Molecular epidemiology of Ornithobacterium rhinotracheale

Ornithobacterium rhinotracheale is a recently described gram-negative rod-shaped bacterium associated with respiratory tract infections in poultry. In order to determine the molecular epidemiology of this bacterium, we characterized 55 O. rhinotracheale isolates from eight countries on four continents by multilocus enzyme electrophoresis (MLEE), repetitive sequence based-PCR (rep-PCR), and 16S rRNA gene sequencing. MLEE discriminated the O. rhinotracheale isolates into six electrophoretic types (ETs), of which only three ETs were recovered from domesticated poultry. The 16S rRNA gene sequence and rep-PCR analyses confirmed the results obtained by MLEE and indicated limited heterogeneity among isolates of O. rhinotracheale recovered from poultry. Taken together, the results of our analysis demonstrate that the majority of O. rhinotracheale isolates recovered from domesticated poultry throughout the world are represented by a small group of closely related clones and suggest that the bacterium was recently introduced to domesticated poultry from wild bird populations.

Occurrence of multiple genomovars of Burkholderia cepacia in cystic fibrosis patients and proposal of Burkholderia multivorans sp. nov

We performed an integrated genotypic and phenotypic analysis of 128 strains of the genera Burkholderia, Ralstonia, and Pseudomonas in order to study the taxonomic structure of Burkholderia cepacia and its relationships with other Burkholderia species. Our data show that presumed B. cepacia strains isolated from cystic fibrosis patients belong to at least five distinct genomic species, one of which was identified as Burkholderia vietnamiensis. This group of five phenotypically similar species is referred to as the B. cepacia complex. The name Burkholderia multivorans is proposed for one of these genomic species, which was formerly referred to as B. cepacia genomovar II; the remaining B. cepacia groups are referred to as genomovars I, III, and IV, pending additional differential phenotypic tests. The role and pathogenic potential of each of these taxa, particularly in view of the potentially fatal infections in cystic fibrosis patients, need further evaluation. The data presented also demonstrate that Pseudomonas glathei and Pseudomonas pyrrocinia should be reclassified as Burkholderia species.

Campylobacter hyoilei Alderton et al. 1995 and Campylobacter coli Véron and Chatelain 1973 are subjective synonyms

The taxonomic affiliation of Campylobacter hyoilei was reevaluated by examining a variety of phenotypic and genotypic criteria. Whole-cell protein electrophoresis and a comparison of 66 phenotypic characters revealed that reference strains of C. hyoilei were indistinguishable from Campylobacter coli strains. These data were confirmed by a DNA-DNA hybridization level of 67% between the type strains of the two species. Several species-specific assays based on PCR amplification or probe hybridization further substantiated that C. coli strains and C. hyoilei strains are indistinguishable. It is therefore concluded that C. hyoilei and C. coli represent the same species and that the former name should be regarded as a junior synonym of the latter name.

Streptococcus hyovaginalis sp. nov. and Streptococcus thoraltensis sp. nov., from the genital tract of sows

Two groups of strains isolated from sows were shown to belong to new sublines in the genus Streptococcus. Based on phenotypic and phylogenetic analyses, we propose that these bacteria should be classified as two new species, Streptococcus hyovaginalis sp. nov. and Streptococcus thoraltensis sp. nov. These two species are found in the genital tract, but the capnophilic species S. thoraltensis may also occur in the intestinal tract of pigs. The type strain of S. hyovaginalis is SHV515 (= LMG 14710), and S69 (= LMG 13593) is the type strain of S. thoraltensis.

Characterization of some Actinomyces-like isolates from human clinical specimens: reclassification of Actinomyces suis (Soltys and Spratling) as Actinobaculum suis comb. nov. and description of Actinobaculum schaalii sp. nov

Five strains of a hitherto unknown Actinomyces-like bacterium were isolated from human clinical sources, including blood cultures. Biochemical and chemotaxonomic characterization indicated that the strains were distinct from previously described Actinomyces and Arcanobacterium species. A comparative 16S rRNA gene sequence analysis demonstrated that the undescribed strains constitute a new subline within the Actinomyces-Arcanobacterium species complex. The closest known relative of the isolates was found to be Actinomyces suis, although a 16S rRNA sequence divergence value of approximately 6% clearly demonstrated that the unknown bacterium represents a distinct species. Based on the results of the present and earlier phylogenetic investigations, it is proposed that Actinomyces suis should be reclassified in a new genus, the genus Actinobaculum, as Actinobaculum suis comb. nov. In addition, a new species, Actinobaculum schaalii, is proposed for the Actinomyces-like bacterium from human sources. The type strain of Actinobaculum schaalii is CCUG 27420.

Molecular discrimination between Campylobacter jejuni, Campylobacter coli, Campylobacter lari and Campylobacter upsaliensis by polymerase chain reaction based on a novel putative GTPase gene

Polymerase chain reaction (PCR) mediated DNA fingerprinting has resulted in the identification of a novel Campylobacter jejuni gene, encoding a GTPase protein. The gene, consisting of 383 amino acids contained semi-conserved GTP-binding sites (designated G-1 to G-4), that are characteristic for members of the GTPase protein superfamily. Remarkably, this gene from C. Jejuni appears to encode a member of a novel family of GTP-binding proteins, containing two separate putative GTP-binding domains, each comprising a series of semi-conserved GTP-binding motifs. Spacing between these motifs is highly conserved. Based on this novel gene, a general PCR strategy for the identification of C. jejuni, C. coli, C. lari and C. upsaliensis was developed. PCR primers were deduced from GTP-binding motifs G-1 and G-3 of the first GTP-binding domain. These GTP-binding sites flank a variable region of precisely 117 bp in the four Campylobacter spp. that allowed the development of species-specific probes. This PCR-hybridization assay offers a novel tool for rapid molecular detection and specific identification of the thermophilic Campylobacter spp.

Evaluation of arbitrarily primed PCR analysis and pulsed-field gel electrophoresis of large genomic DNA fragments for identification of enterococci important in human medicine

The increasing problems encountered with enterococcal nosocomial infections and the intrinsic and acquired resistance of the enterococci to different antimicrobial compounds highlight the need for a rapid identification technique. Enterococcus faecalis is readily identified by biochemical tests, but species differentiation within the Enterococcus faecium and Enterococcus gallinarum species groups is less well established. In the present study, 66 strains representing the most prevalent human enterococci were used to develop a PCR-based species-specific identification protocol. Whole-cell protein analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis was used as a reference method for species identification. In addition, the genomic SmaI macro-restriction fragment distribution of all of the strains was examined by pulsed-field gel electrophoresis (PFGE). Oligonucleotide D11344-primed PCR was as discriminative as whole-cell protein analysis and resulted in more easily interpreted band patterns. This PCR-based technique allowed identification of clinical isolates by visual examination of the DNA profiles obtained. The inability of both methods to discriminate between Enterococcus casseliflavus and Enterococcus flavescens brought into question the species status of E. flavescens. PFGE did not result in species-discriminative DNA bands or band patterns, but proved to be superior for interpretation of interstrain relationships.

Genotypic diversity of Campylobacter lari isolated from mussels and oysters in The Netherlands

In order to gain insight into the epidemiology of Campylobacter lari infection in The Netherlands due to the consumption of raw mussels and oysters, batches of these shellfish were screened for the presence of Campylobacter spp. during a 6 month period in 1993-1994. Apparently, 41 out of 59 batches of mussels and 11 out of 41 batches of oysters were colonized with Campylobacter spp. A subset of the isolates was further characterized by additional phenotypic tests, numerical analysis of electrophoretic protein patterns, and genotyping by random amplification of polymorphic DNA (RAPD). Protein electrophoretic analysis of 39 Campylobacter spp. cultured from 24 batches of mussels and oysters, revealed that all isolates, except two, were C. lari. Two strains with an aberrant protein pattern were identified as C. coli and C. hyointestinalis, respectively. Nalidixic acid susceptible campylobacters (NASC) and urease-positive thermophylic campylobacters (UPTC) did not form separate clusters and should be considered biovars only. Several strains were both urease positive and nalidixic acid susceptible, which represents a new biovar within C. lari. The results of RAPD demonstrated the presence of 3 distinct genetic variants, implying that even within a single batch of shell fish, relatively extensive DNA polymorphisms can be found. It is therefore apparent that this complex group of C. lari is characterized by a high degree of genetic diversity, implying the presence of a heterogenous population of C. lari in crustacean organisms living in marine waters in a restricted area in The Netherlands.

Streptococcus difficile is a nonhemolytic group B, type Ib Streptococcus

Whole-cell protein electrophoretic analysis of the type strain of Streptococcus difficile (LMG 15799) revealed that this organism was indistinguishable from Streptococcus agalactiae strains. Although LMG 15799T (T = type strain) was originally described as serologically untypeable, we found that this strain was a group B streptococcus belonging to the capsular polysaccharide antigen type Ib group. The biochemical reactivity of S. difficile, which differed from the biochemical reactivity of typical S. agalactiae strains mainly by being less versatile, is similar to the biochemical reactivity of other group B, type Ib streptococci isolated from poikilothermic animals, such as fish and frogs.

Burkholderia cepacia: medical, taxonomic and ecological issues

The increasing challenge posed by multiresistant saprophytes in medical microbiology is strikingly demonstrated by the emergence of Burkholderia (formerly Pseudomonas) cepacia as an opportunist pathogen in immunocompromised patients, particularly individuals with chronic granulomatous disease and cystic fibrosis (CF). Best known previously as a phytopathogen and the cause of soft rot of onions, B. cepacia presents three major problems for the CF community: innate multiresistance to antimicrobial agents; person-to-person transmission of epidemic strains through nosocomial or social contacts; and 'cepacia syndrome', a fulminating fatal pneumonia, sometimes associated with septicaemia, that occurs in approximately 20% of colonised patients, including those with previously mild disease. Accumulated evidence to dispel earlier suggestions that the organism is avirulent and merely a marker of existing lung disease includes: case-controlled studies in CF patients; reports of serious infections in non-CF patients; in-vitro and in-vivo evidence that B. cepacia induces production of pro-inflammatory markers, including the major cytokine TNFalpha; and histopathological evidence that exposure of transgenic CF mice to B. cepacia results in pneumonia. By the early 1990s, the use of selective culture media and DNA-based bacterial fingerprinting confirmed suspicions of epidemic person-to-person spread of B. cepacia. This evidence provided scientific justification for draconian and controversial measures for infection control, in particular, segregation of B. cepacia-colonised patients during treatment at CF centres and their exclusion from social gatherings and national conferences. Recently, molecular analyses of type strains and clinical isolates have revealed that isolates identified previously as B. cepacia belong to at least three distinct species and have increased concern regarding the reliability of current laboratory detection and identification systems. Clarification of the taxonomy of B. cepacia-like organisms and the pathogenic potential of environmental isolates remains a high priority, particularly when the organism's antifungal and degradative properties have created interest in its potential use as a biological control agent to improve crop yields and its use for the bioremediation of contaminated soils.

Presence of vancomycin-resistant enterococci in farm and pet animals

Enterococcus faecium strains with vanA-mediated glycopeptide resistance were isolated by enrichment culture from the intestines and feces of several animal species, mainly horses and dogs (8% positive), chickens (7% positive), and pigs (6% positive). Other vanA-positive enterococcal strains were identified as E. durans in gallinaceous birds, E. faecalis in a horse, and E. gallinarum in a pheasant. Samples from pigeons, cage birds, and ruminants were negative. It was concluded that vancomycin resistance is widespread among isolates from farm and pet animals.

Bordetella trematum sp. nov., isolated from wounds and ear infections in humans, and reassessment of Alcaligenes denitrificans Rüger and Tan 1983

Ten strains recognized on the basis of a computer-assisted numerical comparison of whole-cell protein patterns as members of a novel species belonging to the family Alcaligenaceae were examined by using an integrated phenotypic and genotypic approach. This species, for which we propose the name Bordetella trematum sp. nov., was more closely related to the type species of the genus Bordetella (Bordetella pertussis) than to the type species of the genus Alcaligenes (Alcaligenes faecalis) and had the general characteristics of members of this family (i.e., a DNA base ratio in the range from 57 to 70 mol%, a fatty acid profile characterized by high percentages of 16:0, 17:0 cyclo, and 14:0 3OH, nonsaccharolytic metabolism, and several classical biochemical characteristics, including aerobic and microaerobic growth, catalase activity, assimilation of citrate, an absence of anaerobic growth, and an absence of acetylmethylcarbinol and indole production, gelatin liquefaction, and esculin hydrolysis). A reevaluation of the criteria used to classify Alcaligenes denitrificans Rüger and Tan 1983 and Achromobacter xylosoxidans Yabuuchi and Ohyama 1971 as subspecies of Alcaligenes xylosoxidans and additional evidence provided in recent studies revealed that, consistent with present standards, it is appropriate to consider these two taxa distinct species of the genus Alcaligenes.

Survey of enterococcal susceptibility patterns in Belgium

A national surveillance study was performed in order to identify the enterococci causing important infections, to determine their susceptibilities to first-choice agents for treatment, and to characterize the phenotypes and genotypes of the glycopeptide-resistant strains. A total of 472 isolates were collected between 15 January and 15 April 1993. The ability of the API rapid ID 32 STREP gallery to identify enterococci was evaluated. The majority of the Belgian enterococci were identified as E. faecalis (89.4%). E. faecium and other enterococci were present in small percentages only (9.1 and 1.5%, respectively). The API rapid ID 32 STREP system identified 88.6% of the strains with an excellent or very good identification score. For the majority of the strains with uncertain identification scores, the results of a single test only were aberrant. Only 2.3% of the strains remained unidentified. High-level aminoglycoside resistance was widespread in E. faecalis (streptomycin, 50.8%; gentamicin, 8.7%), and the emergence of ciprofloxacin resistance was found to be associated with aminoglycoside resistance. E. faecium is generally more resistant to a wide range of antibiotics, but glycopeptide-resistant strains (1.5%) have not yet become widespread.

Isolation of Campylobacter concisus from feces of children with and without diarrhea

A prospective study compared fecal isolation rates of Campylobacter concisus for children with diarrhea and without diarrhea by a filter technique in which media were incubated for 4 days in a microaerobic atmosphere. No statistically significant difference in isolation rates was found (13.2% in patients with diarrhea and 9% in controls). Moreover, 35 of 37 children attending the same day care center harbored different C. concisus strains, as was demonstrated by arbitrary primer PCR DNA fingerprinting. These data suggest a lack of a pathogenic role for C. concisus in enteritis.

Taxonomic study of lancefield streptococcal groups C, G, and L (Streptococcus dysgalactiae) and proposal of S. dysgalactiae subsp. equisimilis subsp. nov

Streptococcus dysgalactiae consists of at least five distinct subgroups on the basis of serogroups, biotypes, and hosts. A chemotaxonomic and phenotypic examination of 80 S. dysgalactiae strains representing the known diversity within this species and 49 reference strains representing all members of the streptococcal pyogenic species group revealed two subpopulations of strains within S. dysgalactiae. The name S. dysgalactiae subsp. dysgalactiae is proposed for strains of animal origin. These strains belong to Lancefield serogroups C and L, are alpha-, beta-, or nonhemolytic, and do not exhibit streptokinase activity on human plasminogen or proteolytic activity on human fibrin. The name S. dysgalactiae subsp. equisimilis is proposed for human isolates. These strains belong to Lancefield serogroups C and G, are beta-hemolytic, and exhibit streptokinase activity on human plasminogen and proteolytic activity on human fibrin.

Polyphasic approach to the classification and identification of Gardnerella vaginalis and unidentified Gardnerella vaginalis-like coryneforms present in bacterial vaginosis

A taxonomic study of Gardnerella vaginalis and G. vaginalis-like coryneforms was performed in order to clarify the phylogenetic affiliation of these organisms and to improve future identification. We examined 50 strains by performing whole-cell protein and fatty acid analyses, a 16S rRNA sequence analysis, and an extensive phenotypic characterization analysis. The results of both chemotaxonomic techniques which we used divided the organisms into two main clusters, and the 16S rRNA sequence analysis revealed that the clusters represent different genera, which were easily distinguished by the results of classical phenotypic tests. The cluster I strains were identified as G. vaginalis, which was shown to be a close relative of the genus Bifidobacterium. An improved description of G. vaginalis is presented. The cluster II strains belong to or are closely related to Actinomyces turicensis.

Polyphasic analysis of strains of the genus Capnocytophaga and Centers for Disease Control group DF-3

A polyphasic approach was used to determine the relationships between well-characterized reference strains representing all seven Capnocytophaga species. One Centers for Disease Control (CDC) group DF-3 strain, a presumed relative of the genus Capnocytophaga, and 15 field isolates were included as well. Fourteen isolates were assigned to named Capnocytophaga species, all of which could be differentiated by means of whole-organism protein electrophoresis. A separate position was occupied by the CDC group DF-3 strain and by one field isolate representing a novel Capnocytophaga species. The phylogenetic position of each taxon was determined by means of 16S rRNA sequence analysis. A considerable genotypic heterogeneity within the genus Capnocytophaga was detected in spite of the minimal phenotypic differences. Comparative 16S rRNA sequence analysis revealed that CDC group DF-3 is not a close relative of the capnocytophagas but constitutes a separate genus that clusters together with Bacteroides forsythus and Bacteroides distasonis, two generically misclassified Bacteroides species. The degree of protein similarity correlated with our and published DNA-DNA binding values. Percentage 16S rRNA similarity values of greater than 97% did not guarantee conspecificity. All Capnocytophaga strains had very similar fatty acid contents characterized by significant amounts of 14:0, 15:0 iso (greater than 55%), 16:0, 16:0 3OH, and 17:0 iso 3OH. PCR-mediated DNA fingerprinting allowed discrimination of most species, although some strains could not be classified efficiently because of DNA polymorphisms.

Polyphasic taxonomy, a consensus approach to bacterial systematics

Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question.

Characteristics of Bordetella hinzii strains isolated from a cystic fibrosis patient over a 3-year period

Over a 3-year period, an adult cystic fibrosis patient underwent eight episodes of pulmonary exacerbation of his disease. At least one of two different strains of Bordetella hinzii could be isolated from sputum samples in every instance. The differentiation of B. hinzii from related taxa and its role as an etiologic agent of infections are discussed. The two isolates of B. hinzii reported are the third and fourth human-derived strains described in the literature.

Generation of DNA probes for detection of microorganisms by polymerase chain reaction fingerprinting

Identification of medically relevant microorganisms is important for diagnosis, treatment and prevention of infectious diseases. This has initiated the development of a large number of identification and typing techniques based on phenotypic and genetic characteristics. In general, these last mentioned nucleic acid-mediated techniques provide more detailed and consistent information on strain-specific characteristics. However, the development of clinically useful microbial DNA/RNA probes requires nucleotide sequence information and a set of well defined reference organisms for test validation in comparison with the current gold standard. This is a requirement for the development of accurate nucleic acid hybridisation and/or amplification tests. Recently, it has been demonstrated that polymerase chain reaction (PCR)-mediated genetic typing of microorganisms can lead to the immediate isolation of species-specific DNA probes by comparison of DNA fingerprints. This combines the sensitivity of PCR with the specificity of DNA probing without the need to generate nucleic acid sequence information prior to probe development. The implications of this procedure for clinical microbiology and epidemiological surveillance will be discussed. It is shown that specific probes can be developed for various taxonomic levels and that detection and identification can be combined into a single, fast procedure. The versatility and widely applicable principles of this procedure will be highlighted and exemplified by some newly developed tests and a review of the current literature.

Burkholderia (Pseudomonas) cepacia and cystic fibrosis: the epidemiology in Belgium

Burkholderia cepacia has become an increasingly recognized pathogen among cystic fibrosis (CF) patients and its potential role in declining pulmonary function or unexpected fatal outcome has caused widespread concern. Direct person-to-person transmission has been documented and a segregation policy of CF patients colonized with B.cepacia from non-colonized CF patients is widely adopted. Since this policy has a dramatic impact on social behaviour of CF patients it is imperative that clinical laboratories accurately isolate and identify B.cepacia in the respiratory secretions. In order to comprehend the epidemiology of B.cepacia in the Belgian CF population a multicentre study was conducted during a period of 1 year (March'93-February'94). B.cepacia was isolated in only 12 of 465 CF patients (2.6%). Routine biochemical tests identified these strains as authentic B.cepacia. However, the combined data from protein and DNA-DNA hybridization analyses revealed that the Belgian CF "B.cepacia" isolates showed patterns different from reference B.cepacia isolates and belong to 3 different, newly identified Burkholderia genomovars, but not to B.cepacia. Comparative analysis of the selective media used for recovery of these "B.cepacia" strains from respiratory secretions indicated that the commercial medium (Mast) containing polymyxin B and ticarcillin as the selective agents was the best and most user-friendly. Molecular typing of these Burkholderia isolates by arbitrarily-primed PCR (AP-PCR) and pulsed-field gel electrophoresis (PFGE) showed that spread of a single strain within a same centre occurred but the mode of transmission remains unknown; inter-centre spread of strains was not observed. Interestingly, neither colonization with a distinct or an epidemic strain (belonging to either of the three newly identified Burkholderia genomovars) nor colonization for a prolonged period of time, led to a rapid deterioration of lung function in these CF patients. It appears essential to determine the prevalence of these "new" Burkholderia genomovars in larger populations of CF patients and to evaluate their virulence and other features as this may have important clinical and practical implications.

Campylobacter fetus subspecies fetus septicaemia: SDS-PAGE as an aid to speciation

We describe a case of bacteraemia due to an atypical strain of Campylobacter fetus ssp. fetus. Conventional biochemical and phenotypic characterisation was unhelpful but whole cell protein profiles obtained by means of sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) allowed us to identify this strain.