implanted with depleted uranium pellets. In contrast, urine samples from animals implanted with tantalum did not show a significant enhancement of mutagenic activity in these strains. In depleted uranium-implanted animals, urine mutagenicity increased in a dose- and time-dependent manner demonstrating a strong positive correlation with urine uranium levels (r = 0.995, P < 0.001). There was no mutagenic enhancement of any bacterial strain detected in the sera of animals implanted with either depleted uranium or tantalum pellets. The results suggest that uranium content in the urine is correlated with urine mutagenicity and that urinary mutagenicity might be used as a biomarker to detect exposure to internalized uranium.

Animals↗
PubMed1997

Development and application of monoclonal antibodies for in situ detection of indigenous bacterial strains in aquatic ecosystems.

Strain-specific monoclonal antibodies (MAbs) were developed for three different bacterial isolates obtained from a freshwater environment (Lake Plusssee) in the spring of 1990. The three isolates, which were identified by molecular methods, were as follows: Cytophaga johnsonae PX62, Comamonas acidovorans PX54, and Aeromonas hydrophila PU7718. These strains represented three species that were detected in high abundance during a set of mesocosm experiments in Lake Plusssee by the direct analysis of low-molecular-weight RNAs from bacterioplankton. We developed one MAb each for the bacterial isolates PX54 and PU7718 that did not show any cross-reactivity with other bacterial strains by immunofluorescence microscopy. Each MAb recognized the general lipopolysaccharide fraction of the homologous strain. These MAbs were tested successfully for their ability to be used for the in situ detection and counting of bacteria in lake water by immunofluorescence microscopy. During the spring of 1993, A. hydrophila PU7718 showed a depth distribution in Lake Plusssee with a pronounced maximum abundance at 6 m, whereas Comamonas acidovorans PX54 showed a depth distribution with a maximum abundance at the surface. The application of these MAbs to the freshwater samples enabled us to determine the cell morphologies and microhabitats of these strains within their natural environment. The presence of as many as 8,000 cells of these strains per ml in their original habitats 3 years after their initial isolation demonstrated the persistence of individual strains of heterotrophic bacteria over long time spans in pelagic habitats.

Aeromonas↗
PubMed1989

Detecting aberrant strains in bacterial groups as an aid to constructing databases for computer identification.

Computer assisted identification systems require that databases on the test results of the species are of high quality. One reason for poor quality is the inadvertent inclusion of strains that do not belong to a taxon; this can readily occur in groups where ancillary criteria (e.g. serology) are not available. A possible strategy is to exclude strains that are very atypical in their properties, i.e. that are very outlying, provided an objective criterion can be used. A computer program, OUTLIER, for the detection of outlying strains in bacterial clusters was evaluated. A brief description of the theory and operation of the program is given. The program uses as an objective criterion the degree to which the strain data fits a chi-square. This allows easy identification of aberrant strains that should be excluded in constructing a database. The program utilizes 1.0 data and calculations are based upon a choice of one of four identification coefficients. The relative merits of these four coefficients were examined for eight sets of bacterial data. Two of the coefficients, -log10 Willcox likelihood and Taxonomic distance squared appear to show little significant differences and we recommend these for routine work, with the first being the more useful. The Pattern distance squared was useful in indicating where atypical strains may be metabolically less active or slow-growing members of a cluster rather than true outliers. The Variance-weighted Taxonomic distance squared behaved anomalously and we do not recommend it.

Bacteria↗
PubMed1975

Detection of carcinogens as mutagens: bacterial tester strains with R factor plasmids.

We described previously a simple test on petri plates for detecting chemical carcinogens as mutagens, using an especially sensitive set of bacterial strains to detect mutagenic acitivty and a mammalian liver extract for carcinogen activity. We now extend the utility of the method by introducing two new bacterial strains which can detect with great sensitivity many carcinogens which we did not detect before or detected with less sensitivity. Among these carcinogens are aflatoxin B-1, sterigmatocystin, benzyl chloride, benzo[a]-pyrene, 7,12-dimethylbenzanthracene, 1'-acetoxysafrole, and the nitrofuran food additive furylfuramide (AF-2). The new strains TA100 and TA98 contain an R factor plasmid, pKM101, in our standard tester strains TA1535 and TA1538. The R factor increases mutagenesis with certain mutagens, but not others. We present evidence that the mutagens that become more effective work through an error-prone recombinational repair.

Biological Assay↗
PubMedDate not supplied

Detection of tetracyclines with luminescent bacterial strains.

The performance of two bioluminescent Escherichia coli K-12 strains for the specific detection of the tetracycline family of antimicrobial agents was compared, and the analytical applicability of one of the strains was preliminarily evaluated. One sensor plasmid contained the bacterial luciferase operon of Photorhabdus luminescens under the control of the tetracycline-responsive element from transposon Tn10 (15). An analogous plasmid construction with firefly (Photinus pyralis) luciferase reporter gene was constructed, and these two divergent tetracycline-inducible light-emitting systems were compared for their suitability for the qualitative detection of tetracyclines. Both sensor strains behaved in a similar manner kinetically, and the most sensitive tetracycline response for both sensor strains was achieved in 90-120 min by performing the assay at 37 degrees C. The sensor strain containing the bacterial luciferase operon responded slightly more sensitively to different tetracyclines than the strain containing firefly luciferase gene. The sensor bacteria retained their inducibility in lyophilization, and freeze-dried cells detected tetracyclines as sensitively as freshly cultivated sensor cells. The preliminary results from the analysis of tetracycline-spiked pork serum samples indicated that these sensor bacteria could be used to screen veterinary samples for tetracycline residues in real-time.

Animals↗
PubMed1982

Comparative evaluation of different pairs of DNA repair-deficient and DNA repair-proficient bacterial tester strains for rapid detection of chemical mutagens and carcinogens.

The aim of the present study was to evaluate the usefulness of different pairs of DNA repair-deficient and DNA repair-proficient bacterial tester strains in a mutagenicity/carcinogenicity screen, possibly as complements to the Ames test. 70 carcinogenic and non-carcinogenic compounds, representing a variety of chemical structures, were tested for their DNA-damaging effects, using 6 different DNA-repair-deficient bacterial strains. 2 Bacillus subtilis systems, H17/M45 and HLL3g/HJ-15, were used. The susceptibility of Escherichia coli AB1157 was compared with the susceptibility of 4 recombination-deficient mutants, JC5547, JC2921, JC2926 and JC5519. The test compounds were applied onto paper disks (spot test, ST), or incorporated into a top agar layer (agar-incorporation test, AT). The 2 B. subtilis systems were generally found to be more sensitive and reliable than the assays using E coli. The incorporation of the test compounds in the agar increased the sensitivity of the test for polycyclic aromatic hydrocarbons and other poorly water-soluble compounds. Hydrazines and several other highly polar chemicals could be tested more efficiently when applied onto paper disks. About 30% of the test compounds did not induce any growth inhibition and so could not be tested properly. In order to evaluate the ability of these DNA-repair tests to complement the Ames Salmonella mutagenicity test in a genetic toxicology screening program, results from this study were compared with published data both on mutagenicity in the Ames test and on carcinogenicity. 8 carcinogens generally found to be non-mutagenic for Salmonella were tested: 2 showed DNA-damaging properties (mitomycin C, 1,2-dimethylhydrazine), 5 failed to do so (actinomycin D, griseofulvin, thioacetamide, diethylstilbestrol, safrole), and one (thiourea) was not toxic, so that no classification was possible. 2 non-carcinogenic bacterial mutagens were examined; one, sodium azide, was equitoxic for repair-proficient and -deficient strains, while the other, nitrofurantoin, primarily inhibited repair-deficient strains. The DNA-repair tests failed to indicate the mutagenic and carcinogenic properties of acridine orange. Nalidixic acid, a non-mutagenic DNA synthesis inhibitor, damaged bacterial DNA. Apart from the differences summarized above, carcinogenicity was indicated correctly by the Salmonella S9 assay and most sets of DNA-repair-deficient and DNA-repair-proficient tester strains evaluated in this study. Thus, several more carcinogens could be detected by performing the Ames test and the bacterial DNA-repair tests in tandem than by using either test alone. Nevertheless, the use of both bacterial in vitro systems in a battery of short-term tests for mutagenicity/carcinogenicity evaluation is not considered to be ideal, since the Ames test and the pairs of DNA-repair-deficient and DNA-repair-proficient tester strains used had several shortcomings in common under the conditions of this study.

Bacillus subtilis↗
PubMed2001

Rapid detection and identification of bacterial strains by Fourier transform near-infrared spectroscopy.

The use of Fourier transform near-infrared (FT-NIR) spectroscopy and multivariate pattern recognition techniques for the rapid detection and identification of bacterial contamination in liquids was evaluated. The complex biochemical composition of bacteria yields FT-NIR vibrational transitions (overtone and combination bands) that can be used for classification and identification. Bacterial suspensions (Escherichia coli HB101, E. coli ATCC 43888, E. coli 1224, Bacillus amyloliquifaciens, Pseudomonas aeruginosa, Bacillus cereus, and Listeria innocua) were filtered to harvest the cells and eliminate the matrix, which has a strong NIR signal. FT-NIR measurements were done using a diffuse reflection-integrating sphere. Principal component analysis showed tight clustering of the bacterial strains at the information-rich spectral region of 6000-4000 cm(-1). The method reproducibly distinguished between different E. coli isolates and conclusively identified the relationship between a new isolate and one of the test species. This methodology may allow for the rapid assessment of potential bacterial contamination in liquids with minimal sample preparation.

Bacillus↗
PubMed2004

GATC-specific restriction--modification systems in ruminal bacteria.

The GATC-specific restriction and modification activities were analyzed in 11 major bacterial representatives of ruminal microflora. Modification phenotype was observed in 13 out of 40 ruminal strains. MboI isoschizomeric restriction endonucleases were detected in 10 bacterial strains tested; three strains lacked any detectable corresponding endonuclease activity. The only examined strain of Mitsuokella multi-acida was found to possess a different type of endonuclease activity. This is the first report on restriction activity in ruminal treponemes M. multiacida and Megasphaera elsdenii.

Animals↗
PubMed2006

[Growth and detection of aerobic bacterial pathogens in BacT/Alert FA, BacT/Alert SA, Bactec Plus Aerobic/F and Bactec Standard Aerobic/F].

The article compares the ability of detection and detection times (TTD) of aerobic bacteria in the BacT/Alert FA, BacT/Alert SA, Bactec Plus Aerobic/F and Bactec Standard Aerobic/F bottles. Compared bottles were inoculated at the same time with the identical suspension of bacterial strain. All bottles detected bacterial pathogens even in the case of very low number of inoculated bacteria. The differences of TTD were detected between the bottles of compared hemocultivation systems. Bactec Plus Aerobic/F system is faster in the detection of the members of family Enterobacteriaceae at 1-3 hours, BacT/Aert FA system is faster in the detection of coagulase-negative staphylococci. Most difference was detected at Pseudomanas stutzeri, where the detection in BacT/Alert FA bottles was at 15 hours faster in opposite of Bactec Plus Aerobic/F bottles. In the bottles without sorbent Staphylococcus aureus and Streptococcus sanqui were detected faster in the system Bactec Standard Aerobic/F. The bottles BacT/Alert SA detected faster skin corynebacteria. Detected differences have not a practical importance for the blood stream infection diagnostics.

Bacteria, Anaerobic↗