The selection of lactose-utiljzing,polysaccharide-producing strains ofXanthomonas campestris

Summary A procedure was developed to discriminate between singleXanthomonas campestris colony isolates which differed in growth form on solid media and in viscosity production in liquid media. The method was used to assess degree of variability between colonies and between successive generations of isolates chosen for industrial application.     

Use of the method of enriching of soil samples with calcium carbonate for isolation of Actinomyces

Possible application of a modified procedure for treatment of soil samples with calcium carbonate under humid conditions to isolation of actinomycetes was studied. The procedure proved to be rather efficient in regard to increasing the number of the isolates including representatives of rare genera as compared with the routine methods. The number of microorganisms isolated from the soil samples treated with calcium carbonate under humid conditions was 2 orders higher than that from untreated soil samples. 1033 actinomycete cultures were isolated from the soil samples treated in accordance with the above procedure and only 597 cultures were isolated from the untreated soil samples. The antibiotic activity of the isolates was studied and their taxonomic position at the genus level was determined. The preliminary treatment of soil samples equally stimulated development of actinomycetes belonging to different genera. It is advisable that the described procedure for isolation of actinomycetes from soil samples in screening of cultures producing new antibiotics be used in combination with other selective methods of isolation.     

Nutritionally limited pectinolytic bacteria from the human intestine.

A selective procedure was used to isolate pectinolytic intestinal bacteria from human subjects. The three isolates with the greatest pectinolytic activity utilized pectin and a few related compounds as fermentable substrates for growth but did not utilize any other compound tested. Thus, their substrate utilization pattern was markedly different from that of previously described intestinal pectinolytic isolates. The three isolates are representatives of a nutritionally defined group of bacteria for which the term pectinophilic is proposed.     

Nutritionally limited pectinolytic bacteria from the human intestine

A selective procedure was used to isolate pectinolytic intestinal bacteria from human subjects. The three isolates with the greatest pectinolytic activity utilized pectin and a few related compounds as fermentable substrates for growth but did not utilize any other compound tested. Thus, their substrate utilization pattern was markedly different from that of previously described intestinal pectinolytic isolates. The three isolates are representatives of a nutritionally defined group of bacteria for which the term pectinophilic is proposed.     

Screening of xylanolytic bacteria using a colour plate method

A simple procedure is described for the screening and isolation of xylanolytic bacteria, able to degrade hemicellulose. Bagasse hemicellulose was purified, cross-linked with green dye for use as indicator, and used in a Petri dish assay for the determination of xylanolytic activity. Hydrolysis of the substrate causes the formation of transparent halos around bacterial colonies. The screening procedure was used to select thermoresistant bacteria. The four best isolates were characterized and classified as Bacillus species.     

Direct plating procedure for enumerating Vibrio vulnificus in oysters (Crassostrea virginica).

A procedure for enumerating and identifying Vibrio vulnificus in oysters was developed and evaluated. This method consists of growth on a direct plating medium (VVE medium) for isolating the organism from shellfish tissues, followed by biochemical tests for differentiating and identifying presumptively positive isolates. Densities of V. vulnificus are reliably obtained in 2 to 4 days, and as few as 10 culturable cells per 100 g can be identified. The procedure was evaluated by using a DNA probe technique specific for the cytotoxin-hemolysin gene of V. vulnificus and gas chromatographic analysis of the fatty acid contents of positive isolates. Only 3.2 and 0.4% of the isolates gave false-positive and false-negative results, respectively. The average level of recovery on VVE medium for 33 strains, including both clinical and environmental isolates, was 92% of the level of recovery obtained with brain heart infusion agar supplemented with 1% NaCl. The densities of V. vulnificus in oyster homogenates and individual oysters harvested from gulf and Atlantic coastal waters revealed that seasonally high levels occurred. The VVE medium procedure facilitated enumeration of this pathogen in molluscan shellfish and had a distinct advantage over the widely used most-probable-number procedure for V. vulnificus enumeration, which requires 5 to 7 days and often gives improbable and imprecise results.     

The use of S1 nuclease treatment of hybrid PCR products for the differentiation between PVY isolates

A new strategy based on treating PCR hybrids with S1 nuclease was used to differentiate between two PVY isolates. Mixed denatured and annealed hybrid PCR products of two PVY isolates including a tested strain and a reference N strain were treated with S1 nuclease. Single-stranded mismatched regions were revealed by the S1 nuclease cleavage, yielding a characteristic pattern of bands in polyacrylamide gel by which virus isolates could be matched. Sequence analysis of the relevant PCR products revealed that only part of the mismatched regions were cleaved by the S1 nuclease. Still, the distinct pattern of degradation products enabled the differentiation between the PVY isolates. The general application of this procedure for strain differentiation is discussed.     

High presence of extended-spectrum beta-lactamases and resistance to quinolones in clinical isolates of Escherichia coli

A study was conducted to detect the presence of extended-spectrum β-lactamases (ESBLs) in 706 isolates of Escherichia coli, largely from outpatients (75.2%). The Clinical and Laboratory Standards Institute (formerly NCCLS)-recommended disk diffusion procedure was used to detect ESBL presence; the VITEK 2 system (bioMérieux, Marcy L’Etoile, France) was used to determine the susceptibility to antibiotics of clinical interest, and the ESBLs were characterized by biochemical study, determining the isoelectric point, and by molecular study with PCR. Clonal distribution was studied in eight hospital isolates. There were 115 ESBL-producing isolates (16.3%), with a predominance of CTX-M9 type (58.3%). We draw attention to the high resistance to quinolones (>70%) in CTX-M9 and SHV enzyme producing isolates and the lower aminoglycoside activity in the latter.     

Rapid screening procedure for detection of plasmids in streptococci.

An enrichment procedure, yielding plasmid deoxyribonucleic acid preparations normally containing less than 5% chromosomal contamination, has been devised for the isolation of plasmids from virtually all species of streptococci. The procedure is rapid, reproducible, and inexpensive, requiring no radioisotopes or density gradient centrifugation. The procedure can be used for routine screening of several hundred isolates in a short period of time, and plasmids obtained from 10- to 20-ml cultures can readily be visualized in agarose gels.     

A rapid pulsed-field gel electrophoresis method of genotyping Haemophilus parasuis isolates

Aims: To develop a modified pulsed‐field gel electrophoresis (PFGE) method for characterizing Haemophilus parasuis isolates. Methods and Results: A modified PFGE procedure was designed using CpoI to generate restriction maps of H. parasuis genomic DNA. This approach was used to characterize 47 H. parasuis clinical isolates and 15 reference strains. All strains could be typed by this method, and the procedure was completed in 36 h. A total of 39 different PFGE patterns were identified among 47 epidemiologically unrelated clinical isolates. Conclusions: The modified PGFE described in this report efficiently characterized H. parasuis isolates. This method can be adopted for studying the epidemiology of Glässer’s disease outbreaks in addition to differentiating and classifying previously untypeable H. parasuis isolates. Significance and Impact of the Study: The modified PFGE method described is a novel means of characterizing H. parasuis isolates. It is also a highly discriminatory molecular typing method (discriminatory index of 0·98) that can overcome the limitations of serotyping.     

Application of Random Amplified Polymorphic DNA analysis to differentiate strains of Salmonella typhi and other Salmonella species

A Random Amplified Polymorphic DNA (RAPD) fingerprinting method was developed to differentiate isolates of Salmonella serotype typhi ( S. typhi ) and other Salmonella isolates. A panel of five primers was used to examine 63 isolates of Salm. typhi , including 56 strains isolated in Taiwan and seven strains obtained abroad. Twenty-one RAPD types were revealed using the RAPD fingerprinting method. An RAPD with primer 6032 yielded a polymorphism in a 350 bp fragment that differentiated the attenuated vaccine strain Salm. typhi Ty21a from the rest of the Salm. typhi strains. Strains of Salm. typhi were divided into five types with primer D14307. Primer D14307 also proved capable of discrimination among 65 other Salmonella isolates representing 42 different serotypes. The bacterial DNA used in this RAPD protocol was obtained using a commercially available DNA extraction kit (GeneReleaser). The DNA of various strains of Salmonella from this simple extraction procedure could be discriminated within a few hours using the RAPD technique.     

Continued Surveillance of Serratia marcescens Infections by Bacteriocin Typing: Investigation of Two Outbreaks of Cross-Infection in an Intensive Care Unit

During an 8.5-month period, 198 additional isolates of Serratia marcescens were typed by bacteriocin sensitivity; 154 isolates were typable and were categorized according to our current system of 54 provisional bacteriocin sensitivity patterns. Two outbreaks of nosocomial infection due to S. marcescens occurred in our intensive care unit, involving two and five patients, respectively. The latter outbreak was caused by a strain of S. marcescens which was not sensitive to any of the 10 bacteriocins normally used. Therefore we developed a supplementary procedure based on bacteriocin production rather than bacteriocin sensitivity. Bacteriocin production was induced with mitomycin C, and the crude lysates were applied to 15 provisional bacteriocin indicator strains. The reverse typing procedure was necessary to determine the spread and ultimate subsidence of this particular outbreak of cross-infection.     

Serological identification of group D streptococci using commercial antisera

Three commercial group D streptococcal antisera were tested for the serological identification of 100 group D enterococci; 20 Streptococcus bovis; 5 isolated from each of the following streptococcal groups: A, B, C and G; and 3 isolates from serological group F. Antisera from Difco Laboratories, BBL, and Wellcome Reagents Limited were used in the classic capillary tube precipitin test on extracts prepared using the Rantz and Randall procedure. No false positive precipitin reactions were observed. Of the enterococcal isolates, all 100 reacted with the Wellcome, 99 reacted with the BBL, and 96 reacted with the Difco group D antisera. However, of the 20 S. bovis isolates, only 2 reacted with the BBL, and 1 reacted with both the Difco and the Wellcome antisera. Each antiserum was then used to prepare staphylococcal coagglutination (CoA) reagents and each isolate was subsequently tested. A simple extraction procedure was performed by suspending colonies of an isolate in a loopful of salin on a microscope slide and gently heating the slide directly in the flame of a Bunsen burner. All 100 enterococci and all 20 S. bovis gave positive results with the BBL and the Wellcome CoA reagents. Using the Difco reagent, 2 S. bovis isolates failed to produce postitive results. No false positive results were observed with the non-Group D isolates. Our results indicate that the CoA technique using commercial group D antisera may provide faster and sometimes more sensitive serological identification than the classic capillary tube precipitin test.     

Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces

For the detection and identification of predominant bacteria in human feces, 16S rRNA-gene-targeted group-specific primers for the Bacteroides fragilis group, Bifidobacterium, the Clostridium coccoides group, and Prevotella were designed and evaluated. The specificity of these primers was confirmed by using DNA extracted from 90 species that are commonly found in the human intestinal microflora. The group-specific primers were then used for identification of 300 isolates from feces of six healthy volunteers. The isolates were clearly identified as 117 isolates of the B. fragilis group, 22 isolates of Bifidobacterium, 65 isolates of the C. coccoides group, and 17 isolates of Prevotella, indicating that 74% of the isolates were identified with the four pairs of primers. The remaining 79 isolates were identified by 16S ribosomal DNA sequence analysis and consisted of 40 isolates of Collinsella, 24 isolates of the Clostridium leptum subgroup, and 15 isolates of disparate clusters. In addition, qualitative detection of these bacterial groups was accomplished without cultivation by using DNA extracted from the fecal samples. The goal for this specific PCR technique is to develop a procedure for quantitative detection of these bacterial groups, and a real-time quantitative PCR for detection of Bifidobacterium is now being investigated (T. Requena, J. Burton, T. Matsuki, K. Munro, M. A. Simon, R. Tanaka, K. Watanabe, and G. W. Tannock, Appl. Environ. Microbiol. 68:2420-2427, 2002). Therefore, the approaches used to detect and identify predominant bacteria with the group-specific primers described here should contribute to future studies of the composition and dynamics of the intestinal microflora.     

Classification ofVibrio vulnificusStrains by the Carbohydrate Composition of Their Capsular Polysaccharides

Pathogenic bacteria are often classified on the basis of the complex polysaccharides found on the surface, usually capsular polysaccharides or lipopolysaccharides. It is common in clinical practice to use reactivity with antisera specific to the various cell surface carbohydrates for this purpose. In this work, we describe a chemotyping method for bacterial capsular polysaccharides which is based on a carbohydrate analysis of an acid hydrolysate of the capsule. High-performance anion-exchange chromatography at high pH (HPAE) with electrochemical detection, which is used for analysis of the hydrolysate, shows preferential sensitivity for sugars. A single acid hydrolysis condition is chosen for screening a large collection of bacterial isolates and a computerized autosampler is used to make possible a large number of rapid analyses. This procedure does not yield a quantitative carbohydrate analysis for the sample but produces a fingerprint which can be used to discriminate among isolates which have different capsular polysaccharide structures. The procedure has been applied to a collection of 120 isolates ofVibrio vulnificus,a water-born species common in shellfish which causes septicemia in immunocompromised individuals, most often from eating of raw oysters. The collection of bacterial isolates includes strains from both clinical cases of septicemia and from such environmental sources such as sea water, sediments, and shellfish. Our results show that a number of unusual sugars including many amino sugars are found in these polysaccharides and that a wide variety of capsular carbotypes inV. vulnificusmay be readily distinguished by the HPAE fingerprint.     

The clones of Listeria monocytogenes detected in food depend on the method used

S. LONCAREVIC, W. THAM AND M.-L. DANIELSSON-THAM. 1996. Restriction enzyme analysis (REA) with pulsed-field gel electrophoresis (PFGE) has been used to characterize and compare Listeria monocytogenes strains isolated from foods by two methods, an enrichment procedure and a direct plating procedure. In total 151 isolates from nine foods were investigated. In six of the foods (101 strains investigated) only one clone of L. monocytogenes was found irrespective of the method used. In three foods (50 strains investigated) the direct plating procedure yielded more clones than the enrichment procedure. At the most, five clones were detected in the same food. The results presented here indicate that direct plating from the food reveals more L. monocytogenes clones than revealed by an enrichment procedure.     

Interfertility and genetic variability among European and North American isolates of the basidiomycete fungus Chondrostereum purpureum

The conspecificity of Finnish and western Canadian isolates of the decay fungus Chondrostereum purpureum was investigated by several approaches, including the assessment of genetic variability, mating and progeny analysis, and the analysis of selected phenotypic traits. Eight second-generation single spore strains per fungal isolate pairing were investigated with specific genetic markers developed for both Finnish and Canadian parental isolates. Tests of linkage disequilibrium were used to analyze whether these markers assorted independently among single spore strains. This procedure was similarly applied to the third-generation spore progeny. Finally, global non-metric multidimensional scaling was used to analyze independent random amplified microsatellite marker data to assess the genetic variability of the parental Finnish and Canadian isolates, and their second- and third-generation progeny. Our results revealed that the parental isolates from Finland and western Canada were genetically divergent, but no interfertility barriers were identified between these geographically distant fungi. Furthermore, parental genetic markers used in mating studies demonstrated that second- and third-generation spore progenies underwent normal meiosis and genetic recombination without linkage disequilibrium. Based on this work, the studied C. purpureum isolates from Finland and Canada can be considered as belonging to a single biological species, although genetic and limited phenotypic differentiation was observed.     

Morphological, Biochemical and Molecular Characterization of Trichoderma harzianum Isolates for their Efficacy as Biocontrol Agents

The random amplified polymorphic DNA (RAPD) procedure was used to examine the genetic variability among 8 isolates of Trichoderma harzianum , and their ability to antagonize Sclerotium rolfsii using a dual culture assay was correlated with RAPD profiles. Eight oligodeoxynucleotide primers were selected for the RAPD assays, which resulted in 86 bands for 8 isolates of T . harzianum . The data were entered into a binary matrix and a similarity matrix was constructed using the DICE similarity (SD) index. An unweighted pair grouping mathematical averaging (UPGMA) cluster based on SD values was generated using the NTSYS computer program. A mean coefficient of similarity obtained for pairwise comparisons was c. 30% and it showed that the variability among the isolates of T. harzianum was very high. Using the dual culture method in antagonism experiments, the T. harzianum isolates were classified in to antagonism classes. Further, T. harzianum isolates were screened for chitinase and β-1,3-glucanase activity. RAPD was efficient in demonstrating the high intraspecific genetic variation among isolates. The dendrogram did not show the grouping of isolates by their level of antagonism. Relationship among polymorphism existent, the aggressiveness and the origin of isolates were not found.     

Dual tropism for macrophages and lymphocytes is a common feature of primary human immunodeficiency virus type 1 and 2 isolates.

We have investigated the ability of human immunodeficiency virus type 1 (HIV-1) and HIV-2 isolates to infect and replicate in primary human macrophages. Monocytes from blood donors were allowed to differentiate into macrophages by culture in the presence of autologous lymphocytes and human serum for 5 days before infection. A panel of 70 HIV-1 and 12 HIV-2 isolates were recovered from seropositive individuals with different severities of HIV infection. A majority of isolates (55 HIV-1 and all HIV-2) were obtained from peripheral blood mononuclear cells, but isolates from cerebrospinal fluid, monocytes, brain tissue, plasma, and purified CD4+ lymphocytes were also included. All isolates were able to infect monocyte-derived macrophages, even though the replicative capacity of the isolates varied. Interestingly, isolates with a rapid/high, syncytium-inducing phenotype did not differ from slow/low, non-syncytium-inducing isolates in their ability to replicate in monocyte-derived macrophages. Others have reported that rapid/high, syncytium-inducing isolates have a reduced ability to infect and replicate in monocytes. However, different methods to isolate and culture the monocytes/macrophages were used in these studies and our study. Thus, the ability of HIV isolates to replicate in monocytes/macrophages appears to be strongly influenced by the isolation and culture procedures. It remains to be determined which culture procedure is more relevant for the in vivo situation.