[The use of molecular genetics techniques in clinical microbiology--final report from the workshop of the Molecular Microbiology Working Group TIDE]

In the last decade, there has been a rapid development in the use of molecular genetics methods in clinical microbiology. Novel technologies bring new knowledge and approaches to various disciplines of microbiology--taxonomy, identification of microbes, clinical diagnosis, epidemiology of infectious diseases and antibiotic resistance. This article summarizes the conclusions from the workshop of the Molecular Microbiology Working Group TIDE held during the Second Annual Meeting of the Society for Medical Microbiology of the J. E. Purkyne Czech Medical Association.

The effect of ripening and storage conditions on the distribution of tyramine, putrescine and cadaverine in Edam-cheese

The aim of the work was to describe the development of selected biogenic amines (histamine, tyramine, putrescine and cadaverine) in 4 layers of Dutch-type cheese (Edam-cheese) depending on 3 ripening/storage regimes during a 98-day period. Biogenic amines were analysed by means of ion-exchange chromatography. A further goal was to identify microbial sources of biogenic amines in the material analysed. Phenotype characterization and repetitive sequence-based PCR fingerprinting were used to identify the isolated bacteria. The highest content of tyramine, putrescine and cadaverine was determined in cheeses stored in a ripening cellar at a temperature of 10 degrees C during the whole observation period. Lower biogenic amines content was determined in samples which were moved into a cold storage device (5 degrees C) after 38 days of storage in a ripening cellar (10 degrees C). The lowest concentrations of biogenic amines were detected in cheeses which were moved into a cold storage device (5 degrees C) after 23 days of storage in a ripening cellar (10 degrees C). During the 98-day period, histamine was not detected in any of the regimes. Within the cheeses analysed, non-starter lactic acid bacteria Lactobacillus curvatus, Lactobacillus casei/paracasei and Lactobacillus plantarum were detected as the main producers of the biogenic amines tested. In starter bacteria Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris the decarboxylase activity tested was not detected.

Comparative evaluation of automated ribotyping and RAPD-PCR for typing of Lactobacillus spp. occurring in dental caries

A group of 67 Lactobacillus spp. strains containing Lactobacillus casei/paracasei, Lactobacillus fermentum, Lactobacillus gasseri, Lactobacillus plantarum, Lactobacillus rhamnosus and Lactobacillus salivarius species isolated from early childhood caries and identified to the species level in a previous study (Svec et al., Folia Microbiol 54:53-58, 2009) was characterized by automated ribotyping performed by the RiboPrinter microbial characterization system and by randomly amplified polymorphic DNA fingerprinting (RAPD-PCR) with M13 primer to evaluate these techniques for characterization of lactobacilli associated with dental caries. Ribotyping revealed 55 riboprints among the analysed group. The automatic identification process performed by the RiboPrinter system identified 18 strains to the species level, however cluster analysis divided obtained ribotype patterns into individual clusters mostly corresponding to the species assignment of particular strains. RAPD-PCR fingerprints revealed by the individual Lactobacillus spp. showed higher variability than the ribotype patterns and the fingerprint profiles generated by the analysed species were distributed among one to four clusters. In conclusion, ribotyping is shown to be more convenient for the identification purposes while RAPD-PCR fingerprinting results indicate this method is a better tool for typing of Lactobacillus spp. strains occurring in dental caries.

[Nocardia farcinica as the causative agent of a brain abscess in a patient with interstitial lung disease]

This case report describes a two-step protocol for the identification of the causative agent of nocardiosis in a patient with brain abscess, antibiotic susceptibility testing and etiological treatment after neurosurgery. The patient treated with corticosteroids for pulmonary fibrosis and presenting with multiple neurological manifestations was admitted to a neurosurgery clinic. CT and contrast MRI revealed an expansive multilocular lesion 45 x 35 mm in size in the left parietal lobe, differentially diagnosed as malignant glioma. The lesion was biopsied and the histology showed a brain abscess containing white blood cells and dead tissue. The aspirated pus culture yielded bacteria of the genus Nocardia that were further identified, in the first step, by phenotypic methods (Gram positivity, partial acidoresistance, airborne mycelium detection, growth at 45 degrees C, lysozyme resistance and antibiotic resistance phenotype) as belonging to resistance phenotype V., v.s. N. farcinica (resistance to aminoglycosides except amikacin and to third-generation cephalosporins). In the second step of the polyphasic identification, rDNA was isolated and a 1000 bp part of the 16S rRNA gene was sequenced. Sequence comparison with the GenBank database using BLAST software identified the agent as N. farcinica (100%). The isolate was tested for susceptibility by the NCCLS /CLSI dilution method and showed good susceptibility to co-trimoxazole, amikacin and imipenem. The patient was treated with long-term intravenous cotrimoxazole acid in combination with amikacin and his clinical condition and laboratory parameters of inflammation improved. N. farcinica is among the three most frequently isolated Nocardia species in Europe as well as in the Czech Republic where it was repeatedly recovered from the lungs and respiratory tract of immunocompromised patients with systemic nocardiosis.

16S rRNA gene-based identification of cultured bacterial flora from host-seeking Ixodes ricinus, Dermacentor reticulatus and Haemaphysalis concinna ticks, vectors of vertebrate pathogens

A total of 151 bacterial isolates were recovered from different developmental stages (larvae, nymphs and adults) of field-collected ticks (67 strains from Ixodes ricinus, 38 from Dermacentor reticulatus, 46 from Haemaphysalis concinna). Microorganisms were identified by means of 16S rRNA gene sequencing. Almost 87 % of the strains belonged to G(+) bacteria with predominantly occurring genera Bacillus and Paenibacillus. Other G(+) strains included Arthrobacter, Corynebacterium, Frigoribacterium, Kocuria, Microbacterium, Micrococcus, Plantibacter, Rhodococcus, Rothia, and Staphylococcus. G(-) strains occurred less frequently, comprising genera Advenella, Pseudomonas, Rahnella, Stenotrophomonas, and Xanthomonas. Several strains of medical importance were found, namely Advenella incenata, Corynebacterium aurimucosum, Microbacterium oxydans, M. schleiferi, Staphylococcus spp., and Stenotrophomonas maltophilia. Data on cultivable microbial diversity in Eurasian tick species D. reticulatus and H. concinna are given, along with the extension of present knowledge concerning bacterial flora of I. ricinus.

Lactobacillus spp. associated with early childhood caries

A group of 69 lactobacilli was isolated from caries lesions and root canals of early childhood caries (ECC) affected children treated in the Department of Pedodontics (Children's Teaching Hospital, Brno, Czech Republic). Biochemical and physiological properties of all strains were characterized by API 50 CH kit and conventional tube tests. The rep-PCR fingerprinting with the (GTG)(5) primer was used for genotypic grouping of the isolates. The (GTG)(5)-PCR fingerprinting grouped all analyzed strains into a few clusters in nearly full agreement with phenotype identification results and clarified the taxonomic position of 13 biochemically unidentified strains. In total, 20 strains of Lactobacillus fermentum, 17 L. rhamnosus, 14 L. casei/paracasei, 7 L. gasseri, 7 L. salivarius and 4 L. plantarum were identified. Mixtures of two or even three Lactobacillus spp. were isolated from a few root canal content samples. Results obtained by biotyping and (GTG)(5)-PCR were generally comparable except for L. gasseri strains that were not biochemically identified. The (GTG)(5)-PCR fingerprinting was shown to be quicker, easier to perform and more reliable than biotyping. Our results imply this molecular method as a good tool for screening and identification of Lactobacillus spp. inhabiting dental plaque.

Characterization of Lactococcus lactis subsp. lactis isolated from surface waters

A group of nine presumptive enterococci was isolated on enterococcal selective media Slanetz-Bartley agar and/or kanamycin-esculin-azide agar during a screening of Enterococcus spp. in surface waters. All strains formed a homogeneous cluster separated from all enterococcal species using rep-PCR fingerprinting with the (GTG)5 primer but they matched fingerprints revealed by Lactococcus lactis subsp. lactis representatives. Further identification using extensive biotyping and automated ribotyping with EcoRI (RiboPrinter microbial characterization system) confirmed all strains as L. lactis subsp. lactis in full correspondence with the (GTG)5-PCR. We demonstrated that L. lactis subsp. lactis strains occur in different surface waters and can be confused with enterococci due to their positive growth on selective enterococcal media as well as positive results in tests commonly used for identification of the genus Enterococcus (esculin hydrolysis, acetoin and pyrrolidonyl arylamidase production, growth at 10 degrees C and in 6.5% NaCl). The (GTG)5-PCR fingerprinting was revealed as a reliable and fast method for the identification of L. lactis subsp lactis while automated ribotyping with EcoRI proved to be a good tool for intrasubspecies typing purposes.

Identification of lactic acid bacteria isolated from human blood cultures

Fifteen lactic acid bacterial strains were isolated from blood cultures from 15 different patients in the Faculty Hospital in Brno, Czech Republic. All strains were identified using biochemical tests and repetitive PCR using the (GTG)5 primer. Doubtful identification results were confirmed by whole-cell protein analysis. The strains were assigned to the genera Lactobacillus (eight strains representing seven species), Leuconostoc (six strains representing four species) and Weissella (one strain). Antibiotic susceptibility testing was performed using the E-test and revealed high-level resistance to cotrimoxazol, metronidazole, vancomycin and teicoplanin, but nearly all strains were susceptible to erythromycin, clindamycin, ampicillin and penicillin.

Properties of the strainsEnterococcus haemoperoxidus andE. moraviensis, new species among enterococci

Antibiotic susceptibility or resistance, urease activity, detection of the structural genes for bacteriocin production, bacteriocin activity as well as sensitivity of the isolates to enterocins (Ent) A and M were determined in 23 isolates of new species Enterococcus haemoperoxidus and E. moraviensis. The majority of the strains were antibiotic sensitive and exhibited low urease activity (< 10 nkat/mL). The most frequently detected genes for Ent were entA and entP. However, only the strain 466 of E. haemoperoxidus produced an antibacterial substance with inhibitory activity against 21 G+ indicators. It was partially purified reaching an activity of up to 12 800 AU/mL. This bacteriocin active strain also possessed the genes for EntA and EntP. The other strains did not inhibit the indicator strains. The substance produced by the 466 strain was active even after a 5-months storage at +4 and -20 degrees C. This substance has proteolytic and hydrophilic character, pH optimum of bacteriocin production by this strain being between 4 and 7. While E. moraviensis strains showed sensitivity to EntA (produced by E. faecium EK13) and to EntM (produced by E. faecium AL41), E. haemoperoxidus strains were sensitive to EntA (except strain 382) but less sensitive to the treatment by EntM.

Occurance of Staphylococcus nepalensis strains in different sources including human clinical material

Five isolates of coagulase-negative staphylococci were obtained from human urine, the gastrointestinal tract of squirrel monkeys, pig skin and from the environment. All key biochemical characteristics of the tested strains corresponded with the description of Staphylococcus xylosus species. However, partial 16S rRNA gene sequences obtained from analysed strains corresponded with those of Staphylococcus nepalensis reference strains, except for two strains which differed in one residue. Ribotyping with EcoRI and HindIII restriction enzymes, whole cell protein profile analysis performed by SDS-PAGE and SmaI macrorestriction analysis were used for more precise characterization and identification of the analysed strains. Obtained results showed that EcoRI and HindIII ribotyping and whole cell protein fingerprinting are suitable and reliable methods for the differentiation of S. nepalensis strains from the other novobiocin resistant staphylococci, whereas macrorestriction analysis was found to be a good tool for strain typing. The isolation of S. nepalensis is sporadic, and according to our best knowledge this study is the first report of the occurrence of this species in human clinical material as well as in other sources.

[Aeromonas spp. as the causative agent of acute diarrhoea in children under 1 year of age]

STUDY OBJECTIVE

To establish whether there is a link between cases of acute watery diarrhoea and a specific Aeromonas species.

MATERIALS AND METHODS

Eight strains studied were identified as aeromonads and were further characterized by biochemical tests, fatty acid analysis and ribotyping.

RESULTS

Aeromonads were isolated repeatedly from stool specimens of four children under one year of age with acute diarrhoea, two of whom were admitted to hospital. Of eight isolated aeromonads strains six were identified as A. caviae, one was classified into A. veronii bv. sobria and one could not be identified to the species level. Only two A. caviae strains from one patient were found to be identical by ribotyping while the Aeromonas species (strains) isolated from the other cases differed from one another. Contaminated fresh water, contaminated food and contact with travellers with imported diarrhoea were identified as probable sources of infection.

CONCLUSION

Four cases of acute gastroenteritis in small children document that aeromonads are not rare and can cause serious health problems. However, epidemiological links remain unclear. We did not prove correlation between the four serious cases of acute diarrhoea and specific Aeromonas species but the results suggest the predominant role of A. caviae.

Evaluation of (GTG)5-PCR for identification of Enterococcus spp

A set of reference strains and a group of previously unidentified enterococci were analysed by rep-PCR with the (GTG)(5) primer to evaluate the discriminatory power and suitability of this method for typing and identification of enterococcal species. A total of 49 strains representing all validly described species were obtained from bacterial collections. For more extensive evaluation of this identification approach 112 well-defined and identified enterococci isolated from bryndza cheese were tested. The (GTG)(5)-PCR fingerprinting assigned all strains into well-differentiated clusters representing individual species. Subsequently, a group including 44 unidentified enterococci isolated from surface waters was analysed to evaluate this method for identification of unknown isolates. Obtained band patterns allowed us to identify all the strains clearly to the species level. This study proved that rep-PCR with (GTG)(5) primer is a reliable and fast method for species identification of enterococci.

Ribotyping of Lactobacillus casei group strains isolated from dairy products

A series of lactobacilli isolated from dairy products were characterized using biotyping and ribotyping with EcoRI and HindIII restriction enzymes. Biotyping assigned 14 strains as Lactobacillus casei, 6 strains as Lactobacillus paracasei subsp. paracasei and 12 as Lactobacillus rhamnosus. The obtained ribotype patterns separated all analyzed strains into two clearly distinguished groups corresponding to L. rhamnosus and L. casei/L. paracasei subsp. paracasei. The HindIII ribotypes of individual strains representing these two groups were visually very similar. In contrast, EcoRI ribotyping revealed high intraspecies variability. All ribotypes of L. casei and L. paracasei subsp. paracasei dairy strains were very close and some strains even shared identical ribotype profiles. The type strains L. casei CCM 7088T (= ATCC 393T) and Lactobacillus zeae CCM 7069T revealing similar ribopatterns formed a separate subcluster using both restriction enzymes. In contrast, the ribotype profile of L. casei CCM 7089 (= ATCC 334) was very close to ribopatterns obtained from the dairy strains. These results support synonymy of L. casei and L. paracasei species revealed by other studies as well as reclassification of the type strain L. casei CCM 7088T as L. zeae and designation of L. casei CCM 7089 as the neotype strain.

Identification ofStaphylococcus piscifermentans from dog feces

The AD 2 strain isolated from feces of a healthy dog in Slovakia was characterized phenotypically by the conventional tests and commercial identification kits API Staph and ID32 Staph. Results of biochemical tests identified the strain as S. piscifermentans, fully corresponding with the species description. Further characterization by whole-cell protein profile analysis (SDS-PAGE) confirmed the identification based on biochemical tests and showed that the AD 2 strain is S. piscifermentans; lactic acid production, urease activity, bacteriocin production and the antibiotic susceptibility of it were also determined. S. piscifermentans AD 2 isolated first from an animal source was deposited in the Czech Collection of Microorganisms as Staphylococcus piscifermentans CCM 7165.

Characterization of Rhodococcus wratislaviensis strain J3 that degrades 4-nitrocatechol and other nitroaromatic compounds

The bacterial strain J3 was isolated from soil by selective enrichment on mineral medium containing 4-nitrocatechol as the sole carbon and energy source. This strain was identified as Rhodococcus wratislaviensis on the basis of morphology, biochemical, physiological and chemotaxonomic characterization and complete sequencing of the 16S rDNA gene. The isolated bacterium could utilize 4-nitrocatechol, 3-nitrophenol and 5-nitroguaiacol as sole carbon and energy sources. Stoichiometric release of nitrites was measured during degradation of 4-nitrocatechol both in growing cultures and for stationary phase cells. The J3 strain was unable to degrade 4-nitroguaiacol, 2-nitrophenol, 4-nitrophenol, 2,4-dinitrobenzoic acid, 4,5-dimethoxy-2-nitrobenzoic acid and 2,3-difluoro-6-nitrophenol. The J3 strain is deposited in the Czech Collection of Microorganisms as CCM 4930.

Characterization of esculin-positivePseudomonas fluorescens strains isolated from an underground brook

A group of sixteen esculin-positive fluorescent pseudomonads isolated from an underground brook flowing through a cave complex was characterized by biotyping, multiple enzyme restriction fragment length polymorphism analysis of 16S rDNA (MERFLP), ribotyping and whole-cell fatty-acid methyl-esters analysis (FAME). All strains were phenotypically close to Pseudomonas fluorescens, but they revealed high biochemical variability as well as some reactions atypical for P. fluorescens species. Because identification of pseudomonads by of biochemical testing is often unclear, further techniques were employed. Fingerprints obtained by MERFLP clearly showed that all strains represent P. fluorescens species. Ribotyping separated the strains analyzed into four groups corresponding almost completely (with the exception of one strain) to the clustering based on biochemical profiles. FAME analysis grouped all the strains into one cluster together with the P. putida (biotype A, B), P. chlororaphis and P. fluorescens biotype F representatives, but differentiated them from other FAME profiles of all pseudomonads included in the standard library TSBA 40 provided by MIDI, Inc.

Ribotyping of lactobacilli isolated from spoiled beer

Twenty-nine Lactobacillus strains contaminating beers in different Czech breweries as well as representative type strains obtained from the Czech Collection of Microorganisms were characterized using ribotyping with EcoRI and a probe made complementary to 16S and 23S rRNA genes. Biochemical test results assigned the 29 strains to the species L. brevis, L. plantarum, L. buchneri and L. paracasei subsp. paracasei. Ribotyping separated L. brevis, L. plantarum and L. paracasei subsp. paracasei strains into species-specific ribogroups in full correspondence with biotyping; L. buchneri strains were split into two ribogroups. Characteristic band patterns for each species and even typical bands of certain sizes were observed.

Molecular typing of exfoliative toxin-producing Staphylococcus aureus strains involved in epidermolytic infections

Genotyping of sixteen exfoliative toxin-producing (ET-positive) strains of Staphylococcus aureus isolated in maternity units of two distant hospitals was accomplished by PFGE, ribotyping, PCR ribotyping, and prophage carriage. Three strains secreted combined ETA + ETB, and the remaining produced ETA and enterotoxin C, or TSST-1. The comparison of various genomic profiles resulted in the identification of nine genotypes. The presence of one prevailing genotype was demonstrated in each hospital. Evidence was given that the outbreak-related ET-positive strains causing the skin disease pemphigus neonatorum disseminated in both the hospitals did not originate from a single source or a common ancestor.

Characterization of yellow-pigmented and motile enterococci isolated from intestines of the garden snail Helix aspersa

AIMS

Enterococci associated with garden snails (Helix aspersa) were studied in order to obtain reliable species identification and characterization.

METHODS AND RESULTS

Twelve yellow-pigmented and motile enterococci, isolated from the intestines of garden snails, were phenotypically close to Enterococcus casseliflavus, but they showed certain unusual biochemical characteristics. tRNA intergenic length polymorphism analysis (tDNA-PCR) divided all strains studied into two groups, in full agreement with biochemical test results. 16S rDNA sequencing, DNA base composition analysis and DNA-DNA hybridization results showed unambiguously that the enterococci studied belonged to the species Ent. casseliflavus. The representative strains of described ecovars were deposited in the Czech Collection of Microorganisms (CCM) as Ent. casseliflavus CCM 4868, 4869, 4870 and 4871.

CONCLUSIONS

Enterococcus casseliflavus associated with garden snails can be subdivided into groups.

SIGNIFICANCE AND IMPACT OF THE STUDY

Enterococcus casseliflavus differs from other enterococcal species in that it is typically associated with plants, soil, water and invertebrate animals. The different groups that can be found in these widely occurring bacteria are possibly source-specific ecovars, as exemplified by the Ent. casseliflavus inhabiting the intestines of snails.

Rhodococcus jostii sp. nov., isolated from a medieval grave

The taxonomic position of a bacterial strain isolated from the femur of the remains of Jost Lucemburský, margrave in Moravia, Brno (Czech Republic), was investigated by phenotypic, chemotaxonomic and molecular taxonomic methods. The chemotaxonomic characteristics, including the cell-wall amino acid and sugar compositions, the quinone system and the fatty acid profile, were in good agreement with those of the genus Rhodococcus. The G+C content of the DNA was 67.4 mol%. Comparative 16S rRNA gene sequencing demonstrated that the unknown strain represents a distinct line of descent within the genus Rhodococcus. The nearest relatives of the bacterium were Rhodococcus opacus and Rhodococcus percolatus. The unknown bacterium was readily distinguished from these species by using phenotypic methods. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Rhodococcus jostii sp. nov. The type strain is strain IFO 16295T (= CCM 4760T).

Evaluation of ribotyping for characterization and identification of Enterococcus haemoperoxidus and Enterococcus moraviensis strains

Seven Enterococcus moraviensis and 16 Enterococcus haemoperoxidus as well as nine reference cultures of other enterococcal species obtained from the Czech Collection of Microorganisms were characterized using ribotyping with EcoRI and HindIII in the present work. The ribopatterns obtained by both restriction enzymes clearly distinguished all E. moraviensis and E. haemoperoxidus strains from the other enterococci (E. faecalis, E. faecium, E. avium, E. raffinosus, E. pseudoavium, E. malodoratus) and they differentiated both species from each other as well. Although all strains were isolated from different sampling sites, many strains shared the same band patterns. E. moraviensis formed four ribogroups using EcoRI and two ribogroups using HindIII restriction enzyme. E. haemoperoxidus gave six different patterns with EcoRI and five using the HindIII restriction enzyme.

Enterococcus haemoperoxidus sp. nov. and Enterococcus moraviensis sp. nov., isolated from water

A polyphasic taxonomic approach was used to study atypical enterococci isolated from surface waters. All strains were characterized by physiological and biochemical tests as well as by genotyping. The results of biochemical tests and tRNA intergenic length polymorphism analysis (tDNA-PCR) divided all studied strains uniformly into two groups. Because these groups were clearly separated from all enterococcal species described to date, 16S rDNA sequence analysis, DNA base composition analysis and DNA-DNA hybridization of representative strains were done to elucidate the taxonomic position of the analysed groups. On the basis of the results obtained, the names Enterococcus haemoperoxidus (type strain CCM 4851T = LMG 19487T) and Enterococcus moraviensis (type strain CCM 4856T = LMG 19486T) are proposed for the two hitherto undescribed species. The type strains and reference cultures have been deposited in the Czech Collection of Microorganisms (CCM), Masaryk University, Brno, Czech Republic, and in the BCCM/LMG Culture Collection, Ghent University, Belgium.

Dehalogenation of haloalkanes by Mycobacterium tuberculosis H37Rv and other mycobacteria

Haloalkane dehalogenases convert haloalkanes to their corresponding alcohols by a hydrolytic mechanism. To date, various haloalkane dehalogenases have been isolated from bacteria colonizing environments that are contaminated with halogenated compounds. A search of current databases with the sequences of these known haloalkane dehalogenases revealed the presence of three different genes encoding putative haloalkane dehalogenases in the genome of the human parasite Mycobacterium tuberculosis H37Rv. The ability of M. tuberculosis and several other mycobacterial strains to dehalogenate haloaliphatic compounds was therefore studied. Intact cells of M. tuberculosis H37Rv were found to dehalogenate 1-chlorobutane, 1-chlorodecane, 1-bromobutane, and 1,2-dibromoethane. Nine isolates of mycobacteria from clinical material and four strains from a collection of microorganisms were found to be capable of dehalogenating 1,2-dibromoethane. Crude extracts prepared from two of these strains, Mycobacterium avium MU1 and Mycobacterium smegmatis CCM 4622, showed broad substrate specificity toward a number of halogenated substrates. Dehalogenase activity in the absence of oxygen and the identification of primary alcohols as the products of the reaction suggest a hydrolytic dehalogenation mechanism. The presence of dehalogenases in bacterial isolates from clinical material, including the species colonizing both animal tissues and free environment, indicates a possible role of parasitic microorganisms in the distribution of degradation genes in the environment.

Occurrence of Enterococcus spp. in waters

We studied 630 bacterial strains isolated from surface waters and determined as enterococci on the basis of their growth on Slanetz-Bartley agar in typical colonies. The strains were tested and characterized by several key conventional tests for basic differentiation of enterococci and by commercial test kits. We identified 135 strains of E. foecium (21%), 115 E. faecalis (18%), 30 E. mundtii (5%), 27 E. hirae (4%), 22 E. casseliflavus (3%), 21 E. gallinarum (3%), 17 E. durans-E. hirae complex (3%), 5 E. durans (1%), and 1 strain of E. avium. 150 strains were classified only as Enterococcus sp. (25%) and 107 strains (17%) isolated from Slanetz-Bartley agar were not enterococci. We found that the non-enterococcal group consisted of other Gram-positive cocci and Gram-positive and Gram-negative rods. Based on the identification we tried to find a relation between taxonomic position of isolated strains and their colony morphology on Slanetz-Bartley agar. Our of the total of 523 identified enterococci, 345 strains (66%) formed purple colonies, 136 red colonies (26%), 37 pink colonies (7%) and 5 cream colored colonies (1%). There was no correlation among the color, size or colony morphology and the taxonomic characterization of enterococcal strains.

Complex genomic and phenotypic characterization of the related species Staphylococcus carnosus and Staphylococcus piscifermentans

On the basis of numerical analysis of 100 phenotypic features, the strains of two species, Staphylococcus carnosus and Staphylococcus piscifermentans, were differentiated into two separate phenons corresponding with the macrorestriction patterns of their genomic DNA, as well as with the results of ribotyping and PCR amplification of enterobacterial repetitive intergenic consensus sequences. One of the S. carnosus strains, the F-2 strain, was shown to be marginal, exhibiting the lowest genomic and phenotypic similarity to the S. carnosus type strain DSM 20501T. Two of the strains studied (strains S. carnosus SK 06 and S. piscifermentans SK 05) were phenotypically convergent, forming a separate phenon. They were phenotypically similar, even though the genomic DNA of one of them was homologous with that of the S. carnosus type strain, whereas that of the other was homologous with the genomic DNA of the S. piscifermentans type strain. In such cases, fingerprinting methods (particularly macrorestriction analysis and ribotyping) served as important correctives, as they allow phenotypically convergent strains to be distinguished on the basis of their genomic profiles. The results of this paper support the proposal for the new species Staphylococcus condimenti as well as the new subspecies Staphylococcus carnosus subsp. utilis.

Selective isolation of Pseudomonas stutzeri from vertebrate faeces on Rambach agar

Faecal samples collected from 308 wild birds of 25 species and 19 rodents of 3 species in South Moravia (Czechland) were pre-incubated in Müller-Kauffmann tetrathionate broth at 42 degrees C for 24 h and then streaked onto Rambach agar plates which were incubated at 37 degrees C for 48 h. Seventeen out of 22 isolates forming orange-red colonies on Rambach agar were identified as Pseudomonas stutzeri, the rest as Pseudomonas sp. and Alcaligenes sp. The colonies of P. stutzeri were either dry, wrinkled and adherent to the agar (resembling Bacillus) or smooth, less adherent (mimicking Salmonella). P. stutzeri was recovered from five species of vertebrates caught in farmland habitats: the house sparrow (Passer domesticus), the tree sparrow (P. montanus), the great warbler (Acrocephalus arundinaceus), the wood mouse (Apodemus sylvaticus) and the common vole (Microtus arvalis). The overall isolation rate was 4.5% in birds (12.6% in house sparrows) and 15.8% in rodents. The procedure can be useful for the isolation of P. stutzeri in clinical and environmental studies.

[Use of the Streptotest kit for identification of enterococci isolated from human clinical material]

Enterococci are part of the common microflora of man and are isolated in large numbers also from the environment. Recently their presence in clinical material is increasing and they have become an important causal agent of nosocomial infections. From human clinical material (urine, vaginal smears, wounds) a total of 164 strains of enterococci was isolated. Identification of these isolates by means of the commercial STREPTOtest kit was not very successful (71.3%). The use of several supplementary tests and evaluation by the TNW programme improved successful identification (98.8%). The dominating species in clinical material was E. faecalis (94.5%), the second most frequent isolated species was E. faecium (3%). To achieve better identification of enterococci the authors recommend to supplement the kit by further tests (acidification of arabinose, ribose and pyruvate assimilation).

[Identification of aeromonads from water sources]

A total of 102 Aeromonas strains isolated from water were identified by both commercial ENTEROtest 1 & 2 kits and by several conventional tests. 83 strains (81.4%) were identified to the species level according to a differentiation table. A. hydrophila (36 strains), A. caviae (26 strains) and A. sobria (10 strains) species were isolated most frequently. Strains identified as A. allosaccharophila, A. eucrenophila, A. jandaei, A. media and A. trota were very rare. The remaining 19 strains could not be identified. The ENTEROtest kit without additional tube test was insufficient for the identification of Aeromonas strains to the species level. The arginine dihydrolase test and hydrolysis of esculin from the ENTEROtest kit were found to be the least reliable tests.

Genetic relationship of strains of Haemophilus aphrophilus, H. paraphrophilus, and Actinobacillus actinomycetemcomitans studied by ribotyping

Strains of H. aphrophilus, H. paraphrophilus, and A. actinomycetemcomitans are phenotypically very similar. Ribotyping of 24 strains of H. aphrophilus, 22 strains of H. paraphrophilus, 8 strains of A. actinomycetemcomitans, and one strain each of the species Pasteurella aerogenes, H. parahaemolyticus, and the genus Capnocytophaga was studied using a non-radioactive digoxigenin labelled probe based on E. coli 16S- and 23S-ribosomal RNA. Restriction fragments were generated using restriction enzyme EcoRI. The ribotypes were analysed by a numerical approach using UPGMA clustering. Two major clusters were seen: One contained all A. actinomycetemcomitans strains, the other all H. aprophilus and all except one H. paraphrophilus strain intermingled between each other. The H. paraphrophilus strain not found in the H. aphrophilus/H. paraphrophilus cluster, the H. parahaemolyticus, P. aerogenes, and the Capnocytophaga strains clustered separately from each other and the two major clusters. The H. paraphrophilus strain with the deviating ribotype was atypical in other respects: it neither did ferment lactose nor mannose and it was isolated from a deer in contradiction to the remaining H. paraphrophilus strains, which were human isolates. This study supports the view that H. aphrophilus and H. paraphrophilus should be regarded as one species separated from A. actinomycetemcomitans.

[Identification of enteric bacteria using the ENTEROtest 1 and 2 and the ENTERO-Rapid systems]

The identification efficacy of two systems, ENTEROtest 1 & 2 and ENTERO-Rapid (fy. Lachema a. c., Brno), was compared. A total 123 well known strains of enteric bacteria were tested. The ENTEROtest 1 & 2 system correctly identified 87.0% tested strains to the species level, the ENTERO-Rapid system correctly identified 76.4% of these strains.

[Use of the Streptotest for identification of enterococci and viridans-type streptococci]

The new identification system STREPTOtest (fy. Lachema, Brno) was evaluated. A total 118 well-known strains of genus Enterococcus, Streptococcus, Aerococcus, Stomatococcus and Gemella were tested. The STREPTOtest system rapidly and reliably distinguished genus Enterococcus from genus Streptococcus. This method identified correctly to the species level 65.9% of enterococci strains and 52.5% of streptococci strains. The STREPTOtest was used for identification of A. viridans and S. mucilaginosus and it was possible to separate these strains from similar ones. A new differentiation chart for identification of all 13 recently described enterococcal species was proposed.

Identification of Staphylococcus and Micrococcus species with the STAPHYtest system

A collection of 216 well-characterized strains of Staphylococcus, Micrococcus and Stomatococcus was examined by a commercially available STAPHYtest system (Lachema, Brno, Czechoslovakia). The results of STAPHYtest agreed with those of conventional tests. The STAPHYtest permitted a clear-cut separation of Staphylococcus from Micrococcus and Stomatococcus strains and correctly identified 104 of 145 (72%) Staphylococcus strains after 24 h of incubation. However, it allowed the identification only of 19 of 29 validly published Staphylococcus species. The STAPHYtest proved to be a simple and rapid system for the separation of staphylococci from micrococci and for the identification of most frequent clinically significant staphylococci.