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Journal of Clinical Microbiology, September 2005, p. 4758-4765, Vol. 43, No. 9
0095-1137/05/$08.00+0 doi:10.1128/JCM.43.9.4758-4765.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Department of Environment and Primary Prevention,1 Department of Food and Veterinary Medicine, Istituto Superiore Sanità Roma, Rome, Italy,2 Department of Anthrax Reference Institute of Italy at Istituto Zooprofilattico Sperimentale di Puglia e Basilicata, Foggia, Italy3
Received 10 February 2004/ Returned for modification 21 September 2004/ Accepted 4 May 2005
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When comparison of complete genome sequences was still not possible, numerous studies demonstrated the lack of molecular polymorphism within B. anthracis (12). Later, sequencing projects accelerated improvement in molecular typing of these pathogens. An eight-locus multilocus variable-number tandem repeat (VNTR) analysis (8-MLVA) has become the gold standard for the assessment of genetic relationships within the representative worldwide clones (13). The 8-MLVA approach provided a multiple-factor genetic analysis with six chromosomal, one pXO1 locus, and one pXO2 locus markers, with a discriminatory power of 42 alleles. A comparative genome sequencing for discovery of novel polymorphisms in B. anthracis (20) provided a powerful new tool for investigating infectious disease outbreaks. A total of 64 new polymorphic sites, including single-nucleotide polymorphism, VNTR, single-nucleotide repeats, and insertions, were reported. A recent approach (14) showed the usefulness of a nested hierarchical approach, applicable to a wide range of pathogens, that uses a progression of diagnostic genomic low-resolution loci and, ultimately, high-resolution loci.
For safety reasons and ease of handling in the laboratory, many investigators have used attenuated vaccine strains carrying one of the two plasmids in studies of toxin and capsule gene expression. The widely studied Sterne (pXO1+/pXO2) is nonencapsulated and toxigenic, whereas Pasteur I type (pXO1/pXO2+) is encapsulated and nontoxigenic. However, atypical Pasteur vaccine strains isolated previously (21) showed the pXO1+/pXO2+ profile, and one of them, the Pasteur II strain, was recently used in real-time PCR studies of pag and cap genes (15). Reference data report that two of three B. anthracis vaccine strains formerly used as antianthrax vaccine strains for cattle in Argentina showed the two-plasmid pattern (5). In Italy an atypical B. anthracis vaccine strain, Carbosap (pXO1+/pXO2+), has been used since 1949 for immunization of cattle and sheep. Although it carries both plasmids, it shows virulence in guinea pigs and mice and is not pathogenic for rabbits (1, 7).
In order to evaluate the mechanism of attenuation in the B. anthracis vaccine strain Carbosap, a previous study (1) sequenced the structural genes encoding for the major virulence factors (cya, lef, and pagA), two trans-acting regulatory genes (atxA and pagR), and the gerX operon involved with germination within macrophages. No molecular differences were found compared to a B. anthracis virulent strain. An approach using real-time PCR for the lef gene (17) led to similar results.
It is important to be able to use advanced methods to distinguish B. anthracis strains isolated from anthrax outbreaks in areas where Carbosap vaccination is common practice. As far as the PCR test to assess the virulence of B. anthracis is concerned, the Organization International Épizooties (OIE) (18) suggests using biomolecular tests which, however, are not able to distinguish wild strains from vaccines with the Carbosap plasmidic profile pXO1+/pXO2+.
The main aim of the present study was to reinforce the gold standard 8-MLVA protocol by adding another locus selected with the help of computational analyses of the numerous polymorphic loci recently discovered in B. anthracis.
Carbosap, some representative wild Italian B. anthracis strains and other reference strains, such as Pasteur I, Pasteur II, and Sterne strain, were included in the present study.
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Standard 8-MLVA analysis. All samples were genotyped according to the gold standard 8-MLVA (13) with slight modifications (Table 1). Forward primer CG3 was tet labeled instead of ned labeled because the latter was not available from our provider (Primm, Milan, Italy). Typically, 10-µl portions of the PCR products were electrophoretically analyzed on ethidium bromide-agarose gels in order to test the success of the reaction. The remaining 40 µl was used for sequencing and for fragment analysis. All PCRs were performed with Platinum Taq (Invitrogen Corp.) under the same assay conditions as in the original method and using a GeneAmp PCR System 9700 (Applied Biosystems, Foster City, CA) that is certified annually by the European Repair Centre (Applera Europe BV, Nieuwerkerk aan den Ijssel, The Netherlands), according to the standards of the Dutch Council for Accreditation (NKO).
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TABLE 1. Gold standard 8-MLVAa
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In silico computational analysis of the known polymorphic loci. All of the available finished or unfinished (contigs) B. anthracis strain sequences were downloaded from GenBank and from the TIGR website. In addition to the B. anthracis prototype, the following genomes were included: Ames Ancestor 0581, Ames Florida A2012, A0039, A1055, Australia-94, CNEVA-9066, France, Kruger-B, Vollum, and Western North America USA6153. One of the four Florida files was released by TIGR after a direct request from one of the authors and was particularly useful. It consisted of a set of 1,000-bp regions centered on each reported polymorphism in order to allow investigators to identify and test these markers on any other anthrax strain.
All of the sequences were scanned using the FINDPATTERNS program of the Wisconsin GCG package (Accelrys, Ltd., Cambridge, United Kingdom) with a complete panel of pattern data (data not shown) for each known polymorphic site. The pattern-data for VX2-3 was "CCGACCT(A){5,}CATACTACC." The brackets indicate some constraints according to a general Unix code: {5,} from a minimum of "5" (A) to
. Flanking sequences were constraints able to identify exactly the VX2-3 locus in all of the examined sequences. The MAPSORT and MAPPLOT programs of the GCG package were used to reconstruct the map of polymorphic loci. This procedure allowed us to map the pXO2 plasmid with the known polymorphic loci (Fig. 1).
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FIG. 1. B. anthracis map of the pXO2 (af188935) plasmid polymorphic loci. The origin and end (96231) of the plasmid are shown on the outer circle. The arrows show the two loci of pXO2 plasmid analyzed here. The corresponding PCR alias names are reported in brackets. All of the potential polymorphic loci are mapped with FINDPATTERN as described in Materials and Methods. The loci name are reported unabridged as indicated in a previous article (19). For convenience, the locations of the known virulent genes are mapped in the inner circle. Abbreviations: VX, variable number tandem repeats; IX, insertions; PS, single nucleotide polymorphism; pXO2, plasmid pXO2; -at, tandem repeats of dinucleotides AT; -A, single A repeats.
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TABLE 2. Primers used for pXO2-A locus test of the VX2-3 locus shown in the plasmid mapa
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Automated genotype analysis. Fragment analysis in denaturing conditions was carried out by using the capillary automatic sequencer ABI PRISM 310 Genetic Analyzer (Applied Biosystems). As a size marker, the PRISM GeneScan-500 ROX (usually called ROX500; Applied Biosystems) was used. This standard is a mixture of a carboxy rhodamine-labeled fragments ranging from 35 to 500 bp, which are generally displayed as red peaks (Fig. 2).
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FIG. 2. B. anthracis genotype 3 polymorphisms. This figure reports a combined screen capture image of capillary fluorescent electrophoresis of the pXO2-A test. Colors of samples (blue), Carbosap (green), and ROX500 (red) correspond to different fluorescent labels. The Carbosap-hex and Carbosap-fam runs are not reported here because peaks perfectly overlapped, similarly to those shown in panel G. All of the graphs were compared after normalization of the profiles with the genotype program according to the internal standard. The heights of the peaks were adjusted to the same range of absorbance, as shown on the left side of each picture. The keys shown in the figure are those reported in Table 3, i.e., sample 424 Carbosap, sample 472, B. anthracis strain 10 and so on. On the top of the figure, the 300- and 340-bp marker sizes of ROX500 are shown. From panels A to H the computed peak shift "sample/Carbosap" values were 5, 4, 3, 2, 1, 0, and +1 bp, respectively.
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The separation of fragments was carried out at 15,000 V at 50°C in a 47-cm-by-50-µm capillary filled with POP4 matrix.
Data analysis. Genescan and genotype software packages (Applied Biosystems) were used to quickly analyze the electropherograms. The computing of molecular size of VNTR loci was usually performed with Genotyper software analysis in a complete automatic style. This method was unfortunately not able to intercept the vrrC1 and vrrC2 values, which were out of the ROX500 range; they were therefore calculated by sequencing. Because the apparent electrophoretic sizes of the DNA fragments were not always exactly the same as the size determined by DNA sequencing, these two and the other six loci were adjusted according to the standard genotypes selected from the references (13). No reference data were available for the 9th locus, so it has been reported as determined experimentally by fragment analysis. As shown in Table 3, using the values of all of the runs (column 7), a mean value of Carbosap-hex internal standard was computed, and therefore the sample data (column 4) were normalized (column 5) by using a correction factor (column 8).
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TABLE 3. Genotyping results of pXO2-A testa
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FIG. 3. Phylogenetic representation of 9-MLVA. Computed base pair lengths for all nine loci were reported in the START spreadsheet from which a UPGMA (unweighted pair-group method with arithmetic averages) tree was inferred. The 8-MLVA was central to determining three major phylogenetic patterns, corresponding to the genotypes 1, 12, and 3. The progressive hierarchical addition of the high-resolution pXO2-A assay results, maximizing the phylogenetic accuracy, subdivided the 23 isolates of genotype 3 into eight unique subtypes. Both genotypes 1 and 12 were divided into two subtypes. Allelic profiles are shown along with the isolate names. The pXO1- or pXO2-deficient strains were not included due to incomplete 8-MLVA patterns. The linkage distance attempts to measure the detected association between alleles at different loci (16).
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The improved 9-MLVA had the new locus located within the 300- and 340-bp peaks of the ROX500 standard (Fig. 2). Numerical results for all of the loci are reported in Fig. 3, displayed along with the isolate codes. Genotyper software showed a good linearity of size markers, which were well distributed and predicted an accurate estimation of pXO2-A fragment size. As shown in Table 3, the mean value of the Carbosap pXO2-A fragment was 323.11 bp with a standard deviation, calculated on 30 different independent runs, of 0.34 bp. All of the values were approximate after normalization (Table 3, column 5). The results were confirmed in duplicate experiments.
Eight subtypes were observed for genotype 3, two were observed for genotype 1, and two were observed for genotype 12. Subtypes of genotype 3 were tentatively named, for convenience, A-H (column 6, Table 3). These subtypes corresponded to fragments ranging from 317 to 325 bp. Carbosap and two samples (samples 458 and 457) were grouped into subtype G. For convenience, Pasteur I, even if it has an incomplete pattern and cannot be genotyped like the other samples, was included in the G group. All of the genotype 3 samples were different from Carbosap and were subtyped in seven groups (A, B, C, D, E, F, and H). The genotype 1 (samples 419 and 420) and genotype 12 samples (samples 421 and 425) also showed heterogeneity, confirming the usefulness of the pXO2-A test in hierarchically subtyping strains.
Representative electropherograms from 8 independent runs of genotype 3 are reported in Fig. 2. The Carbosap-hex (sample 424) internal standard and samples-fam (samples 472 [A], 466 [B], 460 [C], 462 [D], 464 [E], 422 [F], 457 [G], and 427 [H]) are shown in different colors. The ROX500 profile (red peaks) is also reported for convenience. As shown in group F of Fig. 2, differences of 1 bp between sample 22 and Carbosap sample 424 were well shown in our experimental conditions. Differences of more than 1 bp, as shown in group A, gave very distinct peaks. Two wild samples, 457 and 458, and Pasteur I (pXO1/pXO2+) have the 323 allele of Carbosap. As shown in group G of Fig. 2, the representative B. anthracis, strain 10 (sample 457) overlapped perfectly with Carbosap-hex (sample 424). These results were consistent with sequencing data (data not shown). As expected, the Pasteur II strain 74.12 used in the present study showed the two-plasmid pattern pXO1+/pXO2+, a finding consistent with the reference data (15, 21). More interestingly, when pXO2-A profile of Pasteur II (sample 427) was compared to Carbosap_hex (sample 424) a shift in the peaks (Fig. 2, group H) was revealed that was clearly due to a different A contents of VX2-3 poly(A). These data were confirmed by sequencing analysis (data not shown).
When the pXO2-A test was performed as nested PCR by using PCRs 24 and 28 sequentially, it became highly sensitive, with an increase by 103 in the second round of reactions. Because this aspect was beyond the aims of our work, we did not go further with these sensitivity tests. As a rule, pXO2-A 28 was executed directly on the sample DNA without preamplification. Carbosap labeled in two different ways, PCR 28 (fam) and PCR 29 (hex), yielded perfectly overlapping peaks in the predicted range.
In order to confirm results in another range of molecular weights, the reverse primer 420-r of the above-mentioned sets was substituted with primer 464-r in a parallel set of PCRs (pXO2-A, PCR 27). The fluorescent fragments peaked just between the 200- and 245-kb size markers (data not shown). Because no improvement of the resolution was obtained in this location, no further experiments were carried out with these alternative tests.
As expected, Stern vaccine (pXO1+/pXO2) used as negative control for pXO2 plasmid tests showed no signal.
Figure 3 reports all of the genotyping results in a single graph. The START freeware programs turned out to be a very reliable tool for showing taxonomic relationships among strains. An unweighted pair group method with arithmetic means was easily applied starting from a data spreadsheet. It is generally not considered a good algorithm for construction of phylogenetic trees since it requires rates of evolution among different lineages to be approximately equal. Even if phylogenetic inferences could not be drawn from the clustering pattern seen with this method, it may prove useful as a quick guide for identifying similar isolates.
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The confirmation of a two-plasmid pattern in the attenuated B. anthracis strain Pasteur type II strain 74.12, such as Carbosap, is consistent with their similar biological properties related to attenuation characteristics and residual pathogenicity. It could be hypothesized that plasmid-encoded and chromosomal genes act synergistically in the global virulence of B. anthracis. Therefore, mechanisms still unknown could play a role in the attenuation of the B. anthracis.
These data are very interesting because they further underline the importance of being able to distinguish between Carbosap and Pasteur strain type II. In fact, OIE tests are not able to adequately identify vaccine strains closely related to Carbosap and Pasteur II strain 74.12. This method may therefore complete the diagnostic techniques required by OIE (18) for test confirmation of the virulence of strains isolated from anthrax outbreaks.
Although the method may be less useful in countries where the Sterne vaccine is widely used, the pXO2-A marker may be adopted everywhere as an alternative to the identification test recommended by the European Pharmacopeia (6), since it is more informative, less expensive, and faster.
In conclusion, the molecular method presented here could follow the 8-MLVA as a second step of a new hierarchical standard protocol intended to differentiate Carbosap live vaccine from pathogen strains of B. anthracis belonging to genotype 3. Future efforts will be necessary to find other loci that enable us to also differentiate subtype G samples, which have the same pXO2-A profile as Carbosap, for more accurate forensic and epidemiological analyses of natural anthrax cases.
This study was partly supported by the project "Potabilizzazione Delle Acque e Rischi Sanitari Emergenti (PARSE): Marcatori genetici di microrganismi patogeni e diagnostica PCR" of the Italian Ministry of Health (ISS protocol N. 3 ANF).
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