Discrimination of Burkholderia gladioli from other Burkholderia species detectable in cystic fibrosis patients by PCR

Unique Presentations of Burkholderia gladioli Infections in Several Strains of Immunocompromised Mice

Four strains of experimentally naïve mice (NOD. Cg-Prkdc scid Il2rg tm1Wjl /SzJ [NSG], NOD. Cg- Rag1 tm1Mom Il2rg tm1Wjl /SzJ [NRG], B6.129S(Cg)-Stat1 tm1Dlv/J [STAT1 -/-], and B6.129S7- Ifngr1 tm1Agt/J[IFNγR -/-] housed in a barrier facility developed unusual and seemingly unrelated clinical signs. Young NSG/NRG mice (n = 49, mean age = 4 ± 0.4 mo) exhibited nonspecific clinical signs of moderate-to-severe lethargy, hunched posture, decreased body condition, and pallor. In contrast to the NSG/NRG mice, the STAT1-/- and IFNγ R-/- mice (n = 5) developed large subcutaneous abscesses on the head and neck. These mice were euthanized, and samples were collected for culture. NSG/NRG mice had moderate-markedly enlarged livers (20 of 49, 40%) and spleens (17 of 49, 35%). The livers contained multiple, variably-sized, tan regions throughout all lobes. Histology revealed necrotizing hepatitis (13 of 17, 77%), splenic and hepatic extramedullary hematopoiesis (17 of 17, 100%), glomerular histiocytosis (6 of 17, 35%), and metritis (6 of 11, 55%) with perivascular inflammation, suggesting hematogenous spread Differentials for these lesions included mouse hepatitis virus, ectromelia virus, Pseudomonas aeruginosa, Salmonella spp., and Clostridium piliforme. Burkholderia gladioli was cultured from liver lesions and subcutaneous abscesses and confirmed with 16S ribosomal RNA sequencing. After completing systematic testing of the environment, failure of the water autoclave cycle was suspected as the cause of the outbreak. To address the situation, individually ventilated racks were sanitized and new breeders were purchased; these actions dramatically reduced B. gladioli infections. The current literature contains few reports of B. gladioli infections in immunocompromised mice, and its typical presentation is torticollis and rolling. B. gladioli infection is a potential differential for subcutaneous abscesses, hepatitis, and splenomegaly in immunocompromised mice. Careful monitoring of sterilization techniques is essential to prevent such infections in a barrier facility.

Research on the establishment and application of protein fingerprint spectrum database of Burkholderia pseudomallei in Hainan Province China

Burkholderia pseudomallei (B. pseudomallei) is the etiologic agent of melioidosis. The aim of this study was to establish a SuperSpectrum of B. pseudomallei in Hainan and evaluate its application value in the rapid identification of clinical isolates of B. pseudomallei. In total, 99 isolates of B. pseudomallei were obtained between 2010-2019 in different regions of Hainan Province, multilocus sequence typing (MLST) was performed, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was applied for spectrum acquisition. A SuperSpectrum was created based on the selection of 80 representative average spectra for 17 isolates of B. pseudomallei. Then we validated the SuperSpectra with 82 strains of B. pseudomallei, eight strains of Burkholderia thailandensis, two strains of Burkholderia cepacia, one strain of Burkholderia cenocepacia and one strain of Burkholderia multivorans, as well as one strain of Burkholderia gladioli identified by MLST typing, 16S rRNA gene sequencing and Vitek 2 Compact. The results showed that all samples in this study were confirmed at the species level. Protein fingerprints spectra showed that specific peaks occurred in B. pseudomallei from the Hainan region. The result of clustering typing indicated that B. pseudomallei and its closely related species could be well classified by MALDI-TOF MS at the protein level.

Discrimination of Burkholderia gladioli pv.alliicola and B. cepacia complex using the gyrB gene of B. gladioli pv. alliicola

The aim of the present study was to investigate the efficiency of the gyrB gene derived from Burkholderia gladioli pv.Alliicola (Bga) on the identification of Bga from the B. cepacia complex (Bcc) based on the COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy. A set of primers used for the specific amplification of the gyrB gene in Bga were designed according to the CODEHOP principle. A total of 1,644 bp of the gyrB gene sequence of Bga were acquired by CODEHOP amplification. The sequence was blasted in GenBank and it revealed an average of 86% similarity with the gyrB gene of nine genomovars of Bcc. A phylogenetic tree was constructed using the gyrB gene sequences. The microarray method was adopted to discriminate Bga from Bcc based on the specific probes designed upon the gyrB gene, and five genomovars of Bcc demonstrated a good discrimination from Bga on the microarray chip. CODEHOP strategy succeeded in amplification of the gyrB gene of Bga, which made it possible for the identification of Bga from five genomovars of Bcc.

Laboratory diagnosis of melioidosis: past, present and future

Melioidosis is an emerging, potentially fatal disease caused by Burkholderia pseudomallei, which requires prolonged antibiotic treatment to prevent disease relapse. However, difficulties in laboratory diagnosis of melioidosis may delay treatment and affect disease outcomes. Isolation of B. pseudomallei from clinical specimens has been improved with the use of selective media. However, even with positive cultures, identification of B. pseudomallei can be difficult in clinical microbiology laboratories, especially in non-endemic areas where clinical suspicion is low. Commercial identification systems may fail to distinguish between B. pseudomallei and closely related species such as Burkholderia thailandensis. Genotypic identification of suspected isolates can be achieved by sequencing of gene targets such as groEL which offer higher discriminative power than 16S rRNA. Specific PCR-based identification of B. pseudomallei has also been developed using B. pseudomallei-specific gene targets such as Type III secretion system and Tat-domain protein. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolutionary technique for pathogen identification, has been shown to be potentially useful for rapid identification of B. pseudomallei, although existing databases require optimization by adding reference spectra for B. pseudomallei. Despite these advances in bacterial identification, diagnostic problems encountered in culture-negative cases remain largely unresolved. Although various serological tests have been developed, they are generally unstandardized "in house" assays and have low sensitivities and specificities. Although specific PCR assays have been applied to direct clinical and environmental specimens, the sensitivities for diagnosis remain to be evaluated. Metabolomics is an uprising tool for studying infectious diseases and may offer a novel approach for exploring potential diagnostic biomarkers. The metabolomics profiles of B. pseudomallei culture supernatants can be potentially distinguished from those of related bacterial species including B. thailandensis . Further studies using bacterial cultures and direct patient samples are required to evaluate the potential of metabolomics for improving diagnosis of melioidosis.

Evaluation of Onion Cultivars for Resistance to Enterobacter cloacae in Storage

Sixty-nine storage onion (Allium cepa) cultivars (seven white, five red, and 57 yellow cultivars) were evaluated in the Washington State University Onion Cultivar Trials in the semiarid Columbia Basin of central Washington in 2007-08 and/or 2008-09. Each cultivar was inoculated with Enterobacter cloacae, cured, stored under commercial storage conditions, and evaluated for bacterial storage rot symptoms approximately 4.5 months after storage. Noninoculated bulbs of each cultivar served as a control treatment in each experiment. In addition, bulbs injected with water served as a second control treatment in the 2008-09 experiment. Inoculation of onion bulbs with E. cloacae resulted in significantly higher incidence and severity of Enterobacter bulb decay compared to noninoculated bulbs and bulbs injected with sterile water. For bulbs inoculated with E. cloacae, mean severity of bacterial storage rot per cultivar ranged from 5 to 19% of the cross-section evaluated for each onion bulb in 2007-08 and from 9 to 29% in 2008-09. For noninoculated bulbs, mean severity ranged from 0 to 1% in 2007-08 and 0 to 3% in 2008-09. For bulbs injected with water in the 2008-09 experiment, severity of bulb rot ranged from 0 to 10% per cultivar, with four cultivars (OLYX05-26, RE-E, Redwing, and Talon) displaying bulb rot ratings significantly greater than 0%. For the 33 cultivars included in both experiments, a significant correlation in bulb rot severity ratings was detected for the 2007-08 versus 2008-09 experiments (r = 0.43 at P = 0.013). Redwing, Red Bull, T-433, Centerstone, and Salsa had low severity ratings in both experiments; whereas Montero, OLYS05N5, Caveat, and Granero had severe bulb rot ratings in both experiments. The results demonstrate that it should be possible to select for increased resistance to Enterobacter bulb decay in storage onion cultivars.

Microbiological and epidemiological features of clinical respiratory isolates of Burkholderia gladioli

Burkholderia gladioli, primarily known as a plant pathogen, is involved in human infections, especially in patients with cystic fibrosis (CF). In the present study, the first respiratory isolates recovered from 14 French patients with CF and 4 French patients without CF, identified by 16S rRNA gene analysis, were tested for growth on B. cepacia selective media, for identification by commercial systems, and for their antimicrobial susceptibilities, and were compared by pulsed-field gel electrophoresis (PFGE). Patients' data were collected. All 18 isolates grew on oxidation-fermentation-polymyxin B-bacitracin-lactose medium and Pseudomonas cepacia agar, but only 13 grew on Burkholderia cepacia selective agar. API 20NE strips did not differentiate B. gladioli from B. cepacia, whereas Vitek 2 GN cards correctly identified 15 isolates. All isolates were susceptible to piperacillin, imipenem, aminoglycosides, and ciprofloxacin and were far less resistant to ticarcillin than B. cepacia complex organisms. Fifteen PFGE types were observed among the 18 isolates, but shared types were not identified among epidemiologically related patients. The microbiological follow-up of CF patients showed that colonization was persistent in 3 of 13 documented cases; B. gladioli was isolated from posttransplantation cultures of blood from 1 patient. Among the patients without CF, B. gladioli was associated with intubation (three cases) or bronchiectasis (one case). In summary, the inclusion of B. gladioli in the databases of commercial identification systems should improve the diagnostic capabilities of those systems. In CF patients, this organism is more frequently involved in transient infections than in chronic infections, but it may be responsible for complications posttransplantation; patient-to-patient transmission has not been demonstrated to date. Lastly, B. gladioli appears to be naturally susceptible to aminoglycosides and ciprofloxacin, although resistant isolates may emerge in the course of chronic infections.

Two cases of keratitis and corneal ulcers caused by Burkholderia gladioli

We report two cases of protracted keratitis complicated by corneal ulcer. Burkholderia gladioli, primarily known as a plant pathogen, was cultured from corneal swabs. The epithelial defects healed after extended adequate antibiotic therapy. Despite identical patterns of both strains in restriction fragment length polymorphism analysis, a common infection source was not detectable.

Selection of nitrogen-fixing deficient Burkholderia vietnamiensis strains by cystic fibrosis patients: involvement of nif gene deletions and auxotrophic mutations

Burkholderia vietnamiensis is the third most prevalent species of the Burkholderia cepacia complex (Bcc) found in cystic fibrosis (CF) patients. Its ability at fixing nitrogen makes it one of the main Bcc species showing strong filiations with environmental reservoirs. In this study, 83% (29 over 35) of the B. vietnamiensis CF isolates and 100% of the environmental ones (over 29) were found expressing the dinitrogenase complex (encoded by the nif cluster) which is essential in N(2) fixation. Among the deficient strains, two were found growing with ammonium chloride suggesting that they were defective in N(2) fixation, and four with amino acids supplements suggesting that they were harbouring auxotrophic mutations. To get insights about the genetic events that led to the emergence of the N(2)-fixing defective strains, a genetic analysis of B. vietnamiensis nitrogen-fixing property was undertaken. A 40-kb-long nif cluster and nif regulatory genes were identified within the B. vietnamiensis strain G4 genome sequence, and analysed. Transposon mutagenesis and nifH genetic marker exchanges showed the nif cluster and several other genes like gltB (encoding a subunit of the glutamate synthase) to play a key role in B. vietnamiensis ability at growing in nitrogen-free media. nif cluster DNA probings of restricted genomic DNA blots showed a full deletion of the nif cluster for one of the N(2)-fixing defective strain while the other one showed a genetic organization similar to the one of the G4 strain. For 17% of B. vietnamiensis clinical strains, CF lungs appeared to have favoured the selection of mutations or deletions leading to N(2)-fixing deficiencies.

CARACTERIZACIÓN BIOQUIMICA Y PERFIL DE SENSIBILIDAD ANTIMICROBIANA IN VITRO DE MUESTRAS DE BURKHOLDERIA MALLEI AISLADAS DE ÉQUIDOS DE LA REGIÓN NORDESTE DE BRASIL

RESUMEN En este estudio fueron aisladas y caracterizadas bioquímicamente siete muestras deBurkholderia mallei de secreción de nódulos cutáneos cerrados de equinos y asininos naturalmente infectados por la B. mallei y procedentes del Estado de Pernambuco, Nordeste de Brasil. Las muestras de B. mallei fueron sometidas a pruebas bioquímicas para su clasificación y posteriormente a varias pruebas de sensibilidad in vitro a diferentes drogas antimicrobianas. Se observo variación en el bioquimismo entre las muestras bacterianas, principalmente referente a la fermentación de los carbohidratos. Se observácion además, mayor sensibilidad in vitro al clorofenicol, doxaciclina, enrofloxacina, florfenicol, gentamicina, netilmicina, nitrofurantoína, oxalinato, sulfa+trimetoprim y tetraciclina. A pesar de la sensibilidad observada para algunos antimicrobianos, no se indica el tratamiento de los animales enfermos con estos por la posibilidad de que se tornen portadores y mantenedores de la bacteria en el ambiente.

Nosocomial bloodstream infections with Burkholderia stabilis

Burkholderia stabilis was grown from blood cultures of seven patients presenting with signs and symptoms of septicaemia in the intensive care unit at Mersin University Hospital, Mersin, Turkey between July and October 2002. Four patients had one B. stabilis-positive blood culture, two patients had two, and one patient had four. Isolates from six of seven patients had the same resistotype and random amplified polymorphic DNA analysis type. Despite treatment with ciprofloxacin and imipenem, to which the strains were susceptible, all patients died one to eight days after isolation of B. stabilis from their blood. B. stabilis should be regarded as an opportunistic pathogen that may cause nosocomial bloodstream infections.

Invasion of spores of the arbuscular mycorrhizal fungus Gigaspora decipiens by Burkholderia spp

Burkholderia species are bacterial soil inhabitants that are capable of interacting with a variety of eukaryotes, in some cases occupying intracellular habitats. Pathogenic and nonpathogenic Burkholderia spp., including B. vietnamiensis, B. cepacia, and B. pseudomallei, were grown on germinating spores of the arbuscular mycorrhizal fungus Gigaspora decipiens. Spore lysis assays revealed that all Burkholderia spp. tested were able to colonize the interior of G. decipiens spores. Amplification of specific DNA sequences and transmission electron microscopy confirmed the intracellular presence of B. vietnamiensis. Twelve percent of all spores were invaded by B. vietnamiensis, with an average of 1.5 x 10(6) CFU recovered from individual infected spores. Of those spores inoculated with B. pseudomallei, 7% were invaded, with an average of 5.5 x 10(5) CFU recovered from individual infected spores. Scanning electron and fluorescence microscopy provided insights into the morphology of surfaces of spores and hyphae of G. decipiens and the attachment of bacteria. Burkholderia spp. colonized both hyphae and spores, attaching to surfaces in either an end-on or side-on fashion. Adherence of Burkholderia spp. to eukaryotic surfaces also involved the formation of numerous fibrillar structures.

Molecular analysis of Burkholderia cepacia complex isolates from a Portuguese cystic fibrosis center: a 7-year study

This work reports results of a systematic molecular analysis involving 113 Burkholderia cepacia complex isolates obtained from 23 cystic fibrosis (CF) patients under surveillance over a 7-year period at the major Portuguese CF center, the Santa Maria Hospital in Lisbon. The majority of the isolates were serial isolates from persistently infected patients (more than one-half of the population examined). In agreement with previous studies, B. cenocepacia (formerly genomovar III) was the most prevalent species; it was isolated from 52% of the patients infected with B. cepacia complex isolates. Contrasting with previous studies, a very significant percentage of the Portuguese CF subpopulation examined was infected with B. cepacia genomovar I (36%) and B. stabilis (18%). B. multivorans was recovered from two of the infected patients. All four of the species or genomovars were associated with poor clinical outcome, including the cepacia syndrome, and gave rise to chronic and transient infections, with the clinical condition depending on the patient and other still-unidentified factors. The B. cepacia epidemic strain marker region was found exclusively in genomovar III strains, while cblA was detected in genomovars I and III, only. There was no clear relation between the presence of these markers and transmissibility. Altogether, our results indicate that the use of these markers or the genomovar status in identifying patients at higher risk for infection is uncertain.

Use of 16S rRNA gene sequencing for identification of nonfermenting gram-negative bacilli recovered from patients attending a single cystic fibrosis center

During 1999, we used partial 16S rRNA gene sequencing for the prospective identification of atypical nonfermenting gram-negative bacilli isolated from patients attending our cystic fibrosis center. Of 1,093 isolates of nonfermenting gram-negative bacilli recovered from 148 patients, 46 (4.2%) gave problematic results with conventional phenotypic tests. These 46 isolates were genotypically identified as Pseudomonas aeruginosa (19 isolates, 12 patients), Achromobacter xylosoxidans (10 isolates, 8 patients), Stenotrophomonas maltophilia (9 isolates, 9 patients), Burkholderia cepacia genomovar I/III (3 isolates, 3 patients), Burkholderia vietnamiensis (1 isolate), Burkholderia gladioli (1 isolate), and Ralstonia mannitolilytica (3 isolates, 2 patients), a recently recognized species.

Comparative evaluation of the BD Phoenix and VITEK 2 automated instruments for identification of isolates of the Burkholderia cepacia complex

We evaluated two new automated identification systems, the BD Phoenix (Becton Dickinson) and the VITEK 2 (bioMérieux), for identification of isolates of the Burkholderia cepacia complex (BCC). The test sample included 42 isolates of the highly virulent and epidemic genomovar III, 45 isolates of B. multivorans, and 47 isolates of other members of the BCC. Rates of correct identification by the BD Phoenix and VITEK 2 were similar when all BCC isolates were considered (50 and 53%, respectively) but differed markedly for genomovar III (71 and 38%; P < 0.01) and for B. multivorans (58 and 89%; P < 0.001). For the BD Phoenix as well as the VITEK 2, taking all 134 isolates of the BCC together, rates of correct identification of clinical isolates (56 and 55%, respectively; n = 85) were higher than those of environmental isolates (21 and 39%, respectively; n = 28). Clinical isolates of genomovar III (n = 27) showed correct identification rates of 81% (BD Phoenix) and 48% (VITEK 2) (P < 0.01). Rates of misidentification for BD Phoenix and VITEK 2 were 9 and 17% for genomovar III, 22 and 7% for B. multivorans, and 36 and 13% for the other BCC members (P < 0.01), respectively. More than half of the isolates misidentified by each instrument were identified as Ralstonia pickettii, Ralstonia paucula (CDC IV C-2 group), Alcaligenes faecalis, Achromobacter spp., or, for the VITEK 2, "various nonfermenters." This study reemphasizes that confirmatory identification of BCC, preferably by molecular methods, is highly recommended.

Microbiological characterisation of Burkholderia cepacia isolates from cystic fibrosis patients: investigation of the exopolysaccharides produced

Eleven strains of Burkholderia cepacia were isolated directly from clinical specimens: 10 from sputum of cystic fibrosis patients, and one from a vaginal swab. They were biochemically identified using API20NE and confirmed by a PCR-based assay. The genomovar characterisation obtained by specific PCR amplification revealed seven strains belonging to genomovar I, three belonging to genomovar IIIA and one belonging to genomovar IV. All isolates were also typed by ribotyping and random amplification of polymorphic DNA analysis. Some of the characterised strains were examined for the ability to produce exopolysaccharides, with the aim of correlating the genomovar with the exopolysaccharide structure. The polysaccharides were analysed by means of methylation analysis and 1H-NMR spectroscopy in order to determine structural similarities. It was shown that different strains are capable of producing chemically different polysaccharides.

Burkholderia gladioli: recurrent abscesses in a patient with cystic fibrosis

We describe a case of an adult patient with cystic fibrosis who developed chronic pulmonary infection and multiple episodes of soft tissue abscesses with Burkholderia gladioli; this organism should be added to the list of potential pathogens for individuals with cystic fibrosis.

Unusual respiratory bacterial flora in cystic fibrosis: microbiologic and clinical features

Pulmonary infections continue to be a significant source of morbidity and mortality among patients with cystic fibrosis. Although our understanding of the pathogenesis and clinical consequences of pulmonary infections with Pseudomonas aeruginosa has increased greatly in recent years, very little is known about potentially emerging pathogens such as Burkholderia cepacia complex, Stenotrophomonas maltophilia, Alcaligenes xylosoxidans, and methicillin-resistant Staphylococcus aureus. In this review, the authors discuss methods for appropriate identification of these "unusual" organisms and their epidemiologic and clinical features. Multicenter surveillance studies are needed to more clearly establish the pathogenicity of these organisms.

DNA-Based diagnostic approaches for identification of Burkholderia cepacia complex, Burkholderia vietnamiensis, Burkholderia multivorans, Burkholderia stabilis, and Burkholderia cepacia genomovars I and III

Bacteria of the Burkholderia cepacia complex consist of five discrete genomic species, including genomovars I and III and three new species: Burkholderia multivorans (formerly genomovar II), Burkholderia stabilis (formerly genomovar IV), and Burkholderia vietnamiensis (formerly genomovar V). Strains of all five genomovars are capable of causing opportunistic human infection, and microbiological identification of these closely related species is difficult. The 16S rRNA gene (16S rDNA) and recA gene of these bacteria were examined in order to develop rapid tests for genomovar identification. Restriction fragment length polymorphism (RFLP) analysis of PCR-amplified 16S rDNA revealed sequence polymorphisms capable of identifying B. multivorans and B. vietnamiensis but insufficient to discriminate strains of B. cepacia genomovars I and III and B. stabilis. RFLP analysis of PCR-amplified recA demonstrated sufficient nucleotide sequence variation to enable separation of strains of all five B. cepacia complex genomovars. Complete recA nucleotide sequences were obtained for 20 strains representative of the diversity of the B. cepacia complex. Construction of a recA phylogenetic tree identified six distinct clusters (recA groups): B. multivorans, B. vietnamiensis, B. stabilis, genomovar I, and the subdivision of genomovar III isolates into two recA groups, III-A and III-B. Alignment of recA sequences enabled the design of PCR primers for the specific detection of each of the six latter recA groups. The recA gene was found on the largest chromosome within the genome of B. cepacia complex strains and, in contrast to the findings of a previous study, only a single copy of the gene was present. In conclusion, analysis of the recA gene of the B. cepacia complex provides a rapid and robust nucleotide sequence-based approach to identify and classify this taxonomically complex group of opportunistic pathogens.

Identification of members of the Burkholderia cepacia complex by species-specific PCR

Definitive identification of the species in the Burkholderia cepacia complex by routine clinical microbiology methods is difficult. Phenotypic tests to identify B. multivorans and B. vietnamiensis have been established; more recent work indicates B. stabilis may also be identified by growth characteristics and biochemical tests. However, attempts to identify genomovars I and III have, thus far, proved unsuccessful. Previously, we demonstrated the utility of two primer pairs, directed to the rRNA operon, to specifically identify the B. cepacia complex in a PCR. One of these primer pairs, G1-G2, only amplified a DNA fragment from genomovars I and III and B. stabilis in a PCR with genomic DNA isolated from prototypical strains representing the five genomovars. Sequence analysis of the rRNA operon for all the genomovars indicated that this primer pair targeted a region shared by these isolates. Further analysis revealed a region of heterogeneity between genomovar III and B. stabilis internal to the amplified product of G1-G2. Primers designed to target this region were tested with prototypical strains following an initial amplification with the G1-G2 primer pair. New primers specific for the prototypical genomovar III and B. stabilis were designated SPR3 and SPR4, respectively. Analysis of 93 isolates representing 18 genomovar I, 13 B. multivorans, 36 genomovar III, 11 B. stabilis, and 15 B. vietnamiensis isolates was performed. DNA from all isolates of genomovars I and III and B. stabilis was amplified by G1-G2. Genomovar III isolates yielded a product with SPR3/G1 while B. stabilis amplified with SPR4-G1. Genomovar I isolates were amplified by either SPR3-G1 or SPR4-G1, but not both. B. multivorans yielded a product with SPR3-G1 but not G1-G2, and B. vietnamiensis isolates were negative in all PCRs. Thus using an algorithm with G1-G2, SPR3-G1, and SPR4-G1 primers in a PCR analysis, genomovar III isolates can be separated from B. stabilis and the identity of B. multivorans and B. vietnamiensis can be confirmed.

Distinguishing species of the Burkholderia cepacia complex and Burkholderia gladioli by automated ribotyping

Several species belonging to the genus Burkholderia are clinically relevant, opportunistic pathogens that inhabit major environmental reservoirs. Consequently, the availability of means for adequate identification and epidemiological characterization of individual environmental or clinical isolates is mandatory. In the present communication we describe the use of the Riboprinter microbial characterization system (Qualicon, Warwick, United Kingdom) for automated ribotyping of 104 strains of Burkholderia species from diverse sources, including several publicly accessible collections. The main outcome of this analysis was that all strains were typeable and that strains of Burkholderia gladioli and of each species of the B. cepacia complex, including B. multivorans, B. stabilis, and B. vietnamiensis, were effectively discriminated. Furthermore, different ribotypes were discerned within each species. Ribotyping results were in general agreement with strain classification based on restriction fragment analysis of 16S ribosomal amplicons, but the resolution of ribotyping was much higher. This enabled automated molecular typing below the species level. Cluster analysis of the patterns obtained by ribotyping (riboprints) showed that within B. gladioli, B. multivorans, and B. cepacia genomovar VI, the different riboprints identified always clustered together. Riboprints of B. cepacia genomovars I and III, B. stabilis, and B. vietnamiensis did not show distinct clustering but rather exhibited the formation of loose assemblages within which several smaller, genomovar-specific clusters were delineated. Therefore, ribotyping proved useful for genomovar identification. Analysis of serial isolates from individual patients demonstrated that infection with a single ribotype had occurred, despite minor genetic differences that were detected by pulsed-field gel electrophoresis of DNA macrorestriction fragments. The automated approach allows very rapid and reliable identification and epidemiological characterization of strains and generates an easily manageable database suited for expansion with information on additional bacterial isolates.

Molecular typing and exopolysaccharide biosynthesis of Burkholderia cepacia isolates from a Portuguese cystic fibrosis center

This work describes the first epidemiological survey of Burkholderia cepacia involved in pulmonary infections among the Portuguese population with cystic fibrosis (CF) who attended the major CF treatment Center in Lisbon at Sta. Maria Hospital from 1995 to the end of 1997. The characterization of the genomic relatedness of the isolates was based on the analysis of their ribopatterns (with EcoRI) followed by construction of a ribotype-based phylogenetic tree. This study was complemented with macrorestriction fragment analysis by pulsed-field gel electrophoresis. After optimization of the solid growth medium, we found that exopolysaccharide (EPS) production by B. cepacia CF isolates is not as rare a phenomenon as was thought before; indeed, 70% of the isolates examined were EPS producers.

Species-specific PCR as a tool for the identification of Burkholderia gladioli

Burkholderia gladioli colonizes the respiratory tracts of patients with cystic fibrosis and chronic granulomatous disease. However, due to the high degree of phenotypic similarity between this species and closely related species in the Burkholderia cepacia complex, accurate identification is difficult. Incorrect identification of these species may have serious repercussions for the management of patients with cystic fibrosis. To develop an accurate procedure for the identification of B. gladioli, a molecular method to discriminate between this species and other species commonly isolated from the sputa of patients with cystic fibrosis was investigated. The 23S ribosomal DNA was cloned from several clinical isolates of B. gladioli, and the nucleotide sequence was determined. Computer-assisted sequence comparisons indicated four regions of the 23S rRNA specific for this species; these regions were used to design three primer pairs for species-specific PCR. Two of the primer pairs showed 100% sensitivity and specificity for B. gladioli when tested against a panel of 47 isolates comprising 19 B. gladioli isolates and 28 isolates of 16 other bacterial species. One of the primer pairs was further assessed for species specificity by using a panel of 102 isolates obtained from the Burkholderia cepacia Research Laboratory and Repository. The species-specific PCR was positive for 70 of 74 isolates of B. gladioli and was negative for all other bacterial species examined. Overall, this primer pair displayed a sensitivity and specificity of 96% (89 of 93) and 100%, respectively. These data demonstrate the potential of species-specific PCR for the identification of B. gladioli.

Identification of Burkholderia spp. in the clinical microbiology laboratory: comparison of conventional and molecular methods

Cystic fibrosis (CF) predisposes patients to bacterial colonization and infection of the lower airways. Several species belonging to the genus Burkholderia are potential CF-related pathogens, but microbiological identification may be complicated. This situation is not in the least due to the poorly defined taxonomic status of these bacteria, and further validation of the available diagnostic assays is required. A total of 114 geographically diverse bacterial isolates, previously identified in reference laboratories as Burkholderia cepacia (n = 51), B. gladioli (n = 14), Ralstonia pickettii (n = 6), B. multivorans (n = 2), Stenotrophomonas maltophilia (n = 3), and Pseudomonas aeruginosa (n = 11), were collected from environmental, clinical, and reference sources. In addition, 27 clinical isolates putatively identified as Burkholderia spp. were recovered from the sputum of Dutch CF patients. All isolates were used to evaluate the accuracy of two selective growth media, four systems for biochemical identification (API 20NE, Vitek GNI, Vitek NFC, and MicroScan), and three different PCR-based assays. The PCR assays amplify different parts of the ribosomal DNA operon, either alone or in combination with cleavage by various restriction enzymes (PCR-restriction fragment length polymorphism [RFLP] analysis). The best system for the biochemical identification of B. cepacia appeared to be the API 20NE test. None of the biochemical assays successfully grouped the B. gladioli strains. The PCR-RFLP method appeared to be the optimal method for accurate nucleic acid-mediated identification of the different Burkholderia spp. With this method, B. gladioli was also reliably classified in a separate group. For the laboratory diagnosis of B. cepacia, we recommend parallel cultures on blood agar medium and selective agar plates. Further identification of colonies with a Burkholderia phenotype should be performed with the API 20NE test. For final confirmation of species identities, PCR amplification of the small-subunit rRNA gene followed by RFLP analysis with various enzymes is recommended.

Discrimination of Burkholderia multivorans and Burkholderia vietnamiensis from Burkholderia cepacia genomovars I, III, and IV by PCR

We present a PCR procedure for identification of Burkholderia cepacia, Burkholderia multivorans, and Burkholderia vietnamiensis. 16S and 23S ribosomal DNAs (rDNAs) of B. multivorans and B. vietnamiensis were sequenced and aligned with published sequences for definition of species-specific 18-mer oligonucleotide primers. Specific antisense 16S rDNA primers (for B. cepacia, 5'-AGC ACT CCC RCC TCT CAG-3'; for B. multivorans, 5'-AGC ACT CCC GAA TCT CTT-3') and 23S rDNA primers (for B. vietnamiensis, 5'-TCC TAC CAT GCG TGC AA-3') were paired with a general sense primer of 16S rDNAs (5'-AGR GTT YGA TYM TGG CTC AG-3') or with a sense primer of 23S rDNA (5'-CCT TTG GGT CAT CCT GGA-3'). PCR with these primers under optimized conditions is appropriate to specifically and rapidly identify B. multivorans, B. vietnamiensis, and B. cepacia (genomovars I, III, and IV are not discriminated). In comparison with the polyphasic taxonomic analyses presently necessary for species and genomovar identification within the B. cepacia complex, our procedure is more rapid and easier to perform and may contribute to clarifying the clinical significance of individual members of the complex in cystic fibrosis.

THE THREE DS OF PCR-BASED GENOMIC ANALYSIS OF PHYTOBACTERIA: Diversity, Detection, and Disease Diagnosis

The advent of molecular biology in general and the polymerase chain reaction in particular have greatly facilitated genomic analyses of microorganisms, provide enhanced capability to characterize and classify strains, and facilitate research to assess the genetic diversity of populations. The diversity of large populations can be assessed in a relatively efficient manner using rep-PCR-, AFLP-, and AP-PCR/RAPD-based genomic fingerprinting methods, especially when combined with computer-assisted pattern analysis. Genetic diversity maps provide a framework to understand the taxonomy, population structure, and dynamics of phytobacteria and provide a high-resolution framework to devise sensitive, specific, and rapid methods for pathogen detection, plant disease diagnosis, as well as management of disease risk. A variety of PCR-based fingerprinting protocols such as rDNA-based PCR, ITS-PCR, ARDRA, T-RFLPs, and tRNA-PCR have been devised, and numerous innovative approaches using specific primers have been adopted to enhance both the detection and identification of phytobacteria. PCR-based protocols, combined with computer-based analysis, have provided novel fundamental knowledge of the ecology and population dynamics of bacterial pathogens, and present exciting new opportunities for basic and applied studies in plant pathology.

Molecular procedure for rapid detection of Burkholderia mallei and Burkholderia pseudomallei

A PCR procedure for the discrimination of Burkholderia mallei and Burkholderia pseudomallei was developed. It is based on the nucleotide difference T 2143 C (T versus C at position 2143) between B. mallei and B. pseudomallei detected in the 23S rDNA sequences. In comparison with conventional methods the procedure allows more rapid identification at reduced risk for infection of laboratory personnel.