Methods for the differentiation of microorganisms

Synergistic Impacts of Plant-Growth-Promoting Bacteria and Selenium Nanoparticles on Improving the Nutritional Value and Biological Activities of Three Cultivars of Brassica Sprouts

Due to the growing world population and increasing environmental stress, improving the production, nutritional quality, and pharmaceutical applications of plants have become an urgent need. Therefore, current research was designed to investigate the impact of seed priming using plant-growth-promoting bacteria (PGPB) along with selenium nanoparticles (SeNPs) treatment on chemical and biological properties of three Brassica oleracea cultivars [Southern star (VA1), Prominence (VA2), Monotop (VA3)]. With this aim, one out of five morphologically different strains of bacteria, namely, JM18, which was further identified via 16S rRNA gene sequencing as a Nocardiopsis species with strong plant-growth-promoting traits, isolated from soil, was used. To explore the growth-promoting potential of Nocardiopsis species, seeds of three varieties of B. oleracea were primed with JM18 individually or in combination with SeNP treatment. Seed treatments increased sprout growth (fresh and dry weights) and glucosinolate accumulation. The activity of myrosinase was significantly increased through brassica sprouts and consequently enhanced the amino-acid-derived glucosinolate induction. Notably, a reduction in effective sulforaphane nitrile was detected, being positively correlated with a decrease in epithiospecifier protein (EP). Consequently, the antioxidant activities of VA2 and VA3, determined by the ferric reducing antioxidant power (FRAP) assay, were increased by 74 and 79%, respectively. Additionally, the antibacterial activities of JM18-treated cultivars were improved. However, a decrease was observed in SeNP- and JM18 + SeNP-treated VA2 and VA3 against Serratia marcescens and Candida glabrata and VA1 against S. marcescens. In conclusion, seed priming with the JM18 extract is a promising method to enhance the health-promoting activities of B. oleracea sprouts.

Isolation, characterization, and molecular identification of soil bacteria showing antibacterial activity against human pathogenic bacteria

BACKGROUND

The present study dealt with the screening of soil bacteria with antibacterial activity from different locations in Bangalore, India. Antibiotics play the role of self-defense mechanism for the bacteria and are produced as secondary metabolites to protect themselves from other competitive microorganisms. The need for new antibiotics arose as the pathogenic bacteria acquire resistance to various antibiotics meant for treating human diseases. Given the importance of antibiotics of bacterial origin, standard techniques have been used to isolate and characterize the soil bacteria which showed antibacterial activity.

RESULTS

The isolated bacteria were tested against human pathogenic bacteria like Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae by primary and secondary screening methods. The isolates PR1, PR2, and PR3 were confirmed to have antibacterial activity against S. aureus, E. coli, P. aeruginosa, and K. pneumoniae by both methods. Studies on the effect of filter sterilization, autoclaving, and proteinase K treatment on culture filtrates showed filter sterilization as the best method. The effect of different carbon and nitrogen sources on the antibacterial activity showed that preference by each isolate differed for carbon and nitrogen requirements. The isolates PR1, PR2, and PR3 were identified as Bacillus aryabhattai strain PR-D07, Arthrobacter humicola strain PR-F07, and Neomicrococcus lactis strain PR-F11 through 16S rRNA sequencing.

CONCLUSION

Findings from this research work are encouraging and could proceed further to applied aspects. Only 3 bacterial isolates out of 263 isolates from soil samples displayed antibacterial activity against human pathogens S. aureus, E. coli, P. aeruginosa, and K. pneumoniae. They were identified as B. aryabhattai, A. humicola, and N. lactis by 16S rRNA studies and all of them are Gram-positive. Each isolate preferred different carbon and nitrogen sources for their enhanced antibacterial activity. Efficacy of the culture filtrates of these isolates was tested by filter sterilization, autoclaving, and proteinase K treatment. Filter-sterilized culture filtrates showed higher antibacterial activity than other treatments. A comparison of the antibacterial activity of culture filtrates and antibiotic streptomycin produced an inhibition zone of 18.5 mm and 15.5 mm respectively. This is the first report on the antibacterial activity of all the 3 bacterial strains (B. aryabhattai strain PR-D07, A. humicola strain PR-F07, and N. lactis strain PR-F11), against all the human pathogens, mentioned earlier. It is also found that the antibiotic factor is proteinaceous as proteinase K considerably reduced the antibacterial activity of the culture filtrates. With the above significant results, these 3 bacteria are considered to be promising candidates for the isolation of new antibacterial agents.

Biochemical identification techniques and antibiotic susceptibility profile of lipolytic ambiental bacteria from effluents

Abstract Different methodologies have been developed throughout the years to identify environmental microorganisms to improve bioremediation techniques, determine susceptibility profiles of bacteria in contaminated environments, and reduce the impact of microorganisms in ecosystems. Two methods of bacterial biochemical identification are compared and the susceptibility profile of bacteria, isolated from residential and industrial wastewater, is determined. Twenty-four bacteria were retrieved from the bacteria bank of the Environmental Microbiology Laboratory at the Institute of Biology (IB) of the Universidade Federal de Pelotas, Pelotas, Brazil. Bacteria were identified by conventional biochemical tests and by the VITEK ®2 automated system. Further, the susceptibility profile to antibiotics was also determined by the automated system. Six species of bacteria (Raoutella planticola, K. pneumoniae ssp. pneumoniae , Serratia marcescens, Raoutella sp., E. cloacae and Klebsiella oxytoca) were identified by conventional biochemical tests, while three species of bacteria (K. pneumoniae ssp. pneumoniae, S. marcescens and K. oxytoca ) were identified by VITEK®2 automated system. VITEK ®2 indicated agreement in 19 (79.17%) isolates and difference in five (20.83%) isolates when compared to results from conventional biochemical tests. Further, antibiotic susceptibility profile results showed that all isolates (100%) were resistant to at least one out of the 18 antibiotics tested by VITEK®2. Thus, no multi-resistant bacteria that may be used in effluent treatment systems or in bioremediation processes have been reported. Results indicate VITEK ® 2 automated system as a potential methodology in the determination of susceptibility profile and identification of environmental bacteria.

Evaluation of effect of high frequency electromagnetic field on growth and antibiotic sensitivity of bacteria

This study was aimed to evaluate the impact of high frequency electromagnetic fields (HF-EMF at 900 and 1800 MHz) on DNA, growth rate and antibiotic susceptibility of S. aureus, S. epidermidis, and P. aeruginosa. In this study, bacteria were exposed to 900 and 1800 MHz for 2 h and then inoculated to new medium when their growth rate and antibiotic susceptibility were evaluated. Results for the study of bacterial DNA unsuccessful to appearance any difference exposed and non-exposed S. aureus and S. epidermidis. Exposure of S. epidermidis and S. aureus to electromagnetic fields mostly produced no statistically significant decrease in bacterial growth, except for S. aureus when exposure to 900 MHz at 12 h. Exposure of P. aeruginosa to electromagnetic fields at 900 MHz however, lead to a significant reduction in growth rate, while 1800 MHz had insignificant effect. With the exception of S. aureus, treated with amoxicillin (30 µg) and exposed to electromagnetic fields, radiation treatment had no significant effect on bacterial sensitivity to antibiotics.

Growth of Paecilomyces variotii in B0 (diesel), B100 (biodiesel) and B7 (blend), degradation and molecular detection

The introduction of biodiesel to diesel may allow the fuel to be more susceptible to microorganism growth, especially during incorrect storage. To evaluate the effect of adding biodiesel in pure diesel on the growth of Paecilomyces variotii, microcosms containing pure diesel (B0), blend diesel/biodiesel (B7) and pure biodiesel (B100) were used. In microcosm with minimal mineral medium and B0, B7 or B100, after 60 days, the biomass (dry weight) formed at interface oil-water in B7 and B100 was significantly higher when compared to that of B0. Infrared analysis showed reduction of the carbonile fraction in B7 and B100 suggesting formation of intermediate compounds in B7. To monitor possible contamination of fuel storage tank by P. variotii samples were collected and analysed by specific-PCR assay for detection of P. variotii spores in the aqueous phase. This method was able to detect a minimum of 103 spores ml-1, corresponding to 0.0144 ng µl-1 of DNA. Specificity was tested against Aspergillus fumigatus and Pseudallescheria boydii.

Microbial control of the cotton leafworm Spodoptera littoralis (Boisd.) by Egyptian Bacillus thuringiensis isolates

Four local Bacillus thuringiensis (Bt) isolates that had been serologically identified as Bt var. kurstaki (Btk2, Btk3, and Btk66) and Bt var. mexicanensis (Btm27), in addition to two reference strains (4D20 and 4AC1), were laboratory assayed as microbial control agents against the Egyptian cotton leafworm Spodoptera littoralis (Boisd.). Polymerase chain reaction (PCR) amplification analysis revealed that each of the six experimental strains carries, at least, a cry1 type gene which expresses a protein toxin active against lepidopterous insects. Additionally, PCR amplification results demonstrated that 4D20 and Btk66 contain the Lepidoptera- and Diptera-active cry2 type gene and that Btk66 contains Coleoptera-active cry7 and cry8 genes. Among the six strains, Btk66 and Btm27 were the most promising microbial control agents against S. littoralis. The present findings were the first to report that Btm27 (classified as B. thuringiensis var. mexicanensis) is a very potent microbial control agent against S. littoralis-tested larvae. For more characterization of these two isolates, the sspO gene was investigated as a molecular chronometer. The DNA sequencing results proved that Btk66 and Btm27 carry sspO open reading frames with identical nucleotide sequences, suggesting a strong phylogenetic relationship between the two strains.

Characterization of Enterococcus spp. from human and animal feces using 16S rRNA sequences, the esp gene, and PFGE for microbial source tracking in Korea

Contamination from human and animal fecal waste is a primary cause of water pollution. Microbial source tracking (MST) may be a useful tool for high-quality environmental management and for assessing human health risks associated with water pollution. The goal of this study was to evaluate Enterococcus spp. as a target organism for MST. Thirty-four fecal samples were collected from five different sources (human, chicken, pig, cow, and goose) in South Korea. In total, 237 Enterococcus spp. were isolated from feces using membrane- Enterococcus indoxyl-beta-d-glucoside agar. The 16S rRNA gene and the whole genome were analyzed using nucleic acid sequencing and pulsed-field gel electrophoresis (PFGE), respectively. Both phylogenetic analysis and principal coordinate analysis using UniFrac were performed on the nucleic acid sequences of the 16S rRNA gene. According to P-tests from UniFrac, significant differences existed between Enterococcus spp. isolated from human feces and those from animal feces. In addition, we evaluated whether the esp gene of Enterococcus faecium could be a specific target for Enterococcus spp. isolated from human feces. Of 58 E. faecium isolates tested, only three were esp-positive. The specificity of the esp gene of E. faecium isolated from human feces was 100%, but the sensitivity was <10%. These results suggest that Enterococcus spp. have different molecular characteristics according to their fecal source and that these characteristics can be further identified by analyzing the esp gene and 16S rRNA sequences, whereas PFGE provides limited information on the fecal sources of Enterococcus spp.

Strain-specific genotyping of Bifidobacterium animalis subsp. lactis by using single-nucleotide polymorphisms, insertions, and deletions

Several probiotic strains of Bifidobacterium animalis subsp. lactis are widely supplemented into food products and dietary supplements due to their documented health benefits and ability to survive within the mammalian gastrointestinal tract and acidified dairy products. The strain specificity of these characteristics demands techniques with high discriminatory power to differentiate among strains. However, to date, molecular approaches, such as pulsed-field gel electrophoresis and randomly amplified polymorphic DNA-PCR, have been ineffective at achieving strain separation due to the monomorphic nature of this subspecies. Previously, sequencing and comparison of two B. animalis subsp. lactis genomes (DSMZ 10140 and Bl-04) confirmed this high level of sequence similarity, identifying only 47 single-nucleotide polymorphisms (SNPs) and four insertions and/or deletions (INDELs) between them. In this study, we hypothesized that a sequence-based typing method targeting these loci would permit greater discrimination between strains than previously attempted methods. Sequencing 50 of these loci in 24 strains of B. animalis subsp. lactis revealed that a combination of nine SNPs/INDELs could be used to differentiate strains into 14 distinct genotypic groups. In addition, the presence of a nonsynonymous SNP within the gene encoding a putative glucose uptake protein was found to correlate with the ability of certain strains to transport glucose and to grow rapidly in a medium containing glucose as the sole carbon source. The method reported here can be used in clinical, regulatory, and commercial applications requiring identification of B. animalis subsp. lactis at the strain level.

Comparison of molecular typing methods for the differentiation of Salmonella foodborne pathogens

Bacteria belonging to the genus Salmonella are among the leading causes of foodborne disease of bacterial etiology. These bacteria are also widely disseminated throughout the animal kingdom. The ability to identify the food source from which a human pathogen originated would be of great value in reducing the incidence of foodborne disease and the extent of disease outbreaks due to Salmonella. To date, efforts to identify the origin of these pathogens have centered on phenotypic and genotypic characterization of Salmonella isolates. This review focuses molecular or genotypic techniques that are currently being used for typing, and examines their strengths and weaknesses for determining the source of Salmonella foodborne infections.

Comparison of one-tube multiplex PCR, automated ribotyping and intergenic spacer (ITS) sequencing for rapid identification of Acinetobacter baumannii

Acinetobacter baumannii has emerged as a serious cause of nosocomial infections. Rapid identification of this pathogen is required so that appropriate therapy can be given and outbreaks controlled. This study evaluated a multiplex PCR and an automated ribotyping system for the rapid identification of Acinetobacter baumannii. In total, 22 different reference strains and 138 clinical isolates of Acinetobacter spp., identified by 16S-23S rRNA intergenic spacer (ITS) sequence analysis, were evaluated. All A. baumannii isolates (82 clinical isolates and one reference strain) were identified by the multiplex PCR method (specificity 100%). The sensitivity and specificity of the ribotyping system for identification of A. baumannii were 85.5% (71/83) and 93.5% (72/77), respectively. An additional 100 clinical isolates belonging to the Acinetobacter calcoaceticus-A. baumannii complex were used to compare these two methods for identification of A. baumannii, and this comparison revealed a level of disagreement of 14% (14 isolates). The accuracy of the multiplex PCR was 100%, which was confirmed by sequence analysis of the ITS and recA gene of these isolates. Thus, the multiplex PCR method dramatically increased the efficiency and speed of A. baumannii identification.

Technical note: a rapid pulsed-field gel electrophoresis method for analysis of bifidobacteria

Pulsed-field gel electrophoresis (PFGE) is a widely used and highly discriminatory molecular typing method that has been applied to bifidobacteria. However, published PFGE protocols used with bifidobacteria require between 5 and 7 d to complete. A rapid PFGE method was developed that can be completed within 24 h.

Comparison of isolation rate of Borrelia burgdorferi sensu lato in MKP and BSK-II medium

Different media have been utilized for borrelial cultivation. The aim of the present study was to evaluate the isolation rate of Borrelia burgdorferi sensu lato from two commonly used media, i.e. modified Kelly-Pettenkofer (MKP) and Barbour-Stoenner-Kelly II (BSK-II) medium, and to compare the isolated strains with regard to their phenotypic and genotypic characteristics. Skin biopsy specimens of 2 x 2 x 4 mm were taken from the peripheral site of human solitary erythema lesions and were divided in two pieces, one of which was inoculated into MKP and the other one into BSK-II medium. Species analysis of the obtained strains was performed and their plasmid and protein profiles were determined. Borrelia strains were isolated from 48/96 patients (50%) with erythema migrans. We obtained in 26/48 patients (54%) from MKP as well as from BSK-II, in 11 patients (23%) only from MKP, and in another 11 (23%) only from BSK-II medium a positive result. B. afzelii was isolated from 43 patients (23 were positive in both media, nine in MKP only and 11 in BSK-II medium only), while B. garinii was isolated from five patients (in three from both media, in two from MKP only). All strains of the obtained strain pairs were identical according to species and the type within the species. Plasmid profiles were identical in 17/21 B. afzelii strain pairs (81%) and in 1/3 B. garinii strain pairs; in 6/24 strain pairs, distinctions in the number of plasmids or in their molecular mass were present. Differences in the protein profile were found in 7/24 strain pairs (29%). The distinctions were uniform and were limited to the expression of OspC. In conclusion, our study showed comparable Borrelia isolation rates from MKP and BSK-II medium. The results of the present study indicate that human patients with Lyme borreliosis may simultaneously harbor heterogeneous B. burgdorferi s.l. strains.

Phenotypes of Isolates of Pseudomonas aeruginosa in a Diabetes Care Center

BACKGROUND

Pseudomonas aeruginosa is an invasive organism that frequently causes severe tissue damage in diabetic foot ulcers. A major problem in P. aeruginosa infection may be that this pathogen exhibits a high degree of resistance to a broad spectrum of antibiotics. Some researchers feel that P. aeruginosa is a homogeneous species, whereas others have suggested that they are panmictic. Here we characterized P. aeruginosa populations isolated from diabetic foot ulcer and from hospital environment specimens, both from a tertiary diabetes care center in Chennai, India.

METHODS

Phenotypic methods like antibiotic susceptibility determinations using Kirby-Bauer's disc diffusion test and minimum inhibitory concentration (MIC) as well as outer membrane protein SDS-PAGE analysis of P. aeruginosa were performed.

RESULTS

Twenty three isolates (29.8%) of P. aeruginosa from 77 diabetic foot ulcers and two environmental isolates (13.3%) from 15 different hospital fomites were detected. Both environmental isolates were sensitive to antibiotics than those isolated from clinical specimens by Kirby-Bauer's disk-diffusion method, which correlated the resistance levels by MIC determination. Outer membrane proteins (OMP) corresponding to 21, 23, 43, 46, 50, and 70 kDa were detected.

CONCLUSIONS

The study is captivative as the resistance in P. aeruginosa from diabetic foot ulcers seems very common and because all the isolates were resistant to at least one or more antibiotics tested. Disk-diffusion and MIC results shows that piperacillin, amikacin and imipenem retain high levels of antipseudomonal activities and amikacin two times more active than the aforementioned antibiotics to enable itself as a potent antipseudomonal agent in diabetic foot infections. The OMP profile has revealed that clinical isolates were different from hospital environment isolates, which suggests that the origin of infections by P. aeruginosa is mainly due to growth of bacterial strains acquired by patients prior to hospital admission.

Comparison of Borrelia burgdorferi sensu lato strains isolated from specimens obtained simultaneously from two different sites of infection in individual patients

The aim of the present study was to analyze and compare Borrelia strains isolated from two different specimens obtained simultaneously from individual patients with Lyme borreliosis. Fifty such patients and 50 corresponding pairs of Borrelia isolates (100 low-propagated strains) were subjected to genotypic and phenotypic analysis, including pulsed-field gel electrophoresis for species identification and plasmid profile determination and protein profile electrophoresis for the assessment of the presence and molecular masses of separated proteins. The strains were isolated from two distinct skin lesions (12 patients), skin and blood (28 patients), skin and cerebrospinal fluid (8 patients), and blood and cerebrospinal fluid (2 patients). Out of 100 isolates, 63 were typed as B. afzelii and 37 as B. garinii. From each individual specimen only a single Borrelia species was cultured. Comparison of 50 Borrelia strain pairs isolated from two different specimens of an individual patient revealed that 12/50 (24%) patients were simultaneously infected with two different Borrelia strains; in 3/50 (6%) patients strains differed at the species level, in 4 out of the remaining 47 (9%) patients a strain difference in plasmid profile was established, while 5 out of the remaining 43 (11%) patient strain pairs differed in regard to the protein profiles of the two concurrently isolated strains. The results of the present study indicate that human patients with Lyme borreliosis may simultaneously harbor different B. burgdorferi sensu lato strains.

Performance assessment of DNA fragment sizing by high-sensitivity flow cytometry and pulsed-field gel electrophoresis

The sizing of restriction fragments is the chief analytical technique utilized in the production of DNA fingerprints. Few techniques have been able to compete with pulsed-field gel electrophoresis (PFGE), which is capable of discriminating among bacteria at species and strain levels by resolving restriction fragments. However, an ultrasensitive flow cytometer (FCM) developed in our lab has also demonstrated the ability to discriminate bacteria at species and strain levels. The abilities of FCM warrant a quantitative parallel comparison with PFGE to assess and evaluate the accuracy and precision of DNA fragment sizing by both techniques. Replicate samples of Staphylococcus aureus Mu50 were analyzed along with two clinical S. aureus isolates. The absolute fragment sizing accuracy was determined for PFGE (5% +/- 2%) and FCM (4% +/- 4%), with sequence-predicted Mu50 SmaI fragment sizes used as a reference. Precision was determined by simple arithmetic methods (relative standard deviation for PFGE [RSD(PFGE) ] = 3% +/- 2% and RSD(FCM) = 1.2% +/- 0.8%) as well as by the use of dendrograms derived from Dice coefficient-unweighted pair group method with arithmetic averages (UPGMA) and Pearson-UPGMA analyses. All quantitative measures of PFGE and FCM precision were equivalent, within error. The precision of both methods was not limited by any single sample preparation or analysis step that was tracked in this study. Additionally, we determined that the curve-based clustering of fingerprint data provided a more informative and useful assessment than did traditional band-based methods.

Evaluation of molecular typing methods for Escherichia coli O157:H7 isolates from cattle, food, and humans

Escherichia coli O157:H7, a Shiga toxin-producing E. coli, has been the causative agent of many cases of severe, often life-threatening foodborne illness. Because of the importance of E. coli O157:H7 to public health, many molecular typing methods have been developed to determine its transmission routes and source of infection during epidemiological investigations. Pulsed-field gel electrophoresis (PFGE) is currently used by public health organizations to track infections of E. coli O157:H7 and other foodborne pathogens. In this study, we compared the ability of PFGE, multilocus sequence typing (MLST), and repetitive-element PCR (Rep-PCR) to distinguish among 92 E. coli O157:H7 isolates from cattle, food, and infected humans. Several virulence genes, including the intimin gene (eaeA), the hemolysin gene (hlyA), and the H7 fimbrial gene (fliC), and a housekeeping gene for beta-glucuronidase (uidA) were included in MLST. Rep-PCR reactions were performed using a commercially available typing kit (Bacterial Barcodes Inc., Houston, Tex.) with the provided Uprime-RI primer set. Results of the study indicated that PFGE provided the most discrimination among the techniques, identifying 72 distinct PFGE profiles for the isolates; Rep-PCR elucidated 14 different profiles, whereas MLST generated five profiles. Additionally, there did not appear to be any correlation among the typing methods examined in this study. Therefore, to date, PFGE remains the technique of choice for molecular subtyping of E. coli O157:H7.

Acute hepatitis C: high rate of both spontaneous and treatment-induced viral clearance

BACKGROUND & AIMS

Acute hepatitis C virus infection accounts for approximately 20% of cases of acute hepatitis today. The aim of this study was to define the natural course of the disease and to contribute to the development of treatment strategies for acute hepatitis C virus.

METHODS

The diagnosis of acute hepatitis C virus in 60 patients was based on seroconversion to anti-hepatitis C virus antibodies or clinical and biochemical criteria and on the presence of hepatitis C virus RNA in the first serum sample.

RESULTS

Fifty-one of 60 (85%) patients presented with symptomatic acute hepatitis C virus. In the natural (untreated) course of acute symptomatic hepatitis C (n = 46), spontaneous clearance was observed in 24 patients (52%), usually within 12 weeks after the onset of symptoms, whereas all asymptomatic patients (n = 9) developed chronic hepatitis C. The start of antiviral therapy (interferon-alpha with or without ribavirin) beyond 3 months after the onset of acute hepatitis induced sustained viral clearance in 80% of treated patients.

CONCLUSIONS

The management of acute hepatitis C has to take into account the high rate of spontaneous viral clearance within 12 weeks after the onset of symptomatic disease. Treatment of only those patients who remain hepatitis C virus RNA positive for more than 3 months after the onset of disease led to an overall viral clearance (self-limited and treatment induced) in 91% of patients, and unnecessary treatment was avoided in those with spontaneous viral clearance. Patients with asymptomatic acute hepatitis C virus infection are unlikely to clear the infection spontaneously and should be treated as early as possible.

Pyrosequencing for microbial typing

Pyrosequencing is a real-time DNA sequencing technique generating short reads rapidly and inexpensively. This technology has the potential advantage of accuracy, ease-of-use, high flexibility and is now emerging as a popular platform for microbial typing. Here, we review the methodology and the use of this technique for viral typing, bacterial typing, and fungal typing. In addition, we describe how to use multiplexing for accurate and rapid typing.

Genetic competence and transformation in oral streptococci

The oral streptococci are normally non-pathogenic residents of the human microflora. There is substantial evidence that these bacteria can, however, act as "genetic reservoirs" and transfer genetic information to transient bacteria as they make their way through the mouth, the principal entry point for a wide variety of bacteria. Examples that are of particular concern include the transfer of antibiotic resistance from oral streptococci to Streptococcus pneumoniae. The mechanisms that are used by oral streptococci to exchange genetic information are not well-understood, although several species are known to enter a physiological state of genetic competence. This state permits them to become capable of natural genetic transformation, facilitating the acquisition of foreign DNA from the external environment. The oral streptococci share many similarities with two closely related Gram-positive bacteria, S. pneumoniae and Bacillus subtilis. In these bacteria, the mechanisms of quorum-sensing, the development of competence, and DNA uptake and integration are well-characterized. Using this knowledge and the data available in genome databases allowed us to identify putative genes involved in these processes in the oral organism Streptococcus mutans. Models of competence development and genetic transformation in the oral streptococci and strategies to confirm these models are discussed. Future studies of competence in oral biofilms, the natural environment of oral streptococci, will be discussed.

Rapid DNA fingerprinting of pathogens by flow cytometry

BACKGROUND

A new method for rapid discrimination among bacterial strains based on DNA fragment sizing by flow cytometry is presented. This revolutionary approach combines the reproducibility and reliability of restriction fragment length polymorphism (RFLP) analysis with the speed and sensitivity of flow cytometry.

METHODS

Bacterial genomic DNA was isolated and digested with a rare-cutting restriction endonuclease. The resulting fragments were stained stoichiometrically with PicoGreen dye and introduced into an ultrasensitive flow cytometer. A histogram of burst sizes from the restriction fragments (linearly related to fragment length in base pairs) resulted in a DNA fingerprint that was used to distinguish among different bacterial strains.

RESULTS

Five different strains of gram-negative Escherichia coli and six different strains of gram-positive Staphylococcus aureus were distinguished by analyzing their restriction fragments with DNA fragment sizing by flow cytometry. Fragment distribution analyses of extracted DNA were approximately 100 times faster and approximately 200,000 times more sensitive than pulsed-field gel electrophoresis (PFGE). When sample preparation time is included, the total DNA fragment analysis time was approximately 8 h by flow cytometry and approximately 24 h by PFGE.

CONCLUSIONS

DNA fragment sizing by flow cytometry is a fast and reliable technique that can be applied to the discrimination among species and strains of human pathogens. Unlike some polymerase chain reaction (PCR)-based methods, sequence information about the bacterial strains is not required, allowing the detection of unknown, newly emerged, or unanticipated strains.