DISCRIMINATION OF Burkholderia mallei/pseudomallei FROM Burkholderia thailandensis BY SEQUENCE COMPARISON OF A FRAGMENT OF THE RIBOSOMAL PROTEIN S21 (RPSU) GENE

Comparison of Mast Burkholderia Cepacia, Ashdown + Gentamicin, and Burkholderia Pseudomallei Selective Agar for the Selective Growth of Burkholderia Spp

Reliable identification of pathogenic Burkholderia spp. like Burkholderia mallei and Burkholderia pseudomallei in clinical samples is desirable. Three different selective media were assessed for reliability and selectivity with various Burkholderia spp. and nontarget organisms.

Mast Burkholderia cepacia agar, Ashdown + gentamicin agar, and B. pseudomallei selective agar were compared. A panel of 116 reference strains and well-characterized clinical isolates, comprising 30 B. pseudomallei, 20 B. mallei, 18 other Burkholderia spp., and 48 nontarget organisms, was used for this assessment.

While all B. pseudomallei strains grew on all three tested selective agars, the other Burkholderia spp. showed a diverse growth pattern. Nontarget organisms, i.e., nonfermentative rod-shaped bacteria, other species, and yeasts, grew on all selective agars. Colony morphology did not allow unambiguous discrimination.

While the assessed selective media reliably allowed the growth of a wide range of B. pseudomallei strains, growth of other Burkholderia spp. is only partially ensured. Growth of various nontarget organisms has to be considered. Therefore, the assessed media can only be used in combination with other confirmative tests in the diagnostic procedure for the screening for melioidosis or glanders.

A Quadruplex Real-Time PCR Assay for the Rapid Detection and Differentiation of the Most Relevant Members of the B. pseudomallei Complex: B. mallei, B. pseudomallei, and B. thailandensis

The Burkholderia pseudomallei complex classically consisted of B. mallei, B. pseudomallei, and B. thailandensis, but has now expanded to include B. oklahomensis, B. humptydooensis, and three unassigned Burkholderia clades. Methods for detecting and differentiating the B. pseudomallei complex has been the topic of recent research due to phenotypic and genotypic similarities of these species. B. mallei and B. pseudomallei are recognized as CDC Tier 1 select agents, and are the causative agents of glanders and melioidosis, respectively. Although B. thailandensis and B. oklahomensis are generally avirulent, both display similar phenotypic characteristics to that of B. pseudomallei. B. humptydooensis and the Burkholderia clades are genetically similar to the B. pseudomallei complex, and are not associated with disease. Optimal identification of these species remains problematic, and PCR-based methods can resolve issues with B. pseudomallei complex detection and differentiation. Currently, no PCR assay is available that detects the major species of the B. pseudomallei complex. A real-time PCR assay in a multiplex single-tube format was developed to simultaneously detect and differentiate B. mallei, B. pseudomallei, and B. thailandensis, and a common sequence found in B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis. A total of 309 Burkholderia isolates and 5 other bacterial species were evaluated. The assay was 100% sensitive and specific, demonstrated sensitivity beyond culture and GC methods for the isolates tested, and is completed in about an hour with a detection limit between 2.6pg and 48.9pg of gDNA. Bioinformatic analyses also showed the assay is likely 100% specific and sensitive for all 84 fully sequenced B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis strains currently available in GenBank. For these reasons, this assay could be a rapid and sensitive tool in the detection and differentiation for those species of the B. pseudomallei complex with recognized clinical and practical significance.

Comparison of Five Commercial Nucleic Acid Extraction Kits for the PCR-based Detection of Burkholderia Pseudomallei DNA in Formalin-Fixed, Paraffin-Embedded Tissues

The extraction and further processing of nucleic acids (NA) from formalin-fixed paraffin-embedded (FFPE) tissues for microbiological diagnostic polymerase chain reaction (PCR) approaches is challenging. Here, we assessed the effects of five different commercially available nucleic acid extraction kits on the results of real-time PCR.

FFPE samples from organs of Burkholderia pseudomallei-infected Swiss mice were subjected to processing with five different extraction kits from QIAGEN (FFPE DNA Tissue Kit, EZ1 DNA Tissue Kit, DNA Mini Kit, DNA Blood Mini Kit, and FlexiGene DNA Kit) in combination with three different real-time PCRs targeting B. pseudomallei-specific sequences of varying length after 16 years of storage.

The EZ1 DNA Tissue Kit and the DNA Mini Kit scored best regarding the numbers of successful PCR reactions. In case of positive PCR, differences regarding the cycle-threshold (Ct) values were marginal.

The impact of the applied extraction kits on the reliability of PCR from FFPE material seems to be low. Interfering factors like the quality of the dewaxing procedure or the sample age appear more important than the selection of specialized FFPE kits.

Correlation of rpsU Gene Sequence Clusters and Biochemical Properties, Gc-Ms Spectra and Resistance Profiles of Clinical Burkholderia Spp. Isolates

This study assessed the variation of phenotypic features of clinical isolates of Burkholderia spp. from common rpsU gene sequence clusters. A total of 41 clinical Burkholderia spp. isolates from German mucoviscidosis patients was subjected to rpsU gene sequencing. Biochemical assessment included the API systems 20 NE and 50 CHE as well as the Micronaut NF system. Fatty acid patterns were assessed using gas chromatography-mass spectrometry (GC-MS). Broth microdilution was used to identify minimum inhibitory concentrations. Five rpsU gene sequence clusters comprised more than one clinical isolate. Altogether, assignments to three species and seven clusters comprising more than one Burkholderia species were performed. Inhomogeneity of biochemical reactions within the clusters ranged from 0/28 to 45/50 reactions. The standard deviation for fatty acid distributions ranged from 0% to 11.5%. Minimum inhibitory concentrations within the clusters showed a wide variation but only minor differences between the clusters. Broad variations within identified rpsU gene sequence clusters regarding biochemical reactions, fatty acid patterns, and resistance patterns of clinical Burkholderia spp. isolates make the application of rpsU gene sequence analysis as a stand-alone procedure for discriminations within the Burkholderia cepacia complex unreliable.

rpsU-based discrimination within the genus Burkholderia

Sequencing of the gene rpsU reliably delineates saprophytic Burkholderia (B.) thailandensis from highly pathogenic B. mallei and B. pseudomallei. We analyzed the suitability of this technique for the delineation of the B. pseudomallei complex from other Burkholderia species. Both newly recorded and previously deposited sequences of well-characterized or reference strains (n = 84) of Azoarcus spp., B. ambifaria, B. anthina, B. caledonica, B. caribensis, B. caryophylli, B. cenocepacia, B. cepacia, B. cocovenenans, B. dolosa, B. fungorum, B. gladioli, B. glathei, B. glumae, B. graminis, B. hospita, B. kururensis, B. mallei, B. multivorans, B. phenazinium, B. phenoliruptrix, B. phymatum, B. phytofirmans, B. plantarii, B. pseudomallei, B. pyrrocinia, B. stabilis, B. thailandensis, B. ubonensis, B. vietnamiensis, B. xenovorans, not further defined Burkholderia spp., and the outliers Cupriavidus metallidurans, Laribacter hongkongensis, Pandorea norimbergensis, and Ralstonia pickettii were included in a multiple sequence analysis. Multiple sequence alignments led to the delineation of four major clusters, rpsU-I to rpsU-IV, with a sequence homology >92%. The B. pseudomallei complex formed the complex rpsU-II. Several Burkholderia species showed 100% sequence homology. This procedure is useful for the molecular confirmation or exclusion of glanders or melioidosis from primary patient material. Further discrimination within the Burkholderia genus requires other molecular approaches.