Phenotypic and genotypic identification of staphylococci isolated from wild small mammals

229 strains of Staphylococcus isolated from the intestines of wild small mammals (Insectivora and rodents) were analysed by phenotypic tests and 16S-23S rDNA intergenic spacer PCR amplification (ITS-PCR). Based on the results of three methods (phenotypical tests, API numerical profiles and ITS-PCR) 65.5% of all staphylococcal strains could be identified. The remaining strains were compared by cluster analysis with reference and identified strains. It is quite possible that, a part of unidentified strains represent hitherto undescribed species, all the more as their ITS types were not found among other members of the genus Staphylococcus. Moreover, the results show that small mammals provides a suitable new habitat for certain staphylococci.     

Phenotypic and genotypic identification of yeasts from cheese

Eighty-five yeast strains isolated from different cheeses of Austria, Denmark, France, Germany, and Italy were identified using physiological methods and genotypically using random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) analysis. Good congruence was found between the phenotypic and genotypic data for 39 of the isolates. However, 26 isolates of Geotrichum could only be identified to the species level using the genotypic methods and 7 isolates were correctly identified to the genus level only using phenotypic identification methods. The phenotypic identification did not agree with the genotypic data for 14 yeast isolates. Using ubiquinone analysis, yeast cell wall sugars and the diazonium blue B test 5 incorrectly identified isolates with phenotypic methods could be identified genotypically. In addition the 7 isolates identified only to the genus level by the phenotypic methods and the 26 Geotrichum strains were identified to the species level using the polyphasic molecular approach mentioned above. Eleven strains remained unidentified. The 76 identified yeast isolates were assigned to 39 species, the most frequent assignments were made to Debaryomyces hansenii, Geotrichum candidum, Issatchenkia orientalis, Kluyveromyces lactis, K. marxianus, Saccharomyces cerevisiae, Yarrowia lipolytica, andCandida catenulata. It is proposed that Debaryomyces hansenii (Zopf) Lodder et Kreger-van Rij and Debaryomyces fabryi Ota should be reinstated. The RAPD-PCR data reinforced the view that the species Galactomyces geotrichum is heterogeneous with all of the Geotrichum isolates from cheese products being assigned G. geotrichum group A sensu M.T. Smith. It is suggested that the name Geotrichum candidum be conserved for this rather common species.     

Phenotypic and genotypic diversity of yeasts isolated from water-buffalo Mozzarella cheese

Water-buffalo Mozzarella (WBM) cheese is one of the several 'pasta filata' or stretched curd cheeses that originated in southern Italy, traditionally manufactured from raw milk employing natural whey starter cultures. Lactose- and galactose-fermenting yeasts isolated from WBM were studied to evaluate their role in the ripening of this cheese. The kinetic parameters of the growth of the yeasts as well as their principal metabolic end-products showed a great variability depending on the species. Moreover, the genetic polymorphism of the yeasts was studied for their differentiation at species level by means of the polymerase chain reaction (PCR) fingerprinting and mitochondrial DNA (mtDNA) restriction analysis. While the differentiation based on metabolic traits was not able to discriminate Kluyveromyces marxianus, Candida kefyr and C. sphaerica, the PCR analysis with primers M13 and RF2 resulted in a reliable and rapid method for differentiating at species level Saccharomyces cerevisiae, K. marxianus, K. lactis and their anamorphic species. Furthermore, mtDNA analysis proved to be more discriminating at strain level.     

Phenotypic and genotypic identification of bacteria from the Burkholderia cepacia complex

AIM: Evaluation of the diagnostic value of pheno- and genotypic characteristics of B. cepacia strains collection. MATERIALS AND METHODS: Phenotypic and genetic methods of identification and differentiation of 25 strains of the B. cepacia complex. RESULTS: Polyphasic taxonomic approach utilizing multiple diagnostic tests was used for accurate identification of Burkholderia species. Algorithm for identification of microorganisms from the B. cepacia complex was developed. CONCLUSION: Combined use of phenotypic and molecular genetic tests, such as recA gene PCR, is recommended for differentiation of the B. cepacia complex genomovars.     

Phenotypic and genotypic homogeneity of the strains of Rickettsia japonica isolated from patients with Oriental spotted fever.

Nine pathogenic strains of Rickettsia japonica isolated from patients with Oriental spotted fever were compared phenotypically and genotypically. Constitution and antigenicity of the proteins demonstrated to be the same among strains. Polymerase chain reaction (PCR) amplification of the two major outer membrane protein genes (ompA and ompB) and an intracellular spotted fever group-common antigen protein gene (rps120) produced the same sizes of products for all strains. Restriction fragment length polymorphism of the PCR products showed the same pattern among strains with each endonuclease. Thus, these strains belong to a single type, the same as the type strain YH (=ATCC VR-1363).     

Phenotypic and genotypic characterization of some Moorella sp. strains isolated from canned foods

Six anaerobic thermophilic strains isolated from various spoiled cans including fish soups and cooked meats were characterized using a polyphasic approach. These strains were closely related to Moorella thermoacetica or Moorella thermoautotrophica species. Except the spacer region between the 16S and the 23S rRNA genes, which exhibited two PCR profiles distinguishing both species, the genotypic and phylogenetic analyses grouped these isolates, the type strains, and all sequences of Moorella thermoacetica and Moorella thermoautotrophica species contained in the GenBank database within a unique cluster. Moreover, all 16S rDNA sequences shared two characteristic DNA fragments, which were highly specific of Moorella thermoacetica/Moorella thermoautotrophica strains. However, taken together, the phenotypic, physiological and genotypic methods were conflicting, and did not enable affiliation of the isolates with one or the other species. To our knowledge, this study represents the first report of characterization of Moorella species isolated from spoiled cans. These results and previous work, very strongly argue in favor of questioning the taxonomic status of the two species.     

Phenotypic and genotypic discrepancy of Streptococcus pneumoniae strains isolated from Asian countries

Non-typeable isolates of Streptococcus pneumoniae collected from Asian countries were characterized by optochin susceptibility test, bile solubility test, multilocus sequence typing of housekeeping genes, amplification of virulence-related genes, 16S rDNA-RsaI digestion, and 16S rDNA sequencing. Six of 54 non-typeable pneumococcal isolates showed divergence of gene sequences of recP and xpt from typical pneumococcal strains. Of these six atypical pneumococcal strains, two showed different results in optochin susceptibility or bile solubility test from typical pneumococcal strains. All six isolates showed high sequence dissimilarities of multilocus sequence typing, 16S rDNA sequences, and lytA sequences from typical S. pneumoniae strains. Data from this study suggest that classic tests such as optochin susceptibility and bile solubility tests may lead to incorrect identification of S. pneumoniae. These atypical strains may belong to different bacterial species from S. pneumoniae.     

Phenotypic and genotypic characterization of Salmonella spp. Isolated from pigs and their farm environment in Korea

This study's objective was to determine the prevalence of Salmonella spp. in pigs and their farm environments in Korea, and to investigate the relationship between the strains based on their phenotypic and genotypic characteristics. A total of 36 Salmonella spp. were isolated in this study: 18 isolates from 492 pigs (3.7%) and 18 isolates from 418 (4.3%) farmhouse environmental samples from 16 different pig farms. Of the Salmonella strains isolated from the numerous environmental samples, the highest prevalence was observed in slurry or manure, followed by partitions, farmer's hands, floors, water/ nipples, ventilation sources, and feed, respectively. All the Salmonella isolates originating from different farms were genetically distinct. In three farms, however, identical phage types and pulse-field gel electrophoresis patterns were observed among Salmonella isolates from pig feces and environmental samples. This study suggests that environments contaminated with Salmonella could pose an infection risk to pigs on pig farms.     

Phenotypic characterization and antibiotic resistance of Acinetobacter spp. isolated from aquatic sources

A total of 99 Acinetobacter isolates from sewage, freshwater aquaculture habitats, trout intestinal contents and frozen shrimps was characterized phenotypically and antibiotic susceptibility patterns determined. One group of genomic species, including Ac. johnsonii, Ac. lwoffi and spp. 15TU, was detected in all sample types and represented the majority of the isolates (n = 54). Isolates belonging to the Acb complex (Ac. calcoaceticus, Ac. baumannii and genomic species 3) were detected in sewage (n = 6) and frozen shrimps (n = 1), Ac. haemolyticus in frozen shrimps (n = 6) and trout intestinal contents (n = 2) and genomic species 11 in freshwater aquaculture habitats (n = 6) and trout intestinal contents (n = 1). Acinetobacter junii (n = 5), genomic species 10 (n = 2), 14BJ (n = 8) and 16BJ (n = 4) were only isolated from sewage. Acinetobacter isolates from sewage were generally more biochemically reactive and resistant to antimicrobial agents compared with isolates from other sample types. Different strains, often belonging to different genomic species, were isolated from sites situated upstream and downstream of the discharge point of a pharmaceutical plant. This finding supported the hypothesis that the waste effluent from the pharmaceutical plant was likely to cause a change in the distribution of Acinetobacter spp. by selecting and/or introducing antibiotic-resistant strains into the recipient sewers.     

Phenotypic characteristics of root-nodulating bacteria isolated from Acacia spp. grown in Libya

Thirty isolates of root-nodulating bacteria obtained from Acacia cyanophylla, A. karroo, A. cyclops, A. tortilis (subsp.raddiana), Faidherbia albida and Acacia sp., grown in different regions of Libya, were studied by performing numerical analysis of 104 characteristics. Three fast- and one slow-growing reference strains from herbaceous and woody legumes were included. Five distinct clusters were formed. The fast-growing reference strains were separated from the isolates whereas the slow-growing was included in cluster 4. With the exception of one cluster, the majority of clusters were formed regardless of the host plant or site of origin. Based on plant tests, generation times, acid production and carbon utilization the isolates were diverse (fast and slow-growing isolates). Like slow-growing isolates, most of the fast-growing isolates appeared to be non-specific, nodulated many species from the same genus notably F. albida, known to nodulate only with slow-growing strains. Most clusters grew at temperatures 35 °C and 37 °C; some grew at temperatures above 40 °C. The majority of isolates grew at acid and alkaline pH and only one isolate grew below pH 4. Most isolates were able to utilize many amino acids as nitrogen sources and to reduce nitrate. Urea was hydrolysed by all clusters. Monosaccharides and polyols were used by slow and fast-growing isolates as the only carbon sources whereas assimilation of disaccharides varied: Some isolates, like slow-growing isolates, failed to utilize these carbon sources. Most isolates were unable to utilize polysaccharides. Regarding tolerance to NaCl on agar medium, the majority of isolates were unable to grow at a concentration of 2% NaCl, but some were highly resistant and there was one isolate which grew at 8% NaCl. Most isolates were resistant to heavy metals and to antibiotics.     

Phenotypic and genotypic characterization of esterase-producing Ureibacillus thermosphaericus isolated from an aerobic digestor of swine waste.

Eight closely related thermophilic strains were isolated from an aerobic and thermophilic treatment of swine wastes. The pleomorphic cells (short and long rods; cocci) showed peritrichous flagella, terminally swollen sporangium, and liberated spores exhibiting hairy appendages. The Gram reaction was negative for both young (4 h) and old (48 h) cultures. Several features, such as colonial morphology, growth between 35 degrees C and 65 degrees C, presence of catalase, presence of spores, and strictly aerobic metabolism (except for one strain), are similar to those found for the genus Bacillus. The inability of the strains to use sugars, except esculin, as source of carbon and energy and the whole cell fatty acid composition are similar to those found in Bacillus thermosphaericus DSM 10633. Sequence analysis of the 16S rRNA gene revealed 99.8%-99.9% identity for seven of the thermophilic strains with this species. A new genus, Ureibacillus, was recently proposed for type strain B. thermosphaericus DSM 10633 The last strain exhibits 97.8% and 97.3% identity with Ureibacillus terrenus DSM12654 and Bacillus sp. TP-84, respectively. Esterase activities were detected for all strains, and assays on p-nitrophenyl butyrate and p-nitrophenyl caprylate revealed that strains were more active on the shorter substrate.     

Phenotypic and genotypic evaluation of Listeria monocytogenes strains isolated from fish and fish processing plants

The aim of this study was to perform the phenotypic and genotypic evaluation of Listeria monocytogenes strains isolated from fish and equipment used in fish processing plants. The prevalence of selected gene-encoding virulence factors among L. monocytogenes strains was assessed by multiplex PCR. The genetic (PFGE method) and protein similarities (MALDI-TOF MS technique) of isolates were determined. Their drug resistance (disk-diffusion method and MIC values), serogroup classification (multiplex-PCR), and the ability to co-aggregate with Salmonella enteritidis were also evaluated. Among 37 L. monocytogenes isolates, 36 strains were found, one of which included two genetically identical isolates (PFGE method). In all examined strains, the following genes were found: hlyA, plcB, plcA, inlA, inlB, prfA, iap, and actA. The presence of virulence genes, mpl, and fbpA was confirmed in 32 (88.9%) strains. It was reported that 30 (83.3%) of the strains belonged to serogroup 1/2a-3a. It was also found that the rate of coaggregation with S. enteritidis bacilli was 16.5–36.3%. Among the investigated L. monocytogenes strains, 25 (69.4%) were sensitive to all antibiotics used. Resistance to penicillin was reported most often among strains (n = 6, 16.7%). The assessment of L. monocytogenes virulence level is an important aspect for the protection of public health. It was reported that strains isolated from fish contain genes coding for virulence factors and some of them are antibiotic-resistant. In our study, it was found that strains with a high degree of genetic similarity also showed a high degree of similarity at the level of protein profiles.     

米卡芬净对分离自中国的念珠菌和曲霉临床株体外抑菌活性的研究

目的了解新型抗真菌药物米卡芬净(micafungin,MFG)对分离自中国的念珠菌和曲霉临床株的体外抑菌活性。方法参照CLSI(Clinical and Laboratory Standards Institute,以前为NCCLS)制定的M27-A2和M38-A方案测定86株念珠菌和35株曲霉的最低抑菌浓度(MIC)或最低有效浓度(MEC)。结果MFG对大多数念珠菌属和曲霉属均有较好的抑菌作用。对念珠菌属的MIC90从高到低依次为:氟康唑(FLC)敏感的白念珠菌、热带念珠菌、光滑念珠菌为0.125μg/ml,FLC耐药和剂量依赖敏感株为0.25μg/ml,克柔念珠菌为0.5μg/ml,近平滑念珠菌8μg/ml,季也蒙念珠菌>16μg/ml。MFG对烟曲霉的MEC90为≤0.03μg/ml,对非烟曲霉的曲霉属MEC90为0.06μg/ml。MFG与唑类药物、两性霉素B(AMB)不存在交叉耐药,对FLC耐药的念珠菌、伊曲康唑耐药的曲霉、AMB不敏感的曲霉均有好的抑菌活性。结论MFG对多数念珠菌属和曲霉属(包括对唑类耐药和AMB不敏感的菌株)有较好的体外抑菌作用。     

Phenotypic and genotypic characteristics of Arcanobacterium haemolyticum isolated from clinical samples in a Danish hospital

Six Arcanobacterium haemolyticum strains isolated from six patients of two hospitals in Denmark were identified phenotypically, also including matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, and by genotypic methods. The latter were performed by sequencing 16S rDNA and glyceraldehyde 3-phosphate dehydrogenase encoding gene gap and by amplification of an A. haemolyticum specific region of 16S–23S rDNA intergenic spacer region and 23S rDNA. The six A. haemolyticum strains were further investigated for the presence of seven potential virulence genes encoding arcanolysin, phospholipase D, hemolysin A, CAMP factor family protein, collagen binding protein, neuraminidase A and neuraminidase H which appeared to be present in two (seven virulence genes), two (six virulence genes) and two strains (four virulence genes), respectively. The phenotypic and genotypic properties described in the present study might help to reliably identify and further characterize A. haemolyticum isolated from human patients, a species which seems to be of increasing importance.     

Phenotypic and genotypic characterization of encapsulated Escherichia coli isolated from blooms in two Australian lakes

Escherichia coli has long been used as an indicator organism for water quality assessment. Recently there has been an accumulation of evidence that suggests some strains of this organism are able to proliferate in the environment, a characteristic that would detract from its utility as an indicator of faecal pollution. Phenotypic and genotypic characterization of E. coli isolated from blooms in two Australian lakes, separated by a distance of approximately 200 km, identified that the blooms were dominated by three E. coli strains. A major phenotypic similarity among the three bloom strains was the presence of a group 1 capsule. Genetic characterization of a conserved region of the cps gene cluster, which encodes group 1 capsules, identified a high degree of genetic variation within the bloom isolates. This differs from previously described encapsulated E. coli strains which are highly conserved at the cps locus. The phenotypic or genotypic profiles of the bloom strains were not identified in 435 E. coli strains isolated from vertebrates. The occurrence of these encapsulated strains suggests that some E. coli have evolved a free-living lifestyle and do not require a host in order to proliferate. The presence of the same three strains in bloom events in different geographical regions of a temperate climate, and at different times, indicates that free-living E. coli strains are able to persist in these water reservoirs. This study provides further evidence of circumstances where caution is required in using E. coli as an indicator organism for water quality.     

Phenotypic and genotypic analysis of rhizobia isolated from pasture legumes native of Sardinia and Asinara Island

Thirty-five rhizobial strains were isolated from nodules of Lotus edulis, L. ornithopodioides, L. cytisoides, Hedysarum coronarium, Ornithopus compressus and Scorpiurus muricatus growing in Sardinia and Asinara Island. Basic characteristics applied to identification of rhizobia such as symbiotic properties, antibiotic- and salt-resistance, temperate-sensitivities, utilization of different sources of carbon and nitrogen were studied. The results from the 74 metabolic tests were used for cluster analysis of the new rhizobial isolates and 28 reference strains, belonging to previously classified and unclassified fast-, intermediate- and slow-growing rhizobia. All strains examined were divided into two large groups at a linkage distance of 0.58. None of the reference strains clustered with the new rhizobial isolates, which formed five subgroups almost respective of their plant origin. RFLP analysis of PCR-amplified 16S-23S rDNA IGS showed that the levels of similarity between rhizobial isolates from Ornithopus, Hedysarum and Scorpiurus, and the type strains of Rhizobium leguminosarum, Mesorhizobium loti, M. ciceri, M. mediterraneum, Sinorhizobium meliloti and Bradyrhizobium japonicum were not more than 30%. Thus, it can be assumed that these groups of new rhizobial isolates are not closely related to the validly described rhizobial species.     

Phenotypic characteristics and relative proportions of three genotypic variants isolated from a nucleopolyhedrovirus of Spodoptera exigua

US2A, US2D, and US2F are three in vivocloned genotypic variants from the wild-type strain of a Spodoptera exiguanucleopolyhedrovirus (SeMNPV) isolated in Florida (USA) and is the active component of the commercial bioinsecticide Spod-X^®. These variants were compared in terms of pathogenicity (LD₅₀), speed of kill (expressed as mean time to death) and viral progeny productivity (OBs/larva). LD₅₀values were similar for the three cloned genotypes. The mean time to death value for US2D (113.7 h) was significantly higher than those of US2A (31.7 h) and US2F (27.8 h). Virus yield was determined for L₄larvae infected with the estimated LD₉₉. US2D infected larvae attained higher weight than those infected with US2A and US2F, and produced a higher OB yield than larvae infected with US2A or US2F. An outstanding feature of US2F, in contrast to US2A and US2D, was its inability to disrupt the teguments of NPV-killed larvae. To study the relative proportion of the three genotypic variants throughout successive passages, S. exigualarvae were originally infected with a viral inoculum containing a 1:1:1 mixture of the three genotypes. After three successive passages, US2D was no longer detected in either of the three replicate experiments performed, while US2A was the predominant genotype in all of them, and US2F remained at similar proportions throughout the three passages. The influence of the phenotypic characteristics of the three variants on their relative proportions in mixed infections is discussed.