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

Enterococcus moraviensis EMo 1-1Nik of horse origin:characteristics and potential bacteriocin-producing strain

Nowadays, developed more precisious identification techniques have allowed to validate newer enterococcal species. Among them, the species Enterococcus moraviensis was also validated, at first from surface waters. However, in this study, characteristics and potential to bacteriocin production by the strain E. moraviensis EMo 1-1Nik isolated from buccal mucosa of Slovak warm-blood horse breed has been studied. BLASTn analysis allotted this strain to the species E. moraviensis with percentage identity BLASTn 16S rRNA sequence in the strain up to 100% (99.93% similarity with E. moraviensis NR113937.1). The strain EMo 1-1Nik has been provided with GenBank accession number MW326085. It is hemolysis-negative (γ-hemolysis), deoxyribonuclease-negative and gelatinase-negative; absent of virulence factor genes, low-grade biofilm-positive (0.133 ± 0.36), mostly susceptible to tested antibiotics. Moreover, 60% of EMo1-1Nik colonies were found as bacteriocin-producing against the principal indicator Enterococcus avium EA5. The concentrated substance (CS, pH 4.5) of EMo1-1Nik showed the inhibitory activity against EA5 strain (800 AU/mL); CSs with pH 6.3 and 7.3 reached inhibitory activity 100 AU/mL against EA5 strain. CS was thermo-stable and it does not lost activity after enzymes treatment. Oppositelly, EMo 1-1Nik was susceptible to Mundticin EM 41/3 (800 AU/mL) produced by horse fecal strain E. mundtii EM 41/3 and enterocins (up to 51 200 AU/mL). In spite of the preliminary results, it has been shown a potential to produce bacteriocin substance of the safe strain E. moraviensis EMo1-1Nik. The additional studies are in processing.

Description of Pseudomonas jessenii subsp. pseudoputida subsp. nov., amended description of Pseudomonas jessenii and description of Pseudomonas jessenii subsp. jessenii subsp. nov

Fluorescent Pseudomonas putida CCM 3656 (ATCC 11250) was analysed according to the methods of polyphasic approach which were based on sequence analyses involving the rpoB and rrs genes, manual ribotyping using endonuclease HindIII, DNA base composition determination and DNA-DNA hybridization. The results obtained by these genotyping methods showed that the strain CCM 3656 is distant from P. putida taxon, which was supported with phenotype characterization represented by whole-cell protein profile analysis, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry profiling and extended biotyping. The DNA-DNA hybridization experiments performed between the strain CCM 3656 and the closest relatives revealed 77 % similarity with Pseudomonas jessenii. However, the outcomes of sequencing, ribotyping and phenotype characterization allow distinguishing the studied strain from P. jessenii. On the basis of the obtained taxonomic data, we suggest reclassifying strain CCM 3656 to a novel subspecies of P. jessenii and propose naming P. jessenii subsp. pseudoputida subsp. nov. with CCM 3656(T) as type strain. Furthermore, we present an amended description of P. jessenii and proposal of P. jessenii subsp. jessenii subsp. nov.

Enterococcus ureilyticus sp. nov. and Enterococcus rotai sp. nov., two urease-producing enterococci from the environment

A set of 25 urease-producing, yellow-pigmented enterococci was isolated from environmental sources. Phenotypic classification divided the isolates into two phena. Both phena were characterized using 16S rRNA gene sequence analysis, DNA base composition, rep-PCR fingerprinting and automated ribotyping. The obtained data distinguished the isolates from all members of the genus Enterococcus with validly published names and placed them in the Enterococcus faecalis species group. DNA-DNA hybridization experiments, pheS and rpoA sequencing and whole-cell protein electrophoresis provided conclusive evidence for the classification of each phenon as a novel species of the genus Enterococcus, for which the names Enterococcus ureilyticus sp. nov. (type strain CCM 4629(T)  = LMG 26676(T)  = CCUG 48799(T)), inhabiting water and plants, and Enterococcus rotai sp. nov. (type strain CCM 4630(T)  = LMG 26678(T)  = CCUG 61593(T)), inhabiting water, insects (mosquitoes) and plants, are proposed.

Identification of enterococci from broiler products and a broiler processing plant and description of Enterococcus viikkiensis sp. nov

In two previous studies dealing with lactic acid bacteria (LAB) from modified-atmosphere-packaged (MAP) broiler products and a broiler processing plant, several isolates remained unidentified. According to 16S rRNA gene sequence analysis, 36 isolates were assigned to the genus Enterococcus. Numerical analysis of combined HindIII and EcoRI ribopatterns of these isolates resulted in species-specific clusters that were congruent with the clusters obtained by both DNA-directed RNA polymerase subunit A (rpoA) and phenylalanyl-tRNA synthetase α chain (pheS) housekeeping gene analyses. In the analyses, a group of five isolates distinct from any known enterococcal species clustered together. The five isolates were positioned in the Enterococcus avium group, with E. devriesei being the closest phylogenetic neighbor. The DNA-DNA hybridization levels with E. devriesei ranged from 28.8 to 54.3% and indicated that these strains represented a novel species. The name Enterococcus viikkiensis sp. nov. is proposed, with strain DSM 24043(T) (LMG 26075(T)) being the type strain. Our study demonstrated that the identification of enterococci within the E. avium phylogenetic group demands polyphasic taxonomic approaches. The rpoA and pheS gene similarities (99.0 to 99.2% and 94.3 to 95.4%, respectively) between E. viikkiensis and its closest phylogenetic neighbor, E. devriesei, were higher than those previously reported within the enterococci. In addition, the phenotypic profiles of the species in the E. avium group were also highly similar, and some traits were found to be misleading for enterococci, such as E. viikkiensis does not grow at 45°C. The numerical analysis of combined HindIII and EcoRI ribopatterns was of considerable assistance in distinguishing enterococcal species within the E. avium group.

Staphylococcus microti sp. nov., isolated from the common vole (Microtus arvalis)

Two strains of Gram-positive cocci were isolated from viscera of common voles (Microtus arvalis Pallas) with generalized Brucella microti infection in the Czech Republic. Biochemical features and phylogenetic analysis based on 16S rRNA gene sequences showed that the strains are representatives of the genus Staphylococcus and assigned Staphylococcus muscae as the nearest relative. A detailed characterization done by ribotyping, rpoB and hsp60 gene sequencing, whole-cell protein analysis and rep-PCR using the (GTG)(5) primer differentiated the two strains from all described staphylococci. DNA-DNA hybridization with the type strain of S. muscae demonstrated that the two strains should be considered as members of a novel species (26.8 % reassociation). The two analysed strains were found to be coagulase-negative, novobiocin-susceptible, oxidase-negative cultures, phenotypically close to one another, but showing differences in ribotype profiles. The major fatty acids were iso-C(15 : 0), iso-C(17 : 0), anteiso-C(15 : 0), C(18 : 2 )omega6,9c/anteiso-C(18 : 0), C(18 : 0) and C(18 : 1) omega9c. MK-7 was the predominant isoprenoid quinone, with minor amounts of MK-6 and MK-8. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylglycerol and several unknown lipids. These results proved that the two isolates represent a novel staphylococcal species. The name proposed for this novel taxon is Staphylococcus microti sp. nov.; the type strain is 4005-LJ(m)(T) (=CCM 4903(T) =CCUG 55861(T) =DSM 22147(T)).

Classification of brown pigmented aeromonads isolated from river water

Nine Aeromonas strains having a brown exopigment were isolated during the microbiological examination of river water. These brown-pigmented aeromonads were characterized by the phenotyping, fatty-acid methyl-ester analysis and ribotyping. All methods identically confirmed that the group of brown-pigmented aeromonads is quite heterogeneous. Apart from the Aeromonas media taxon, the brown-pigmented aeromonads in river water were represented also by strains of A. allosaccharophila and A. salmonicida subsp. pectinolytica.

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.

Staphylococcus equorum and Staphylococcus succinus isolated from human clinical specimens

A polyphasic identification approach was applied to a group of 11 novobiocin-resistant staphylococci isolated from human clinical materials. Phenotypic characteristics obtained by both commercial and conventional tests assigned eight strains as Staphylococcus xylosus and three strains as ambiguous S. xylosus/Staphylococcus equorum. In contrast to biotyping, ribotyping with EcoRI and HindIII restriction endonucleases and whole-cell protein fingerprinting assigned six analysed strains as S. equorum, and five strains as Staphylococcus succinus. Confirmation of the identification was done by partial 16S rRNA gene sequencing and S. equorum isolates were verified by a PCR assay targeting the sodA gene. From the data it has been implied that ribotyping and whole-cell protein analysis can be used to differentiate between the biochemically almost indistinguishable species S. xylosus, S. equorum and S. succinus. The present study confirms what is believed to be the first occurrence of S. equorum in a relevant human clinical material in the Czech Republic and describes what is believed to be the first-ever isolation of S. succinus from human clinical material.

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.

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.

Reclassification of Staphylococcus pulvereri Zakrzewska-Czerwińska et al. 1995 as a later synonym of Staphylococcus vitulinus Webster et al. 1994

A polyphasic taxonomic approach was applied to strains of the species Staphylococcus vitulinus and Staphylococcus pulvereri in order to clarify their taxonomic relatedness. Four reference strains, representing both species, and seven strains isolated from human clinical material were characterized by biotyping, ribotyping and SDS-PAGE analysis of whole-cell proteins, and none of the screening approaches allowed the two taxa to be distinguished. DNA–DNA hybridization experiments between four selected representative strains, including the type strains, confirmed that Staphylococcus pulvereri is a later synonym of Staphylococcus vitulinus.

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.

Methods used for the isolation, enumeration, characterisation and identification of Enterococcus spp

This paper reviews the methodology applied for the identification and characterisation of enterococci and covers phenotypic, genotypic and phylogenetic techniques. Although conventional phenotypic typing schemes are useful for rapid and simple identification of enterococcal species for routine applications, other methods like standardised sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE), multilocus enzyme electrophoresis (MLEE), antimicrobial susceptibility testing, serotyping, pyrolysis mass spectrometry (pyMS) and vibrational spectroscopic methods allow a more in-depth characterisation of enterococci. Many of the recently described enterococcal species exhibit deviations from hitherto so-called classical enterococci with regard to their phenotypical properties. Therefore, genotypic methods have to be used to clarify their possible assignment to the genus Enterococcus. In this review, special emphasis is given on recently developed polymerase chain reaction (PCR)-based typing methods such as random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), specific and random amplification (SARA) and modifications of PCR-ribotyping as well as pulsed-field gel electrophoresis (PFGE) and partial sequence analysis. The use of PCR and probes for genus and species identification of enterococci is also considered like the application of sequence data of conserved DNA regions (e.g., ribosomal ribonucleic acid (rRNA) genes) in the case of species identification.

Macrococcus brunensis sp. nov., Macrococcus hajekii sp. nov. and Macrococcus lamae sp. nov., from the skin of llamas

Eight strains of Gram-positive, catalase- and oxidase-positive cocci were isolated from the skin of llamas (Lama glama L.) and characterized using a polyphasic approach. These strains were assigned to the genus Macrococcus on the basis of their phenotypic properties (resistance to bacitracin and sensitivity to furazolidone) and DNA base content (40-42 mol% G+C). Phylogenetic analysis based on 16S rDNA confirmed that the strains are members of the genus MACROCOCCUS: They differed from all hitherto described macrococcal species in their production of phosphatase and reduction of nitrate (most strains) and the inability to produce acid from glycerol or to grow in 7.5 % NaCl. Ribotyping (EcoRI), macrorestriction analysis (XbaI) and fatty acid methyl ester analysis divided the strains from llamas into three stable clusters. Moreover, ribotyping differentiated the strains analysed not only from previously described macrococcal species but also from oxidase-positive staphylococci. DNA-DNA hybridization confirmed that the three clusters represent separate genomic groups (similarity values<54 %). All the results showed that the strains represent three novel species, for which the names Macrococcus hajekii sp. nov. (type strain CCM 4809(T)=LMG 21711(T)), Macrococcus brunensis sp. nov. (type strain CCM 4811(T)=LMG 21712(T)) and Macrococcus lamae sp. nov. (type strain CCM 4815(T)=LMG 21713(T)) are proposed.

Geographical variation in ribotype profiles of Escherichia coli isolates from humans, swine, poultry, beef, and dairy cattle in Florida

Waters impacted by fecal pollution can exact high risks to human health and can result in financial losses due to closures of water systems used for recreation and for harvesting seafood. Identifying the sources of fecal pollution in water is paramount in assessing the potential human health risks involved as well as in assessing necessary remedial action. Recently, various researchers have used the ribotyping method to identify sources of bacterial indicators (Escherichia coli and enterococci) in environmental waters. While these studies have identified genotypic differences between human- and animal-derived indicators that are capable of differentiating organisms isolated from humans and various animal hosts, most have focused on organisms collected from a confined geographic area and have not addressed the question of whether these ribotype profiles are watershed specific or if they can be applied universally to organisms from other geographic locations. In this study, E. coli isolates were obtained from humans, beef cattle, dairy cattle, swine, and poultry from locations in northern, central, and southern Florida and were subjected to ribotyping analysis. The intent was to determine (i) if ribotype profiles are capable of discriminating the source of E. coli at the host species level and (ii) if the resulting fingerprints are uniform over an extended geographic area or if they can be applied only to a specific watershed. Our research indicated that, using a single restriction enzyme (HindIII), the ribotyping procedure is not capable of differentiating E. coli isolates from the different animal species sampled in this study. Results indicate, however, that this procedure can still be used effectively to differentiate E. coli as being either human or animal derived when applied to organisms isolated from a large geographic region.

PCR-based methods for identification of Enterococcus species

Two DNA-based techniques were used for species identification of enterococci. PvuII digestion of the genus-specific PCR product yielded four different restriction profiles among 20 enterococcal species; one of them was species-specific for E. faecium. In the second case, 32 reference strains belonging to 20 enterococcal species were divided to 12 groups by amplification of internal transcribed spacer of rRNA operon. Interspecies and some intraspecies profile variability was determined. Both methods gave similar results.