Phenotypic methods for determining genomovar status of the Burkholderia cepacia complex

Recent taxonomic advances have demonstrated that Burkholderia cepacia is a cluster of at least seven closely related genomic species (or genomovars) collectively referred to as the B. cepacia complex, all of which may cause infections among cystic fibrosis patients and other vulnerable individuals. Thus, it is important for clinical microbiologists to be able to differentiate genomovars. Prior to this study, 361 B. cepacia complex isolates and 51 isolates easily confused with B. cepacia complex previously had been identified using a polyphasic approach, and in this study, a comparison of phenotypic and biochemical tests was carried out. It was determined that Burkholderia multivorans and Burkholderia stabilis could reliably be separated from other members of the B. cepacia complex by phenotypic methods. A combination of phenotypic and molecular tests such as recA PCR and 16S rRNA RFLP are recommended for differentiation among the genomovars of the B. cepacia complex. A biochemical reaction scheme for the identification of B. gladioli, Pandoraea species, and Ralstonia pickettii and the differentiation of these species from the B. cepacia complex is also presented.

Burkholderia cepacia genomovar III Is a common plant-associated bacterium

A polyphasic taxonomic study involving DNA-DNA hybridization, whole-cell protein electrophoresis, and 16S ribosomal DNA sequence analysis revealed that a group of Burkholderia cepacia-like organisms isolated from the rhizosphere or tissues of maize, wheat, and lupine belong to B. cepacia genomovar III, a genomic species associated with "cepacia syndrome" in cystic fibrosis patients. The present study also revealed considerable protein electrophoretic heterogeneity within this species and demonstrated that the B. cepacia complex consists of two independent phylogenetic lineages.

Burkholderia cepacia complex: distribution of genomovars among isolates from the maize rhizosphere in Italy

Burkholderia cepacia is a 'complex' in which seven genomic species or genomovars have so far been identified. It appears that all seven B. cepacia genomovars are capable of causing infections in vulnerable persons; in particular, the importance of Burkholderia multivorans (genomovar II) and B. cepacia genomovar III among cystic fibrosis isolates, especially epidemic ones, has been emphasized. In order to acquire a better comprehension of the genomovar composition of environmental populations of B. cepacia, 120 strains were isolated from the rhizosphere of maize plants cultivated in fields located in northern, central and southern Italy. The identification of the different genomovars was accomplished by a combination of molecular polymerase chain reaction (PCR)-based techniques, such as restriction fragment length polymorphism (RFLP) analysis of 16S rDNA (ARDRA), genomovar-specific PCR tests and RFLP analyses based on polymorphisms in the recA gene whole-cell protein electrophoresis. ARDRA analysis allowed us to distinguish between all B. cepacia genomovars except B. cepacia genomovar I, B. cepacia genomovar III and Burkholderia ambifaria (genomovar VII). The latter genomovars were differentiated by means of recA PCR tests and RFLP analyses. Among the rhizospheric isolates of B. cepacia, we found only B. cepacia genomovar I, B. cepacia genomovar III, Burkholderia vietnamiensis (genomovar V) and B. ambifaria. B. cepacia genomovars I and III and B. ambifaria were recovered from all three fields, whereas B. vietnamiensis was detected only in the population isolated from the field located in central Italy. Among strains isolated from northern and southern Italy, the most abundant genomovars were B. ambifaria and B. cepacia genomovar III respectively; in contrast, the population isolated in central Italy showed an even distribution of strains among genomovars. These results indicate that it is not possible to differentiate clinical and environmental strains, or pathogenic and non-pathogenic strains, of the B. cepacia complex simply on the basis of genomovar status, and that the environment may serve as a reservoir for B. cepacia genomovar III infections in vulnerable humans.

A cultured strain of "Helicobacter heilmannii," a human gastric pathogen, identified as H. bizzozeronii: evidence for zoonotic potential of Helicobacter

We compared the characteristics of a cultured human "Helicobacter heilmannii" isolate with those of other helicobacters found in animals. Phenotypic, protein profile, 16S rDNA sequence, and DNA-DNA hybridization analyses identified the human strain as H. bizzozeronii, a species frequently found in dogs. Thus, H. bizzozeronii may have zoonotic potential.

Genotypic and chemotaxonomic evidence for the reclassification of Pseudomonas woodsii (Smith 1911) Stevens 1925 as Burkholderia andropogonis (Smith 1911) Gillis et al. 1995

It was reported before that [Pseudomonas] woodsii and Burkholderia andropogonis are phenotypically indistinguishable and probably represent the same taxon, for which the name B. andropogonis has been proposed. In the present study, it was found that [P.] woodsii and B. andropogonis strains were indistinguishable by whole-cell protein electrophoresis and have a highly similar cellular fatty acid composition. A high DNA-DNA binding value of 95% was found between the type strains of both species. In addition, the 16S rDNA sequence of [P.] woodsii strain LMG 2362T was very similar to that of B. andropogonis LMG 2129T (99.0%). The chemotaxonomic and genotypic data confirm that [P.] woodsii and B. andropogonis represent the same species, for which it is proposed to retain the name B. andropogonis.

Development of a multiplex PCR assay for the simultaneous detection and identification of Arcobacter butzleri, Arcobacter cryaerophilus and Arcobacter skirrowii

A multiplex PCR assay with five primers targeting the 16S and 23S rRNA genes was developed for the simultaneous detection and identification of Arcobacter butzleri, Arcobacter cryaerophilus and Arcobacter skirrowii. The selected primers amplify a 257-bp fragment from A. cryaerophilus, a 401-bp fragment from A. butzleri and a 641-bp fragment from A. skirrowii. No PCR product was generated for closely related bacteria including Campylobacter and Helicobacter species. The assay was useful to identify cultures after in vitro cultivation and to detect and identify A. butlzeri and A. cryaerophilus from poultry samples present in 24-h old enrichment in Arcobacter broth with cefoperazone, amphotericin and teicoplanin (CAT)-supplement.

Pseudomonas antimicrobica Attafuah and Bradbury 1990 is a junior synonym of Burkholderia gladioli (Severini 1913) Yabuuchi et al. 1993

Comparison of the 16S rDNA sequence of Pseudomonas antimicrobica LMG 18920T with published 16S rDNA sequences from other pseudomonads indicated that Pseudomonas antimicrobica belongs to the genus Burkholderia, with Burkholderia gladioli, Burkholderia glumae and Burkholderia plantarii as its closest neighbours. DNA-DNA hybridizations confirmed that Pseudomonas antimicrobica and Burkholderia gladioli represent the same species. Strain LMG 18920T and other Burkholderia gladioli strains were also indistinguishable by SDS-PAGE of whole-cell proteins and had similar biochemical characteristics. The whole-cell fatty acid composition, however, was different from that of other Burkholderia gladioli strains. It is concluded that Pseudomonas antimicrobica is a later synonym of Burkholderia gladioli. As Burkholderia gladioli is known to cause infections in patients with cystic fibrosis and chronic granulomatous disease, the eventual use of strain LMG 18920T as a biological control agent should be approached with caution.

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.

Characterization of Leuconostoc gasicomitatum sp. nov., associated with spoiled raw tomato-marinated broiler meat strips packaged under modified-atmosphere conditions

Lactic acid bacteria (LAB) associated with gaseous spoilage of modified-atmosphere-packaged, raw, tomato-marinated broiler meat strips were identified on the basis of a restriction fragment length polymorphism (RFLP) (ribotyping) database containing DNAs coding for 16S and 23S rRNAs (rDNAs). A mixed LAB population dominated by a Leuconostoc species resembling Leuconostoc gelidum caused the spoilage of the product. Lactobacillus sakei, Lactobacillus curvatus, and a gram-positive rod phenotypically similar to heterofermentative Lactobacillus species were the other main organisms detected. An increase in pH together with the extreme bulging of packages suggested a rare LAB spoilage type called "protein swell." This spoilage is characterized by excessive production of gas due to amino acid decarboxylation, and the rise in pH is attributed to the subsequent deamination of amino acids. Protein swell has not previously been associated with any kind of meat product. A polyphasic approach, including classical phenotyping, whole-cell protein electrophoresis, 16 and 23S rDNA RFLP, 16S rDNA sequence analysis, and DNA-DNA reassociation analysis, was used for the identification of the dominant Leuconostoc species. In addition to the RFLP analysis, phenotyping, whole-cell protein analysis, and 16S rDNA sequence homology indicated that L. gelidum was most similar to the spoilage-associated species. The two spoilage strains studied possessed 98.8 and 99.0% 16S rDNA sequence homology with the L. gelidum type strain. DNA-DNA reassociation, however, clearly distinguished the two species. The same strains showed only 22 and 34% hybridization with the L. gelidum type strain. These results warrant a separate species status, and we propose the name Leuconostoc gasicomitatum sp. nov. for this spoilage-associated Leuconostoc species.

Sensitivity of the Burkholderia cepacia complex and Pseudomonas aeruginosa to transducing bacteriophages

Burkholderia cepacia is now recognised as a life-threatening pathogen among several groups of immunocompromised patients. In this context, the proposed large-scale use of these bacteria in agriculture has increased the need for a better understanding of the genetics of the species forming the B. cepacia complex. Until now, little information has been available on the bacteriophages of the B. cepacia complex. Transducing phages, named NS1 and NS2, were derived from the lysogenic B. cepacia strains ATCC 29424 and ATCC 17616. The frequency of transduction per phage particle ranged from 1.0x10(-8) to 7.0x10(-6) depending on the phage and recipient strain used. The host range of NS1 and NS2 differed but in each case included environmental and clinical isolates, and strains belonging to several species and genomovars of the B. cepacia complex. The host range of both phages also included Pseudomonas aeruginosa. Some B. cepacia complex isolates were sensitive to the well-characterised P. aeruginosa transducing phages, B3, F116L and G101. The lytic activity of NS1 and NS2 was inhibited by B. cepacia lipopolysaccharide suggesting that this moiety is a binding site for both phages. The molecular size of the NS1 and NS2 genomes was approximately 48 kb.

Utility of commercial systems for identification of Burkholderia cepacia complex from cystic fibrosis sputum culture

Performances of several commercial test systems were reviewed to determine their relative levels of accuracy in identifying Burkholderia cepacia complex isolates recovered from cystic fibrosis sputum culture. Positive predictive values ranged from 71 to 98%; negative predictive values ranged from 50 to 82%. All systems misidentified B. cepacia complex. The species most frequently misidentified as B. cepacia was Burkholderia gladioli. These data support the results of previous studies that recommend confirmatory testing, including the use of DNA-based methods, for sputum culture isolates presumptively identified as B. cepacia.

Misidentifying helicobacters: the Helicobacter cinaedi example

Whole-cell protein electrophoresis and biochemical examination by means of a panel of 64 tests were used to identify 14 putative helicobacters to the species level. The results were confirmed by means of DNA-DNA hybridization experiments and were used to discuss misidentification of helicobacters based on 16S rRNA gene sequence data. The data indicated that comparison of near-complete 16S ribosomal DNA sequences does not always provide conclusive evidence for species level identification and may prove highly misleading. The data also indicated that "Helicobacter westmeadii" is a junior synonym of Helicobacter cinaedi and that Helicobacter sp. strain Mainz belongs to the same species. H. cinaedi occurs in various animal reservoirs, including hamsters, dogs, cats, rats, and foxes. Appropriate growth conditions and identification strategies will be required to establish the genuine significance of this widely distributed Helicobacter species.

Misidentification of Burkholderia cepacia in US cystic fibrosis treatment centers: an analysis of 1,051 recent sputum isolates

BACKGROUND

Burkholderia cepacia remains a significant pathogen in persons with cystic fibrosis (CF). The medical and psychosocial consequences of pulmonary colonization with this bacterium are enormous. However, B cepacia may be frequently misidentified from CF sputum culture.

STUDY OBJECTIVES

To determine the rate of misidentification of B cepacia recently recovered from CF sputum culture of persons receiving care in US treatment centers.

DESIGN

Bacterial isolates cultured from CF sputum and putatively identified as B cepacia or other related nonlactose-fermenting Gram-negative species were referred from participating treatment centers. Isolates underwent polyphasic analyses employing phenotypic (selective media and biochemical testing) and genotypic (polymerase chain reaction) assays to determine species identification. Taxonomic evaluations were performed by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins and amplified-fragment length polymorphism analysis.

MEASUREMENTS AND RESULTS

A total of 1,051 isolates recovered from 608 patients were received from 115 treatment centers in 91 US cities. Among the isolates identified as B cepacia by referring laboratories, 11% could not be confirmed as B cepacia by polyphasic analyses. In addition, 36% of isolates not specifically identified by the referring laboratory or identified as a species other than B cepacia were, in fact, found to be members of the B cepacia complex.

CONCLUSIONS

Rates of misidentification of B cepacia remain unacceptably high among US treatment centers. These data suggest the need for increased awareness of this problem among CF centers and their affiliated laboratories, better adherence to recommended protocols for evaluation of CF sputum, and greater use of reference laboratories equipped to provide advanced analyses.

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 characterisation of group A streptococci from invasive and non-invasive disease episodes in Belgium during 1993-1994

Five hundred clinical group A streptococcal (GAS) isolates were collected in Belgium during the period 1 Nov. 1993 to 31 Oct. 1994. Clinical and laboratory data were recorded and isolates were characterised. The presence of the genes encoding streptococcal pyrogenic exotoxin types A (speA), B (speB), C (speC), F (speF) and streptococcal superantigen (ssa) were determined by PCR to target specific sequences. These isolates were also emm-typed and analysed by pulsed-field gel electrophoresis (PFGE) of genomic macrorestriction fragments with the enzyme SmaI. In total, 136 unrelated GAS PFGE types were identified and genetic diversity was clearly demonstrated. Two GAS PFGE types predominated; a first PFGE type comprised 66 (13.2%) emm1 isolates characterised by speA-, speB+, speC-, speF+ and ssa-; the second PFGE type comprised 44 (8.8%) emm12 isolates characterised by speA-, speB+, speC+ (or speC-), speF+ and ssa-. Indistinguishable PFGE types were observed among both invasive and non-invasive isolates. Ten different PFGE types were found among 11 streptococcal toxic shock syndrome (STSS) isolates, and five of these lacked speA. Twenty-five (34.7%) of 72 invasive isolates gave negative results for speA, speC and ssa. This retrospective study confirmed the observation that the dissemination of one specific clone cannot be associated with invasive GAS disease and posed a question regarding the role of SPE A as a major virulence factor. Other streptococcal virulence factors in conjunction with host factors may determine the outcome of invasive GAS infection.

Identification of Campylobacter jejuni, C. coli, C. lari, C. upsaliensis, arcobacter butzleri, and A. butzleri-like species based on the glyA gene

Currently, the detection and identification of Campylobacter and Arcobacter species remains arduous, largely due to cross-species phenotypic similarities and a relatively narrow spectrum of biochemical reactivity. We have developed a PCR-hybridization strategy, wherein degenerate primers are used to amplify glyA fragments from samples, which are then subjected to species-specific oligodeoxyribonucleotide probe hybridizations, to identify and distinguish between Campylobacter jejuni, C. coli, C. lari, C. upsaliensis, Arcobacter butzleri, and an A. butzleri-like species. Evaluation of this strategy with genomic DNA from different type strains suggests that this approach is both specific and sensitive and thus may be applicable in a diagnostic assay to identify and differentiate these highly related species.

Organization of the ribosomal operon 165-235 gene spacer region in representatives of Neisseria gonorrhoeae

Ribosomal rRNA gene fragments (rDNA) encompassing part of the 16S rDNA, the 16S-23S rDNA spacer region and part of the 23S rDNA of 229 Neisseria gonorrhoeae strains were enzymatically amplified using conserved primers. The fragments of approximately 1200 bp were subjected to restriction analysis with HinfI. This revealed 13 patterns (patterns I-XIII) of which patterns I (78 strains), II (32 strains), III (38 strains) and IV (56 strains) were the most abundant, comprising 89.1% of the strains. The obtained restriction patterns consisted of 3 to 8 bands, ranging in size from 32 to 854 bp. The sum of the obtained bands was about 1200 bp for patterns I, II, III, IV, V, IX, and XIII. However, for patterns VI, VII, VIII, X, XI and XII, the sum of the bands well exceeded the estimated size of approximately 1200 bp. We demonstrated that this results from sequence divergence in the 4 rRNA operons, present in the genome of N. gonorrhoeae, giving rise to patterns that are a combination of several other patterns.

Identification and population structure of Burkholderia stabilis sp. nov. (formerly Burkholderia cepacia genomovar IV)

The Burkholderia cepacia complex currently comprises five genomic species, i.e., B. cepacia genomovar I, B. multivorans (formerly known as B. cepacia genomovar II), B. cepacia genomovar III, B. cepacia genomovar IV, and B. vietnamiensis (also known as B. cepacia genomovar V). In the absence of straightforward diagnostic tests for the identification of B. cepacia genomovars I, III, and IV, the last two genomic species were not formally classified as novel Burkholderia species (genomovar I contains the type strain and therefore retains the name B. cepacia). In the present study, we describe differential biochemical tests and a recA gene-based PCR assay for the routine identification of strains currently known as B. cepacia genomovar IV and propose formal classification of this organism as Burkholderia stabilis sp. nov. B. stabilis can indeed be differentiated from all other B. cepacia complex strains by the absence of beta-galactosidase activity, from strains of B. cepacia genomovars I and III and B. vietnamiensis by the inability to oxidize sucrose, and from B. multivorans by the lack of growth at 42 degrees C. In addition, analysis with the recA gene-derived primers BCRG41 (5'-ACCGGCGAGCAGGCGCTT-3') and BCRG42 (5'-ACGCCATCGGGCATGGCA-3') specifically allows the detection of B. stabilis strains in a conventional PCR assay. Examination of a set of 21 B. stabilis strains by means of random amplified polymorphic DNA analysis and pulsed-field gel electrophoresis typing suggested that the genome of this organism is highly conserved, which is in sharp contrast to the generally accepted genomic diversity, variability, and plasticity among B. cepacia strains.

Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb. nov

A polyphasic taxonomic study was performed on a group of isolates tentatively identified as Burkholderia cepacia, Ralstonia pickettii or Ralstonia paucula (formerly known as CDC group IVc-2). The isolates were mainly cultured from sputum of cystic fibrosis patients or from soil. SDS-PAGE of whole-cell proteins and AFLP fingerprinting distinguished at least five different species, and this was confirmed by DNA-DNA hybridizations. 16S rDNA sequence analysis of representative strains indicated that these organisms belong to the beta-subclass of the Proteobacteria, with the genera Burkholderia and Ralstonia as closest neighbours. Based on genotypic and phenotypic characteristics, the organisms were classified in a novel genus, Pandoraea. The DNA base composition of the members of the new genus is between 61.2 and 64.3 mol%. This novel genus includes four new species, Pandoraea apista (the type species) (type strain is LMG 16407T), Pandoraea pulmonicola (type strain is LMG 18106T), Pandoraea pnomenusa (type strain is LMG 18087T) and Pandoraea sputorum (type strain is LMG 18819T), and Pandoraea norimbergensis (Wittke et al. 1997) comb. nov. (type strain is LMG 18379T). The available clinical data indicate that at least some of these organisms may cause chronic infection in, and can be transmitted amongst, cystic fibrosis patients.

Diagnostically and experimentally useful panel of strains from the Burkholderia cepacia complex

Two new species, Burkholderia multivorans and Burkholderia vietnamiensis, and three genomovars (genomovars I, III, and IV) currently constitute the Burkholderia cepacia complex. A panel of 30 well-characterized strains representative of each genomovar and new species was assembled to assist with identification, epidemiological analysis, and virulence studies on this important group of opportunistic pathogens.

Macrolide resistance and erythromycin resistance determinants among Belgian Streptococcus pyogenes and Streptococcus pneumoniae isolates

Resistance of streptococci to macrolide antibiotics is caused by target-site modification or drug efflux. The phenotypic expression of target-site modification can be inducible or constitutive. The prevalence of the three phenotypes among Belgian erythromycin-resistant Group A streptococci (GAS) and Streptococcus pneumoniae isolates was surveyed, their MICs for seven antibiotics were determined and the clonality of the isolates was explored. Of the 2014 GAS isolates tested 131(6.5%) were erythromycin resistant (MIC > 1 mg/L): 110 (84.0%) showed the M-resistance phenotype whereas the remaining 21 strains (16.0%) were constitutively resistant. No inducibly resistant strains were detected. Of 100 S. pneumoniae isolates, 33 were erythromycin resistant (MIC > 1 mg/L). In contrast to the GAS isolates, only 9.1% of the 33 erythromycin-resistant S. pneumoniae isolates showed the M-resistance phenotype. The presence of mefA/E and ermB genes in the M-resistant and constitutively and inducibly resistant strains, respectively, was confirmed by PCR analysis. Genomic analysis based on pulsed-field gel electrophoresis (PFGE) using the restriction enzyme SfiI, revealed 54 different PFGE patterns among the 131 erythromycin-resistant GAS isolates, of which an M6 clone represented 16.0% of the strains; all other clones, exhibiting different M-types, represented <7% of the strains. The S. pneumoniae isolates also appeared to be polyclonally based, as determined by arbitrarily primed PCR. The macrolides miocamycin and rovamycin, the lincosamide clindamycin and the ketolide HMR 3647 showed excellent activity against the M-resistant GAS and S. pneumoniae strains.

Prevalence and molecular epidemiology of glycopeptide-resistant enterococci in Belgian renal dialysis units

The molecular epidemiology of glycopeptide-resistant enterococci (GRE) colonizing the intestinal tracts of Belgian renal dialysis patients was studied among 1318 patients of a population of 1800 dialysis patients from 29 dialysis centers. Of these, 185 patients (14.0%) were colonized with a VANA-positive GRE; GRE harboring the VANB gene were not detected. The majority of the VANA GRE (80.5%) were identified as Enterococcus faecium; 14.8% were identified as E. faecalis; and a limited number were identified as E. avium, E. casseliflavus, E. dispar, E. durans, or E. gallinarum. Genome analysis of 277 VANA-positive GRE by pulsed-field gel electrophoresis revealed a high genetic variability both within the different dialysis centers and within the patients' own GRE flora. No high-level gentamicin-resistant VANA-positive GRE were detected, and most strains remained susceptible to ampicillin. These findings do not support a hospital-driven endemicity of VANA-positive enterococcal isolates in Belgium.

Identification of clinically relevant viridans streptococci by analysis of transfer DNA intergenic spacer length polymorphism

The utility of PCR analysis of transfer DNA intergenic spacer length polymorphism (tDNA-ILP) for the identification to the species level of clinically relevant viridans streptococci was evaluated with a collection of reference strains of 15 species of the salivarius, anginosus, mitis and mutans rRNA homology groups. PCR products generated by using fluorescent, outwardly directed, consensus tDNA primers were analysed by electrophoresis on denaturating polyacrylamide gels and by laser fluorescence scanning. Eleven species showed specific and distinct tDNA patterns: Streptococcus cristatus, Streptococcus gordonii, Streptococcus oralis, Streptococcus mitis, Streptococcus pneumoniae, Streptococcus sanguinis, Streptococcus parasanguinis, Streptococcus anginosus, Streptococcus mutans, Streptococcus criceti and Streptococcus ratti. Indistinguishable patterns were obtained among two groups of species: Streptococcus vestibularis and Streptococcus salivarius on the one hand and Streptococcus constellatus and Streptococcus intermedius on the other. S. mitis strains produced heterogeneous patterns that could be separated into three groups: a group containing S. mitis biovar 1 and two S. mitis biovar 2 groups, one of which clustered with S. parasanguinis strains while the other showed patterns unrelated to other species. These results agree in part with protein electrophoretic analysis showing that S. mitis biovar 2 strains belong to several streptococcal taxa. In conclusion, PCR analysis of tDNA-ILP holds promise for rapid identification of viridans streptococci that are difficult to identify by phenotypic tests.

Identification of Burkholderia species and genomovars from cystic fibrosis patients by AFLP fingerprinting

AFLP is a genomic fingerprinting technique based on the selective amplification of restriction fragments from a total double-digest of genomic DNA. The applicability of this method to differentiate between species and genomovars of the genus Burkholderia was tested, with particular emphasis on taxa occurring in cystic fibrosis patients. In this study, 78 well-characterized strains and field isolates were investigated by two methods of AFLP fingerprinting. In the manual procedure, a radioactively labelled primer was used, amplified fragments were separated by conventional PAGE and the patterns were revealed by autoradiography. In the automated procedure, a fluorescently labelled primer was used in combination with electrophoresis and on-line data collection by means of an automated DNA sequencer. Overall, there was good agreement between the two AFLP procedures and the data were mostly consistent with results obtained from SDS-PAGE of whole-cell proteins and DNA-DNA hybridization experiments. The automated AFLP procedure has considerable technical advantages compared with the manual AFLP procedure, but a thorough visual analysis of the DNA profiles was required to avoid misidentification of some Burkholderia cepacia genomovar III strains.

Phylogenetic characterization of 'Candidatus Helicobacter bovis', a new gastric helicobacter in cattle

Recently helicobacter-like organisms have been reported in the pyloric part of the abomasum of calves and adult cattle. Cultivation of these spiral bacteria has not been successful to date. In the present study, comparative 16S rDNA sequence analysis was used to determine the taxonomic position of these bacteria. Seven abomasal biopsies of adult cattle were sampled from different Belgian and Dutch farms. In all samples the presence of helicobacter-like organisms was demonstrated by biochemical, immunohistochemical and electron microscopical data. Bacterial 16S rDNA was amplified by PCR and sequences were determined either by direct or indirect sequence analysis. Pairwise comparisons revealed all sequences to be more than 99% homologous. Phylogenetic analysis placed the organism, corresponding to the reference sequence R2XA, within the genus Helicobacter. A diagnostic PCR assay was designed, differentiating all of the bovine 16S rDNA sequences from Helicobacter and Wolinella species. The low similarity level towards Helicobacter bilis (92.8%), its closest validly named neighbour, indicates that this novel taxon is indeed a novel Helicobacter species. An in situ hybridization procedure associated the bovine sequences to the helicobacter-like organisms in the abomasum. The name 'Candidatus Helicobacter bovis' is proposed for this new abomasal helicobacter from cattle.