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Infection and Immunity, February 2006, p. 931-939, Vol. 74, No. 2
0019-9567/06/$08.00+0 doi:10.1128/IAI.74.2.931-939.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
K. Cecchini,1,2
S. Frasca Jr.,2 and
S. J. Geary1,2*
Center of Excellence for Vaccine Research,1 Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, Connecticut 062692
Received 26 September 2005/ Returned for modification 28 October 2005/ Accepted 2 November 2005
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In 1995, a global virulence determinant identification technique called signature-tagged mutagenesis was developed in the laboratory of David Holden. Using a pool of uniquely tagged transposons for random mutagenesis, Hensel et al. (17) were able to screen a large mutant population for organisms demonstrating attenuated virulence through negative selection in vivo. This approach allows a comprehensive screening of bacterial genomes for the identification of genes encoding novel virulence determinants. We developed a modification of this technique, termed signature sequence mutagenesis (SSM), and utilized it for the discovery of novel virulence-associated genes in M. gallisepticum. The genome of virulent M. gallisepticum strain R has recently been sequenced and annotated (33) and is the cornerstone of this SSM technique. Signature sequence mutagenesis avoids one of the primary problems of signature-tagged mutagenesis, i.e., the issue of cross-hybridizing transposon tags (19). The Southern hybridization step is replaced with primer sets consisting of a common forward primer annealing at the end of the transposon and a mutant-specific reverse primer annealing in the genomic sequence flanking the transposon. SSM allows the screening of multiple mutants in one animal challenge experiment, thus minimizing the number of animals used. Here, we describe the application of SSM to identify virulence-associated determinants in M. gallisepticum and specifically characterize the dihydrolipoamide dehydrogenase gene (lpd) as a virulence-associated gene.
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carrying pISM2062 (25) was propagated in Luria broth and on plates (10 g tryptone, 5 g yeast extract, and 5 g of NaCl per liter) with ampicillin (100 µg/ml). Nucleic acid extraction. The genomic DNA of each Tn4001mod mutant was extracted from 30 ml of mid-logarithmic-phase culture using the Easy-DNA extraction kit (Invitrogen, Carlsbad, Calif.). DNA concentrations were determined using spectrophotometric-absorbance measurements at 260 nm; purities were verified by absorbance ratios at 260 nm and 280 nm. Plasmid DNA was extracted using the QIAGEN Plasmid Mini kit protocol following the manufacturer's protocol (QIAGEN Inc., Santa Clarita, Calif.).
M. gallisepticum Rlow transformation.
M. gallisepticum Rlow was transformed by electroporation (Bio-Rad Gene Pulser, Hercules, Calif.) with the suicide plasmid pISM2062 (a gift of F. Chris Minion, Iowa State University). This plasmid carries the gram-positive transposon Tn4001mod, which contains the gentamicin resistance gene (5). M. gallisepticum cultures were grown to mid-logarithmic phase at 37°C in 5 ml of Hayflick's broth. The cells were harvested by centrifugation at 12,000 x g for 10 min at room temperature and then resuspended in 1 ml of electroporation buffer (8 mM HEPES, 272 mM sucrose, pH 7.4). After an additional centrifugation at 12,000 x g for 10 min, 60 µl electroporation buffer and 10 µg pISM2062 plasmid DNA were added, and the mixture was incubated on ice for 15 min. The cell-DNA suspension was transferred to a chilled 0.2-cm-gap electroporation cuvette and immediately pulsed (2.5 kV; 25 µF; 100
). One milliliter of cold Hayflick's broth was added, and the mixture was incubated at room temperature for 10 min; the cells were then incubated at 37°C for 2 to 3 h (6, 12, 14). Fifty microliters of the transformation mixture was diluted 1:10, and then 200 µl of that dilution was spread onto Hayflick's agar plates with gentamicin (100 µg/ml). The plates were incubated at 37°C for 7 to 10 days. Single visible colonies were picked and then placed in 500 µl Hayflick's broth with gentamicin and grown to mid-logarithmic phase. These M. gallisepticum transformants were titered and then stored at 80°C as stock cultures.
Transposon insertion site identification. The Tn4001mod M. gallisepticum mutant genomic DNA was extracted and sequenced using the outward primer SG857, annealing 27 bp upstream from the end of the transposon. The primer was designed to utilize the unique BamHI-SmaI cut site located in one of the two insertion sequences (IS256) of the transposon.
Linear sequencing with BigDye Terminator Mix (PE-Applied Biosystems) was used to identify the site of transposon insertion for each Tn4001mod mutant. Each sequencing reaction mixture contained 16 µl BigDye Terminator Mix, 30 pmol of primer, and 2 to 3 µg genomic DNA in a total volume of 32 µl. The following sequencing conditions were used: initial denaturation at 95°C for 5 min, followed by 45 cycles at 95°C for 30 s, 55°C for 20 s, and 60°C for 4 min (15). Excess dye terminators were removed with AutoSeq G-50 spin columns (Amersham Biosciences, Piscataway, NJ), and the samples were vacuum dried. Sequencing was performed by the University of Connecticut Biotechnology Center. Using Artemis v. 5 (Sanger Centre, United Kingdom) and Vector NTI 8 (Invitrogen, Carlsbad, Calif.), the genomic-sequencing results from the mutants were compared to the sequenced and annotated genome of M. gallisepticum strain R (33).
Determining transposon insertion stability. Sterile 1.5-ml microcentrifuge tubes containing 0.5 ml Hayflick's broth were inoculated with 30 µl of Tn4001mod mutant stock and incubated at 37°C until growth was evident. These mutant cultures were passed 30 times in nonselective broth, and on every 10th passage, 30 µl of the culture was transferred and grown in 30 ml of Hayflick's broth with 150 µg/ml gentamicin for genomic-DNA extraction and transposon insertion site sequencing as described above. The resultant sequence was compared to the known insertion site sequence, and any transposon movement was documented. To determine the rate of transposon loss, 30 µl of each mutant was used to inoculate 0.5 ml of nonselective broth, and every day for 14 days, the cultures were passed once. After the 14th passage, the culture was serially diluted and duplicate plated on nonselective Hayflick's plates and those containing 100 µg/ml gentamicin. After incubation at 37°C, the CFU were quantified.
Growth curve analysis of the Tn4001mod mutants. Sterile 250-ml Erlenmeyer flasks containing 69 ml of Hayflick's broth were inoculated simultaneously with 1 ml of equal numbers of pretitered (based on previous optical-density values at 620 nm [OD620]) M. gallisepticum Rlow and each of the individual mutant stock cultures. The cells were incubated at 37°C in a 250-rpm orbital shaking incubator and were harvested at 2, 4, 6, 8, 10, 12, 14, 16, 28, 32, 40, 49, and 54 hours postinoculation. The growth was measured spectrophotometrically by assessing the OD620. All values were graphed semilogarithmically as OD620 values versus time. All growth curve analyses were performed in duplicate.
Design of the unique mutant identifier. The identification of the transposon insertion sites within the M. gallisepticum genome permitted the design of unique reverse primers for each Tn4001mod mutant. These reverse primers were used with the forward primer SG857 and each respective genomic DNA template to produce an amplicon of known size. Each amplicon ranged in size from 300 to 650 bp and represented a unique mutant identifier that distinguished one clone from another.
Animals. Female 4-week-old White Leghorn specific-pathogen-free chickens (SPAFAS, North Franklin, CT) were used in the challenge experiments. The birds were tagged upon arrival and placed in HEPA-filtered isolators (Controlled Isolator Systems, Pittsburgh, PA). After a 1-week period of acclimation (in accordance with approved Institutional Animal Care and Use Committees protocol), all challenge experiments were initiated.
In vivo virulence assay. Three chickens were used in the mutant pool assay. The chickens were challenged with a mixed population of 27 Rlow Tn4001mod mutants (input population) at 1.5 x 106 CFU of each unique transformant. One milliliter of pretitered stock aliquots of each mutant was treated as follows: 100 µl of each mutant culture was transferred to a common 15-ml plug-sealed tube, and the resultant mixed culture was pelleted by centrifugation at 12,000 x g and 4°C for 10 min. The remaining 900 µl of culture in each aliquot was centrifuged as stated above, decanted, and stored at 80°C as a template to produce an input population PCR profile for comparison to the output population PCR profile generated after mutant recovery. The pellet of the mixed culture was then thoroughly resuspended in 100 µl of Hayflick's medium, transferred to a 1.5-ml microcentrifuge tube, and placed on ice in preparation for the challenge. The above procedure was repeated for each chicken in the study. The chickens were infected by intratracheal inoculation using a P200 pipetter carrying 100-µl suspensions of the organism.
Two weeks postchallenge, the chickens were humanely killed by cervical dislocation and immediately necropsied, and samples of the tracheas and air sacs were removed for isolation of M. gallisepticum Tn4001mod mutants. Tissue samples and tracheal swabs were used to inoculate 30 ml of Hayflick's medium containing 150 µg/ml gentamicin, vortexed, and incubated at 37°C for 8 h. The cultures were then passed through 0.45-µm filters and transferred to new plug-sealed tubes, and incubation was continued. Cultures that were acidic (yellow) after being filtered were adjusted to pH 7.4 by the addition of 10 N NaOH, and incubation was continued at 37°C until growth was evident. The genomic DNA of each culture was extracted, and PCR was performed to determine the presence or absence of individual mutants in the output population by using primer sets containing a conserved forward primer (SG857) and a reverse primer specific for each transposon mutant (Table 2). Amplicons were visualized in an ethidium bromide-stained 0.8% agarose gel. The PCR profile of this output population was compared to the input population profile, and those mutants not present in the output population were considered potential virulence mutants.
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TABLE 2. Primer sequences for forward primer SG857 and all 27 mutant-specific reverse primers
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Two weeks postchallenge, the chickens were humanely killed by cervical dislocation and immediately necropsied, and samples of tracheas and air sacs were taken for M. gallisepticum recovery, if present. Tissue samples from groups 1 and 3 were placed in Hayflick's medium, while those from group 2 were grown in gentamicin selective medium. Using sterile instruments, samples of left and right thoracic and abdominal air sacs were removed and either placed in specific culture media (as detailed above) or fixed in 10% neutral buffered formalin for histopathological evaluation. The tracheas were divided into cranial, middle, and caudal thirds; cross-sections 3 to 5 mm in width were fixed in 10% neutral buffered formalin for histopathologic evaluation; and the remaining segments were placed in specific culture media. Formalin-fixed tissue samples were routinely processed, embedded in paraffin blocks, sectioned at 4 µm, and stained with hematoxylin and eosin according to standard histological protocols (39). Histopathological evaluations were performed in a blinded fashion and were based on criteria established by Nunoya et al. (31) and implemented in previous histopathologic studies of M. gallisepticum lesions in the trachea (34) and air sac (32). Lesion scores (LS) were assigned separately to trachea and air sacs.
The LS table adapted to this study to grade tracheal lesions was defined as follows: 0, no significant findings; 0.5, minimal multifocal lymphocytic or lymphofollicular infiltrates amounting to one to three discrete foci; 1, mild mucosal thickening resulting from either mild diffuse lymphocytic infiltrates or multifocal lymphocytic or lymphofollicular infiltrates amounting to four or more discrete foci without edema or heterophils; 2, moderate mucosal thickening resulting from multifocal to diffuse lymphocytic and histiocytic infiltrates with or without lymphofollicular infiltrates, intraepithelial and lamina proprial infiltrates of heterophils, and luminal exudates; and 3, severe mucosal thickening resulting from diffuse infiltrates of lymphocytes, histiocytes, and heterophils with flattening and attenuation of epithelium and luminal exudates. Lesions that had features intermediate in intensity between two scoring values were assigned midrange scores, e.g., 1.5 or 2.5.
The LS table adapted for scoring air sacs was defined as follows: 0, no significant findings; 0.5, minimal multifocal lymphocytic infiltrates with one to three discrete, small, widely separated foci; 1, mild stromal thickening due to either multifocal lymphocytic or lymphofollicular infiltrates amounting to four or more discrete foci or mild diffuse lymphocytic infiltrates without edema or heterophils; 1.5, lesions comparable to 1 with mild heterophilic infiltrates; 2, moderate stromal thickening resulting from multifocal to diffuse lymphocytic, histiocytic, and heterophilic infiltrates that included lymphofollicular aggregates and intraepithelial heterophils; 2.5, lesions comparable to 2 plus significant luminal heterophilic exudates; 3, severe stromal thickening resulting from multifocal to diffuse lymphocytic, histiocytic, and heterophilic infiltrates that might include epithelial attenuation or hyperplasia and luminal heterophilic or granulomatous exudates. In addition to qualitative scoring as described above, the tracheal mucosal width was measured using an ocular micrometer. The widths of the mucosa at four equidistant points along the circumference of each tracheal section were measured using the base of the cilia or the adluminal surface of deciliated or flattened epithelial cells as one boundary and the beginning of the collagenous stroma of the lamina propria-tunica submucosa as the opposite boundary. An average mucosal width was generated for each trachea from measurements of each tracheal section, and average mucosal widths were used in subsequent statistical analyses to determine the relevance of differences in mucosal thickness between inoculated groups.
The genomic DNA of each recovered mutant culture was extracted, and PCR was performed using a primer set containing the conserved forward primer (SG857) and a mutant-specific reverse primer to confirm the identities. Amplicons were visualized by UV transillumination of an ethidium bromide-stained 0.8% agarose gel. If the potential virulence mutant was not recovered at the same rate as wild-type Rlow and demonstrated reduced histopathology compared to wild-type lesion scores, then it was considered to have a virulence deficiency.
Homogenate preparation. Mycoplasma cells were suspended in 1 ml of 40% glycerol, 60% Tris hydrochloride buffer (pH 7.4) (9). The suspension was diluted to 1 mg of protein per ml with Tris hydrocholoride buffer (pH 7.4) containing 1 mM EDTA and 1 mM 2-mercaptoethanol. Three cycles of freeze-thaw and passage through a syringe with an 18-gauge needle were used to homogenize the samples. Total protein was determined by the Bradford assay (2).
Pyruvate dehydrogenase complex activity assay. The pyruvate dehydrogenase complex (PDHC) activity was assayed by a radiochemical method using [1-14C] pyruvic acid-sodium salt (Amersham, Piscataway, NJ) as a substrate. Mycoplasma homogenates containing 100 µg of protein were placed in disposable test tubes in an ice bath and brought to 200 µl with 0.01 M Tris (pH 7.4) containing 1 mM EDTA and 1 mM 2-mercaptoethanol. A 10-µl solution containing coenzyme A (CoA), NAD+, and thiamine pyrophosphate (2 mM each) in Tris buffer was added to each test tube and then mixed. Finally, 20 nmol 1-14C-pyruvic acid was added and mixed. The negative control preparation was immediately inactivated with 15 µl of 50% trichloroacetic acid. The test tubes were stoppered with 1.5-ml microcentrifuge tubes with their bottoms cut off containing paper wicks soaked with 50 µl of 2.5 M NaOH to absorb the evolving CO2. The reaction mixtures were incubated at 37°C and stopped at 15-, 30-, 45-, and 60-min intervals by the addition of 15 µl of 50% trichloroacetic acid. Each time point assessment was performed in duplicate. The tubes were again stoppered and incubated at 37°C in an orbital shaking incubator at 200 rpm for 2 h to collect all evolved CO2. Radioactivity was measured by counting the contents of each tube in 5 ml ScintiSafe (Fisher Chemicals, Fairlawn, NJ) liquid scintillation cocktail in a Beckman LS 3801 scintillation counter (Beckman Coulter, Fullerton, CA). The activity of PDHC was determined by the average decrease of radiolabeled pyruvic acid in the test tube due to decarboxylation, creating 14CO2 that was released from the reaction mixture and collected in the wicks (9).
Statistical analysis. Analysis of variance using the f test was used to determine if there were significant differences between the mean lesion scores of chicken groups. When differences were found, a mean separation analysis using Duncan's multiple-range test was performed. The PDHC activity was analyzed by the paired Student t test to determine significant differences between enzyme activities. Analyses were performed with the statistics program SAS version 8.01 (SAS Institute, Cary, NC).
Sequence analysis.
TMHMM (26), PSIPRED (22, 30), MEMSAT2 (23), and PredictProtein (37) were used to predict protein topology. Sequence homology searches were performed using the PROSITE (11), Pfam (3), PRINTS (1), and BLOCKS (16) databases. Amino acid sequence homologies were considered significant if they possessed
30% identity or similarity.
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TABLE 1. Mapped insertion sites for each Tn4001mod mutant used in the in vivo virulence assay
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FIG. 1. (A) Agarose gel illustrating the input population PCR profile of the in vivo virulence assay using the 27 mutants from Table 1. Each lane consisted of a reaction containing a common forward primer (SG857) and a mutant-specific reverse primer. Molecular size markers are shown in the first lane on the left (M). The arrow indicates the Mg 7 lane. (B) Agarose gel of the output population PCR profile of in vivo virulence assay mutants. This profile is from the trachea of one of three chickens in the potential virulence assay. Molecular size markers are shown in the first lane on the left (M). The arrow indicates the Mg 7 lane.
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TABLE 3. Mycoplasma gallisepticum mutant recovery data from in vivo virulence assays
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Growth curve analysis. Mg 7 did not demonstrate any growth deficiency compared to wild-type Rlow over 54 hours of growth.
Potential virulence mutant assay. Histopathologic evaluation of tracheas from chickens challenged with Mg 7 showed a range of responses, from no significant lesions to mild diffuse lymphocytic infiltrates (LS = 0 to 1) without attenuation or deciliation of the epithelium (Fig. 2A). Chickens challenged with Rlow demonstrated minimal to moderate mucosal thickening (LS = 0.5 to 2) resulting from multifocal to diffuse lymphocytic and histiocytic infiltrates accompanied by heterophils and flattening and attenuation of the epithelium (Fig. 2B). Chickens in the PBS control group had no significant lesions (Fig. 2C). Examination of the tracheal mucosal width revealed a significant difference between the Rlow (60.4 µm)-challenged birds and the Mg 7 (40.6 µm) and PBS (44.6 µm) challenge groups.
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FIG. 2. Histopathologic differences in trachea following challenge with Mg 7 (A), Rlow (B), or 1x PBS (C). The trachea from an Mg 7-challenged bird (A) is minimally thickened by lymphocytic infiltrates (arrowheads), in comparison to the trachea from an Rlow-challenged bird (B) with mucosal thickening due to a dense lymphohistiocytic infiltrate (vertical bar) with scattered heterophils, flattening and attenuation of the epithelium, and loss of cilia. No significant lesions were identified in birds inoculated with 1x PBS (C). The photomicrographs represent the mean lesion score for Mg 7-challenged birds (A), a near-maximum lesion score for Rlow-challenged birds (B), and the minimum lesion score for 1x PBS-challenged birds. Hematoxylin and eosin; magnification, x300.
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FIG. 3. Histopathologic differences in air sacs following challenge with Mg 7 (A), Rlow (B), or 1x PBS (C). Mg 7-challenged birds have few, discrete, widely separated lymphocytic aggregates (asterisk) (A), whereas air sacs from Rlow-challenged birds were moderately thickened by multiple lymphocytic or lymphofollicular aggregates (asterisks) (B). No significant lesions were identified in birds inoculated with 1x PBS (C). The photomicrographs represent the mean lesion score for Mg 7-challenged birds (A) and Rlow-challenged birds (B) and the minimum lesion score for 1x PBS-challenged birds. Hematoxylin and eosin; magnification, x300.
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TABLE 4. Histopathologic-lesion scores from potential virulence mutant assay using Mg 7, 1x PBS, and wild-type Rlow challenges
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FIG. 4. Functional domains of the dihydrolipoamide dehydrogenase enzyme. The Tn4001mod insertion site is located within the extracellular domain. The oxidoreductase active site is represented by the hexagon, and the FAD/NAD binding domain, transmembrane domains, intracellular domains, and oxidoreductase dimerization domain are also depicted.
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FIG. 5. PDHC activity assay. Counts of [14C]pyruvic acid at the 45- and 60-minute time points show a significant difference between the catabolic rates of the Mg 7 (square) and Rlow (triangle) enzyme complexes (standard error bars are shown). The asterisks indicate that the mean value is significantly different (P < 0.05) between Mg 7 and Rlow within the time point.
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The SSM assay allows the comprehensive screening of the genome for CDSs that may play roles in pathogenicity. Due to the random insertion pattern of transposon mutagenesis, it is likely that there will be disruptions of genes involved in pathogenesis. At least 30% of the CDSs in the M. gallisepticum genome sequence are annotated to code for polypeptides of unknown function. Emphasis has focused on the characterization of cytadhesins, such as GapA and CrmA (32, 34, 35), and hemagglutinins, such as the VlhA family of lipoproteins (33), but CDSs of unknown function must be thoroughly investigated as to their potential roles in pathogenicity. The ability to screen a large number of transposon mutants in one challenge experiment greatly accelerates the identification of novel virulence determinants among putative CDSs.
This study has described the identification of Lpd as an important protein in host colonization and pathogenesis. Histopathologic findings demonstrated differences in the severity of lesions caused by Mg 7 compared to Rlow, which were most clearly illustrated by the differences in the lesion scores of air sacs. The lesion scores of air sacs from Mg 7-challenged birds were significantly lower than those of Rlow-challenged chickens and lacked evidence of intense chronic inflammatory responses, such as the presence of lymphofollicular aggregates and epithelial attenuation.
Traditionally, the Lpd protein would be considered a metabolic factor, and therefore, its role in pathogenicity might never have been investigated. It is also important to note that the transposon insertion site in Mg 7 was stable when assayed, and therefore, no secondary transposon-induced mutations occurred during the chicken challenge. The in vitro growth rate of Mg 7 resembled that of wild-type M. gallisepticum, but the lack of the complete enzyme complex greatly affected its ability to colonize and survive within the host.
The Lpd protein is an essential functional subunit of the multienzyme PDHC, with a predicted molecular mass of 51 kDa. The PDHC is normally comprised of multiple copies of the ternary complex of Lpd, dihydrolipoamide transacetylase, and pyruvate dehydrogenase enzymes and is involved in the oxidation of pyruvate, the end product of glycolysis, to acetyl-CoA by the following reaction: pyruvate + CoA + NAD+
acetyl-CoA + CO2 + NADH + H.
The mutation in lpd interrupts the cyclical nature of the enzyme complex, rendering it inoperative after the reaction occurs once. The dihydrolipoamide dehydrogenase enzyme permits the continued function of the pathway by maintaining the correct redox state of the enzymes involved in the bioconversion. The PDHC activity assay confirmed that the protein homogenate from Mg 7 containing the incomplete complex failed to maintain activity, whereas the Rlow homogenate functioned properly.
Acetate is one of the end products of the fermentative metabolism carried out by M. gallisepticum. Through the combined actions of phosphate acetyltransferase and acetate kinase, 1 mole of ATP is generated during the conversion of acetyl-CoA to acetate (36). Without the complete PDHC, acetyl-CoA is not produced at wild-type levels, and the cell loses the ability to make a mole of ATP from the metabolic intermediate, leading to a possible intracellular energy shortage. The reduction in ATP could lower the cumulative activity of the ATP binding cassette transporters upon which the bacterium relies heavily to acquire many of the precursors necessary for its viability. While this feature is easily masked when Mg 7 is grown in the nutrient-rich Hayflick's medium, the deficiency may affect the microorganism's ability to acquire the precursor molecules and cofactors needed to persist and adapt to its host environment.
In a recent report, Haemophilus influenzae type B was shown to be attenuated by a transposon insertion in lpdA, the dihydrolipoamide dehydrogenase gene homolog. When the H. influenzae LpdA mutant was used to challenge 5-day-old infant rats intraperitoneally, it was unrecoverable compared to the wild-type recovery rate (18).
Despite screening of an additional 1,000 M. gallisepticum transposon mutants, a second clone with a mutation in lpd has not been found. Due to the limited molecular tools available for the study of mycoplasma genetics to date, complementation and expression of the wild-type lpd gene via insertion with a second transposon into Mg 7 has been unsuccessful. Although the possibility remains that an undetected second-site mutation may have contributed to the Mg 7 phenotype, we have established that the lpd gene is disrupted and the biologic function impaired. This, coupled with the similar finding in H. influenzae, supports the potential for this to be a valid virulence-associated factor. Further studies are in progress to assess Mg 7 as a vaccine candidate.
This work was supported by USDA grant 58-1940-0-007 to S.J.G. and by the Center of Excellence for Vaccine Research (CEVR).
Present address: TIGR, 9712 Medical Center Drive, Rockville, MD 20850. ![]()
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