Abstract
Burkholderia pseudomallei and B. mallei are two highly pathogenic bacteria, responsible for melioidosis and glanders, respectively. The two are closely related and can also be mistaken for B. thailandensis, a nonpathogenic species. To improve their differential identification, we describe a hydrolysis probe-based real-time PCR method using the uneven distribution of type III secretion system genes among these three species.
Burkholderia pseudomallei is the gram-negative motile bacterium responsible for melioidosis. This saprophyte inhabitant of telluric environments is mainly encountered in Southeast Asia and northern Australia but is sporadically isolated in subtropical and temperate countries (18). Melioidosis is a life-threatening disease that is mainly acquired though skin inoculation or pulmonary contamination, although other routes have been documented. B. mallei, a gram-negative nonmotile bacterium, is the causative agent of glanders. This disease mainly affects horses; humans can be infected after prolonged and close contact with these animals (11). B. pseudomallei and B. mallei are phylogenetically very similar and have nearly identical 16S ribosomal DNA sequences. They have been defined as separate species essentially due to their epidemiological and sanitary features (21). Both species are highly pathogenic and are listed in biological risk class III. Moreover, due to their high virulence by the respiratory route, both are considered potential bioterrorism agents, classified as such in list B by the Centers for Disease Control and Prevention (Atlanta, Ga.) (13). B. thailandensis is a gram-negative, motile saprophyte bacterium. This organism is nonpathogenic for humans and animals but displays phenotypic characteristics that make it appear similar to B. pseudomallei by routine diagnosis tests. Its main specific character is the ability to assimilate l-arabinose. Before being regarded as a definite species (5), B. thailandensis isolates were previously described as arabinose-positive, nonpathogenic variants of B. pseudomallei, as opposed to the arabinose-negative, pathogenic sensu stricto B. pseudomallei strains (14).
As pathogenic Burkholderia isolates are quite infrequent in clinical practice outside of the areas of endemicity, their identification could be missed, even when automated systems are used (9). PCR methods have been proposed, but these suffer from a lack of specificity (7, 15).
The type III secretion system (TTS) is a toxin delivery mechanism that allows pathogenic bacteria to inject toxic substances into the cytoplasm of the host's cells. This “toxin gun” was first described for Salmonella spp. and Shigella flexneri (3, 6) but is now documented in numerous animal- and plant-pathogenic bacteria (8, 22). This mechanism relies on a multiprotein assembly showing strong similarities with the flagella structure (1, 4).
Winstanley et al. (19) reported the first TTS gene cluster, TTS1, in B. pseudomallei. The presence of TTS1 has been correlated with an Ara− phenotype (20) and with pathogenicity (16, 17). An in silico study (12) demonstrated the presence of a partial TTS1 analog in B. mallei. A second type III secretion system (TTS2) has been demonstrated for B. pseudomallei, B. mallei, and B. thailandensis (12); the role of these genes has not yet been elucidated.
The present study shows that the uneven distribution of TTS genes among B. pseudomallei, B. mallei, and B. thailandensis provides a means for distinguishing these three species by PCR.
Primer and probe design.
Real-time PCR assays using hydrolysis probes were designed for three genetic markers: orf11 and orf13 from TTS1 and BpSCU2 from TTS2 (Table 1). The sequences of these open reading frames were obtained from the recently completed B. pseudomallei K96243 genome sequence. These sequence data were produced by the B. pseudomallei Sequencing Group at the Sanger Institute and can be obtained from ftp://ftp.sanger.ac.uk/pub/pathogens/bps/; they are consistent with the TTS1 sequence deposited by Winstanley et al. under the GenBank accession number AF074878. Sequence specificity was checked by (i) BLAST searches for nearly exact matches via the site http://www.ncbi.nlm.nih.gov/BLAST/ and (ii) analysis of the genome sequences of B. mallei (available at The Institute for Genomic Research website http://www.tigr.org) and of B. cenocepacia (available at the Sanger Institute website http://www.sanger.ac.uk/Projects/B_cenocepacia) performed using the BLAST facilities provided at these websites. The three markers studied exhibited identities only with sequences from B. pseudomallei, B. mallei, or B. thailandensis. No significant similarities with sequences from other bacteria, even from beta-proteobacteria, such as members of the B. cepacia complex or Ralstonia species, were found. Primers and probes were designed with Beacon Designer software (Premier Biosoft International, Palo Alto, Calif.).
TABLE 1.
List of PCR primers and hydrolysis probes
| Target gene | Primer | Sequencea (5′-3′) | Reference or source | PCR amplification
|
|||
|---|---|---|---|---|---|---|---|
| B. pseudomallei | B. mallei | B. thailandensis | Other species | ||||
| orf11 | PM122 | ATCGCCAAATGCCGGGTTTC | 12 | + | − | − | − |
| orf11R | CAAATGGCCATCGTGATGTTC | This study | |||||
| orf11pro | FAM-TCGGCGAACGCGATTTGATCGTTC-TAMRA | This study | |||||
| orf13 | orf13f | CACCGGCAGTGATGAGCCAC | This study | + | + | − | − |
| orf13r | ATGCTCCGGCCTGACAAACG | This study | |||||
| orf13pro | FAM-ACGCCCGTCGAAGCCCGAATC-TAMRA | This study | |||||
| BpSCU2 | SCU2F | CTCGAGCTCGTGAAGATGAT | This study | + | + | + | − |
| SCU2R | ACGCGTGCGATCTTGTAATC | This study | |||||
| SCU2pro | FAM-ATGCCACGCACGCGAGCACGA-TAMRA | This study | |||||
FAM, 6-carboxyfluorescein; TAMRA, 6-carboxytetramethylrhodamine.
PCR.
Real-time PCR assays were conducted on a LightCycler apparatus (Roche Applied Science, Penzberg, Gerdany), using FastStart hybridization probe master mixture (Roche) by following the manufacturer's instructions. Primers and probes were obtained from MWG Biotech (Courtaboeuf, France) and were used at final concentrations of 0.5 and 0.2 μM, respectively. Final MgCl2 concentrations were adjusted to 3, 2, and 4 mM for detection of orf11, orf13, and BpSCU2, respectively. Sample volume was 5 μl per assay. Thermal cycling conditions were 5 min at 95°C, followed by 45 cycles of 10 s at 95°C and 45 s at 60°C.
Bacterial strains.
The following species where studied (Table 2; numbers of strains are in parentheses): B. pseudomallei (58), B. mallei (16), B. thailandensis (3), B. andropogonis (1), B. caledonica (1), B. caribensis (1), B. caryophylli (1), B. cepacia (3), B. cenocepacia (1), B. dolosa (1), B. fungorum (1), B. gladioli (1), B. glathei (1), B. glumae (1), B. graminis (5), B. multivorans (1), B. norimbergensis (1), B. phenazinium (1), B. plantarii (1), B. pyrrocinia (1), B. stabilis (1), B. vietnamiensis (1), Pseudomonas aeruginosa (1). Species identification was confirmed by routine phenotypic characterization including Gram staining, motility tests, and biochemical profiles on API 20 NE tests (BioMérieux, Marcy l'Etoile, France) (2).
TABLE 2.
List of strains used in this study
| Species | Strain | Source | ||||
|---|---|---|---|---|---|---|
| B. andropogonis | ATCC 2306 | American Type Culture Collection (Manassas, Va.) | ||||
| B. cepacia | ATCC 25416 | |||||
| B. mallei | ATCC 10399 | |||||
| B. mallei | ATCC 23344 | |||||
| B. pseudomallei | ATCC 11668 | |||||
| B. pseudomallei | ATCC 15682 | |||||
| B. pseudomallei | ATCC 23343 | |||||
| B. thailandensis | ATCC 700388 | |||||
| B. mallei | CIP 52.236 | Collection de l'Institut Pasteur (Paris, France) | ||||
| B. mallei | CIP 64.12 | |||||
| B. mallei | CIP A.187 | |||||
| B. mallei | CIP A.198 | |||||
| B. mallei | CIP A.199 | |||||
| B. mallei | CIP A.200 | |||||
| B. pseudomallei | CIP 52.238 | |||||
| B. pseudomallei | CIP 52.239 | |||||
| B. pseudomallei | CIP 55.135 | |||||
| B. pseudomallei | CIP 60.67 | |||||
| B. pseudomallei | CIP 62.27 | |||||
| B. pseudomallei | CIP 62.28 | |||||
| B. pseudomallei | CIP 68.2 | |||||
| B. pseudomallei | CIP 68.3 | |||||
| B. pseudomallei | CIP A.202 | |||||
| B. pseudomallei | CIP A.203 | |||||
| P. aeruginosa | CIP 100720 | |||||
| B. norimbergensis | DSMZ 11628 | Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (Braunschweig, Germany) | ||||
| B. caledonica | LMG 19076 | Belgian Coordinated Collection of Microorganisms (Ghent, Belgium) | ||||
| B. caribensis | LMG 18531 | |||||
| B. caryophylli | LMG 2155 | |||||
| B. cenocepacia | LMG 12614 | |||||
| B. dolosa | LMG 18941 | |||||
| B. fungorum | LMG 16225 | |||||
| B. gladioli | LMG 2216 | |||||
| B. glathei | LMG 14190 | |||||
| B. glumae | LMG 2196 | |||||
| B. multivorans | LMG 13010 | |||||
| B. phenazinium | LMG 2247 | |||||
| B. plantarii | LMG 10907 | |||||
| B. pyrrocinia | LMG 14191 | |||||
| B. stabilis | LMG 14294 | |||||
| B. vietnamiensis | LMG 10929 | |||||
| B. mallei | NC 00120 | National Collection of Type Cultures (London, United Kingdom) | ||||
| B. mallei | NC 03708 | |||||
| B. mallei | NC 03709 | |||||
| B. mallei | NC 10229 | |||||
| B. mallei | NC 10230 | |||||
| B. mallei | NC 10247 | |||||
| B. mallei | NC 10248 | |||||
| B. mallei | NC 10260 | |||||
| B. pseudomallei | NC 01688 | |||||
| B. pseudomallei | NC 04846 | |||||
| B. pseudomallei | NC 06700 | |||||
| B. pseudomallei | NC 07383 | |||||
| B. pseudomallei | NC 07431 | |||||
| B. pseudomallei | NC 08016 | |||||
| B. pseudomallei | NC 08707 | |||||
| B. pseudomallei | NC 08708 | |||||
| B. pseudomallei | NC 10274 | |||||
| B. pseudomallei | NC 10276 | |||||
| B. pseudomallei | E 090 | Public Health Laboratory Service (London, United Kingdom; strains kindly provided by T. Pitt) | ||||
| B. pseudomallei | E 222 | |||||
| B. pseudomallei | SID 3783 | |||||
| B. pseudomallei | SID 3871 | |||||
| B. pseudomallei | SID 4717 | |||||
| B. pseudomallei | SID 4718 | |||||
| B. pseudomallei | SID 4935 | |||||
| B. pseudomallei | SID 5278 | |||||
| B. thailandensis | E 027 | |||||
| B. thailandensis | E 082 | |||||
| B. pseudomallei | 56.91 | Institut Pasteur (Paris, France; strains kindly provided by A. Dodin) | ||||
| B. pseudomallei | 70061 | |||||
| B. pseudomallei | 77804 | |||||
| B. pseudomallei | A120 | |||||
| B. pseudomallei | Ducruet | |||||
| B. pseudomallei | NT16 | |||||
| B. pseudomallei | PA.1195 | |||||
| B. pseudomallei | W5 | |||||
| B. graminis | AUS 28 | Laboratoire d'Ecologie Microbienne (Université Claude Bernard, Villeurbanne, France; strains kindly provided by B. Cournoyer) | ||||
| B. graminis | AUS 35 | |||||
| B. graminis | C3A1M | |||||
| B. graminis | C4D1M | |||||
| B. graminis | C5A1M | |||||
| B. cepacia | 001/97 | Centre de Recherches du Service de Santé des Armées (Grenoble, France) | ||||
| B. cepacia | 002/97 | |||||
| B. pseudomallei | 008/93 | |||||
| B. pseudomallei | 013/97 | |||||
| B. pseudomallei | 041/97 | |||||
| B. pseudomallei | 042/97 | |||||
| B. pseudomallei | 043/97 | |||||
| B. pseudomallei | 047/98 | |||||
| B. pseudomallei | 050/98 | |||||
| B. pseudomallei | 062/00 | |||||
| B. pseudomallei | 067/00 | |||||
| B. pseudomallei | 089/01 | |||||
| B. pseudomallei | 164/03 | |||||
| B. pseudomallei | 9 | Defense Medical and Environmental Research Institute (Singapore; DNAs kindly provided by May Ann Lee) | ||||
| B. pseudomallei | 11 | |||||
| B. pseudomallei | 22 | |||||
| B. pseudomallei | 59 | |||||
| B. pseudomallei | 15-10 | |||||
| B. pseudomallei | 5/96 | |||||
| B. pseudomallei | 15/96 | |||||
| B. pseudomallei | 497/96 |
Samples.
PCR was performed, with similar qualitative results, on (i) DNA purified by phenol-chloroform extraction by standard procedures (10) and (ii) water-washed or paraformaldehyde-fixed whole bacteria from broth or agar cultures.
Differential identification.
BpSCU2 was amplified from B. pseudomallei, B. mallei, and B. thailandensis. Only the two highly pathogenic species, B. pseudomallei and B. mallei, appeared positive for orf13. Only B. pseudomallei generated the orf11 amplicon. No amplification of the three targets occurred with any of the other species tested (Table 1). These results are consistent with those of BLAST sequences analysis.
Quantification.
The detection limit was 5 fg of B. pseudomallei DNA/μl. When determined on serial 10-fold dilutions of genomic DNA, the quantification was linear between 5 ng/μl and 0.05 pg/μl.
Probe specificity.
No interference was observed when amplifying orf11 from B. pseudomallei 23343 DNA diluted in B. mallei 23344 DNA to a ratio of 1:1,000.
Standards.
Plasmid standards were constructed by cloning fragments amplified from B. pseudomallei 23343 DNA in pCR2.1 TOPO plasmids (Invitrogen, Carlsbad, Calif.) by following the manufacturer's instructions. Purified plasmids were linearized with BamHI endonuclease before use in PCR.
In conclusion, this work provides a means for diagnosis and discrimination between three closely related species, B. pseudomallei, B. mallei, and B. thailandensis, by use of type III secretion system genes. Among the genes studied, orf13 can be regarded as specific for the two highly pathogenic species and orf11 is a specific marker for B. pseudomallei. BpSCU2 is shared by the three species, but, when it is the only marker detected, it provides a means for identification of B. thailandensis in addition to arabinose assimilation.
As hydrolysis probe technology uses standard cycling parameters regardless of the length and sequence of the amplicon, the different markers can be detected during the same LightCycler run. Plasmid standards can be used as positive controls more safely than bacterial cultures or genomic DNA.
This method affords considerable improvements in the specificity and rapidity of the diagnosis of these pathogens and allows rapid discrimination from opportunistic pathogens, such as members of the B. cepacia complex, that routine diagnostic laboratories are more likely to encounter. Moreover, due to the high risks associated with handling of B. pseudomallei and B. mallei, the molecular technique described here can be used by level A laboratories for identification of these potential bioterrorism agents with minimal culture steps.
Acknowledgments
This work was supported by the French Ministry of Defense, DGA/DSP/STTC, grant no. 010808/03-1.
We are indebted to Michèle Palencia for excellent technical assistance.
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