Multiple enzyme restriction fragment length polymorphism analysis for high resolution distinction of Pseudomonas (sensu stricto) 16S rRNA genes

Members of the genus Pseudomonas (sensu stricto) are important phytopathogens and agents of human infections, while other strains and species have beneficial bioremediation and biocontrol activities. Traditionally, these important species have been difficult to differentiate phenotypically; thus, rRNA lineage analyses have often been invoked. In this report, a newly developed approach is described to rapidly detect and distinguish fluorescent Pseudomonas isolates: PCR amplification of a Pseudomonas-specific 990-bp ribosomal RNA gene (rDNA) fragment [Appl. Environ. Microbiol. 64 (1998) 2545.] coupled with multiple enzyme restriction fragment length polymorphism (MERFLP) analysis using a single digestion mixture of AluI, HinfI, RsaI, and Tru9I incubated at 37 degrees C. The method distinguished 116 published sequences and 47 reference strains of authentic Pseudomonas representing 28 nomenspecies. A total of 55% (64/116) of the sequences analyzed by MERFLP were grouped into distinct phylogenetic clusters including Pseudomonas putida, P. syringae, P. aeruginosa, P. stutzeri, and P. fluorescens. The utility of the MERFLPs was confirmed when 100% (33/33) of the above named control reference strains were correctly placed into their phylogenetic clusters. The environmental relevance of the MERFLP method was confirmed when 67% of 28 forest and agricultural soil-derived presumptive Pseudomonas environmental clones and isolates were placed into the five major pseudomonad clusters, one clone fell into the P. agarici cluster, and five clones clustered near related pseudomonads. These data demonstrated that the PCR-MERFLP protocol provides an efficient and powerful tool for distinguishing isolates and rDNA gene libraries of environmental Pseudomonas species.     

Molecular epidemiology of clinical and environmental isolates of the Cryptococcus neoformans species complex reveals a high genetic diversity and the presence of the molecular type VGII mating type a in Colombia

The aim of this study was to investigate the epidemiological relationships of clinical and environmental isolates of the Cryptococcus neoformans species complex in Colombia. The current study reflects data from 1987 to 2004. In Colombia serotypes A and B are most frequently recovered from patients and the environment. Of the 178 clinical isolates studied, 91.1% were of serotype A, 8.4% serotype B and 0.5% serotype C. Of the 247 environmental isolates, 44.2% were of serotype A, 42.6% serotype B and 13.2% serotype C. No serotype D isolates were isolated. Serotype AD has not been recovered in Colombia. PCR fingerprinting with the primers M13, (GACA)4 and (GTG)5 and URA5 gene restriction fragment length polymorphism analysis grouped the majority of clinical serotype A and environmental serotype B isolates into the molecular types VNI (98.1%) and VGII (100%), respectively. Mating type alpha was determined in 99.3% of serotype A isolates, but 96.6% of serotype B isolates were of mating type a. Similar profiles between clinical and environmental isolates suggest that the patients may have acquired the infection from the environment. The data presented form part of the Colombian contribution to the ongoing global survey of the C. neoformans species complex.     

Molecular comparative studies among Blastocystis isolates obtained from humans and animals

This study compared specific polymerase chain reaction (PCR) primers and phylogenetic tree analysis of restriction fragment length polymorphism using the small subunit ribosomal RNA gene in various Blastocystis populations. A phylogenetic tree was constructed using 12 restriction enzymes and a sample pool of 22 isolates, including 2 reference strains and Proteromonas lacertae as an outgroup. The analysis showed that the 22 isolates could be separated into 7 clusters. Four of the 7 clusters were mixed groups that comprised isolates from both humans and nonhuman hosts. The other 3 clusters contained isolates from humans or nonhuman hosts only. The phylogenetic analysis also showed that B. hominis isolates from geographical separated areas did not necessarily cluster in the genetically different groups. The results of genetic homology and phylogenetic tree analysis among Blastocystis isolates from humans and animals indicated that all isolates from animals appear to be B. hominis. Polymerase chain reaction amplifications using previously described and newly defined specific primers mirrored the clusters obtained by the phylogenetic tree analysis. Our results show that primer PCR can be used as a powerful tool for the typing of Blastocystis populations.     

Genetic characterization of Legionella pneumophila serogroup 1 associated with respiratory disease in Australia.

Techniques were developed for genetic characterization of Legionella pneumophila serogroup 1 by using restriction fragment length polymorphism analysis. Allozyme analysis provided an index of the discrimination achieved by restriction fragment length polymorphism. Isolates from human cases of legionellosis were examined by both methods, and their profiles were compared with reference strains of L. pneumophila serogroup 1 obtained from the American Type Culture Collection. Eighteen distinct clones were evident among the isolates examined. Both methods could be used to trace the source of an outbreak of legionellosis caused by L. pneumophila serogroup 1.     

Genetic characterization of Legionella pneumophila serogroup 1 associated with respiratory disease in Australia.

Techniques were developed for genetic characterization of Legionella pneumophila serogroup 1 by using restriction fragment length polymorphism analysis. Allozyme analysis provided an index of the discrimination achieved by restriction fragment length polymorphism. Isolates from human cases of legionellosis were examined by both methods, and their profiles were compared with reference strains of L. pneumophila serogroup 1 obtained from the American Type Culture Collection. Eighteen distinct clones were evident among the isolates examined. Both methods could be used to trace the source of an outbreak of legionellosis caused by L. pneumophila serogroup 1.     

Horizontal gene transfer of a genetic island encoding a type III secretion system distributed in Vibrio cholerae

Twelve Vibrio cholerae isolates with genes for a type III secretion system (T3SS) were detected among 110 environmental and 14 clinical isolates. T3SS‐related genes were distributed among the various serogroups and pulsed‐field gel electrophoresis of NotI‐digested genomes showed genetic diversity in these strains. However, the restriction fragment length polymorphism profiles of the T3SS‐related genes had similar patterns. Additionally, naturally competent T3SS‐negative V. cholerae incorporated the ca. 47 kb gene cluster of T3SS, which had been integrated into a site on the chromosome by recombination. Therefore, it is suggested that horizontal gene transfer of T3SS‐related genes occurs among V. cholerae in natural ecosystems.     

Restriction fragment length polymorphism of 16S-23S rDNA intergenic spacer of Aeromonas spp

We analyzed restriction fragment length polymorphism (RFLP) of 16S-23S rDNA intergenic spacer region (ISR) of Aeromonas species. A total of 69 isolates belonging to 18 DNA hybridization groups (HG; equivalent of genomic species) were used in this study. ISRs were amplified by PCR and the products were digested with four restriction endonucleases: Hin6I, Csp6I, TaqI, and TasI. The RFLP patterns obtained after digesting by particular enzymes revealed ISR polymorphism of isolates allocated to individual genomic species. The combined Hin6I, Csp6I, TaqI, and TasI restriction profiles were examined by Dice coefficient (SD) and unweighted pair group method of clustering (UPGMA). The isolates were allocated into 15 groups, three strains were unclustered. The strains belonging to the following genomic species: A. hydrophila, A. bestiarum, A. salmonicida, A. caviae, A. media, A. schubertii, A. allosaccharophila, A. popoffii, and A. culicicola formed distinct clusters. Strains belonging to HG 6, HG 7, HG 11, and HG 16 revealed similar combined RFLP patterns and constituted one group. Similarly, the strains of A. jandaei (HG 9) and the type strain of A. trota were allocated into one cluster. Two isolates of HG 14 formed distinct cluster. We noticed a genetic diversity among A. veronii isolates, the strains were clustered in two groups. Our study showed that combined ISR-RFLP analysis may be used for identification of some species of Aeromonas.     

Ribotyping and TCP gene cluster analysis of environmental and clinical Vibrio cholerae strains isolated in Iran

The aim of this study was to investigate the presence of TCP gene clusters among clinical and environmental Vibrio cholerae isolates and to explore the genetic relatedness of isolates using ribotyping technique. A total of 50 V. cholerae strains (30 clinical and 20 environmental) were included in this study. Three clinical isolates were negative for TCP cluster genes while the cluster was absent in all of the environmental strains. Ribotyping of rRNA genes with BglI produced 18 different ribotype patterns, three of which belonged to clinical O1 serotype isolates. The remaining 15 ribotypes belonged to clinical non-O1, non-O139 serogroups (two patterns) and environmental non-O1, non-O139 serogroups (13 patterns). Clinical V. cholerae O1 strains from 2004 through 2006 and several environmental non-O1, non-O139 V. cholerae strains from 2006 showed 67.3 % similarity and fell within one single gene cluster. Ribotyping analysis made it possible to further comprehend the close originality of clinical isolates as very little changes have been occurred within rRNA genes of different genotypes of V. cholerae strains through years. In conclusion, ribotyping analysis of environmental V. cholerae isolates showed a substantial genomic diversity supporting the fact that genetic changes within bacterial genome occurs during years in the environment, while only little changes may arise within the genome of clinical isolates.     

Response of Estuarine Biofilm Microbial Community Development to Changes in Dissolved Oxygen and Nutrient Concentrations

The information content and responsiveness of microbial biofilm community structure, as an integrative indicator of water quality, was assessed against short-term changes in oxygen and nutrient loading in an open-water estuarine setting. Biofilms were grown for 7-day periods on artificial substrates in the Pensacola Bay estuary, Florida, in the vicinity of a wastewater treatment plant (WWTP) outfall and a nearby reference site. Substrates were deployed floating at the surface and near the benthos in 5.4 m of water. Three sampling events covered a 1-month period coincident with declining seasonal WWTP flow and increasing dissolved oxygen (DO) levels in the bottom waters. Biomass accumulation in benthic biofilms appeared to be controlled by oxygen rather than nutrients. The overriding effect of DO was also seen in DNA fingerprints of community structure by terminal restriction fragment length polymorphism (T-RFLP) of amplified 16S rRNA genes. Ribotype diversity in benthic biofilms at both sites dramatically increased during the transition from hypoxic to normoxic. Terminal restriction fragment length polymorphism patterns showed pronounced differences between benthic and surface biofilm communities from the same site in terms of signal type, strength, and diversity, but minor differences between sites. Sequencing of 16S rRNA gene clone libraries from benthic biofilms at the WWTP site suggested that low DO levels favored sulfate-reducing prokaryotes (SRP), which decreased with rising oxygen levels and increasing overall diversity. A 91-bp ribotype in the CfoI-restricted 16S rRNA gene T-RFLP profiles, indicative of SRP, tracked the decrease in relative SRP abundance over time.     

Determination of genetic diversity among Indian isolates of Rhizoctonia bataticola causing dry root rot of chickpea

Genetic diversity among 27 isolates (23 from chickpea and 4 from other host crops) of Rhizoctonia bataticola representing 11 different states of India was determined by random amplified polymorphic DNA (RAPD), internal transcribed spacer restriction fragment length polymorphism (ITS-RFLP) and ITS sequencing. The isolates showed variability in virulence test. Unweighted paired group method with arithmetic average cluster analysis was used to group the isolates into distinct clusters. The clusters generated by RAPD grouped all the isolates into six categories at 40% genetic similarity. High level of diversity was observed among the isolates of different as well as same state. Some of the RAPD (OPN 4, OPN 12, and OPN 20) markers clearly distinguished majority of the isolates into the area specific groups. The ITS I, 5.8rDNA and ITS II regions of 11 isolates representing different RAPD groups were amplified with primers ITS 1 and ITS 4 and digested with seven restriction enzymes. The restriction enzymes DraI, MboI, RsaI, and AluI were found to be suitable for differentiating the isolates into five categories by showing isolate specific ITS-RFLP patterns. The isolates were variable in their nucleotide sequences of the ITS regions. This is the first study on genetic diversity among chickpea isolates of R. bataticola.     

Molecular characterization of Korean Bacillus anthracis isolates by amplified fragment length polymorphism analysis and multilocus variable-number tandem repeat analysis

We analyzed the genetic relationships and molecular characteristics of 34 Bacillus anthracis isolates from soil and clinical samples in various regions of Korea and 17 related Bacillus species, using the amplified fragment length polymorphism (AFLP) and multilocus variable-number tandem repeat (MLVA) approaches. Triplicate AFLP profiles of these strains showed high reproducibility and identified 376 polymorphisms. AFLP phylogenetic analysis of B. anthracis isolates showed a high level of similarity, 0.93, and this monomorphic fragment profile proved to be useful to differentiate B. anthracis strains from other Bacillus species. The B. cereus group was separated from other Bacillus species at a level of similarity of 0.68. Among them, some B. cereus strains showed genetic interspersion with B. thuringiensis strains. The evolutionary pattern of nucleotide differences among B. anthracis strains with the eight MLVA markers showed nine MLVA types. Three MLVA types, M1 to M3, were pathogenic B. anthracis isolates and were assigned as new genotypes belonging to the A4 and B3 clusters, compared with 89 genotypes deduced from previous data. This indicates that differences in cluster prevalence and distribution may be influenced more by MLVA markers on two plasmids loci and human activity. Consequently, we suggest that the novel MLVA type may represent significant evidence for historic adaptation to environmental conditions of the Asian continent, particularly Korea. Therefore, MLVA techniques may be available for molecular monitoring on anthrax-release-related bioterrorism and further study is required for the continuous epidemiological study of variable anthrax collections.     

Molecular Characterization of Mycobacterium avium Complex Isolates from Caribbean Patients by DT1/DT6-PCR,Nonradioactive Southern Hybridization,and the Accuprobe System

A genetic fingerprinting analysis of Caribbean isolates of M. avium complex (MAC) from AIDS patients by a Southern blotting technique after Pstl digestion with nonradioactive DNA probes coding for single-copy sequences DT1 and DT6 was performed. In parallel, a selective amplification of a 187-bp fragment within the DT6 sequence with AV6/AV7 primers for Mycobacterium avium and of a 666-bp fragment within the DT1 sequence of M. intracellulare with the IN38/IN41 primers was also performed, and the molecular speciation with these two methods was compared with results obtained with DNA probes of the Accuprobe system. 66 strains investigated comprised 31 international reference isolates of MAC belonging to serovars 1–28 and 42–44, and 35 clinical isolates including 24 strains from Caribbean AIDS patients. 91.43% of the clinical isolates tested gave concordant data with the DT1/DT6 Southern hybridization and PCR as compared with 74.28% for PCR and Accuprobe, and 71.43% for Accuprobe and Southern hybridization. Our results corroborated previous findings showing that the DT1 probe was specific for M. intracellulare, whereas the DT6 probe was specific for M. avium (reference serovars 2 and 3 probed positive both with DT1 and DT6 probes). Contrary to DT1 probe, which did not reveal sufficient polymorphism to discriminate between MAC isolates, DT6 probe showed an interesting polymorphism giving four distinct clusters. Three clusters corresponded to profiles previously reported for reference and/or clinical isolates; however, a fourth cluster was discovered in five Caribbean isolates from four AIDS patients that did not correspond to previously published genetic patterns. When probed with the insertion sequence IS1245, this cluster retained its homogeneity. Received: 9 May 1996 / Accepted: 10 June 1996     

Typing of clinical and environmental Aeromonas veronii strains based on the 16S-23S rDNA spacers

Genetic relationships of Aeromonas veronii strains isolated from human and environmental sources were investigated by restriction fragment length polymorphism (RFLP) of the polymerase chain reaction-amplified intergenic spacer region (ISR) flanked by the 16S and 23S rRNA genes. When using endonucleases AluI, HinfI and CfoI the 16S-23S rDNA-RFLP patterns showed considerable overall similarity, although most strains yielded specific profiles. Several intra-specific lines of descent comprised clinical strains linked to isolates from environmental sources. Strains having identical patterns may be individuals derived from highly similar, if not the same, microorganism. Results suggest that the ISR sequence-based method can be used to demonstrate colonization of a public water supply with a particular microorganism. In addition it could be very useful for tracing recurrent episodes of diarrhea and Aeromonas infection outbreaks.     

Epidemiology of Salmonella sofia in Australia.

In recent years, the incidence of isolation of Salmonella sofia in Australia has risen from 33% of all poultry isolates in 1982 to a peak of 49% of isolates in 1988. A parallel rise has not been seen in S. sofia isolated from humans. In Israel, however, S. sofia has been commonly isolated from both humans and poultry. We investigated the possibility that the Israeli strains may belong to a different clonal group and express virulence determinants not seen in the Australian isolates, accounting for the apparent differences in the virulence seen within this species. A number of S. sofia isolates from Australian chickens and humans, as well as from Israeli humans and chickens, were compared by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of outer membrane proteins, plasmid profiles, and restriction fragment length polymorphism analysis. No reproducible differences could be detected by analysis of outer membrane proteins. A small 6.4-kb plasmid, pIMVS2, was detected in all Australian isolates from chickens but not in the Israeli isolates. Restriction fragment length polymorphism studies with cosmid clones as probes provided the most discrimination among isolates, allowing us to divide them into seven groups. This technique revealed that significant differences exist between Australian and Israeli isolates and provided additional insights into the epidemiology of these Salmonella isolates.     

Epidemiology of Salmonella sofia in Australia.

In recent years, the incidence of isolation of Salmonella sofia in Australia has risen from 33% of all poultry isolates in 1982 to a peak of 49% of isolates in 1988. A parallel rise has not been seen in S. sofia isolated from humans. In Israel, however, S. sofia has been commonly isolated from both humans and poultry. We investigated the possibility that the Israeli strains may belong to a different clonal group and express virulence determinants not seen in the Australian isolates, accounting for the apparent differences in the virulence seen within this species. A number of S. sofia isolates from Australian chickens and humans, as well as from Israeli humans and chickens, were compared by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of outer membrane proteins, plasmid profiles, and restriction fragment length polymorphism analysis. No reproducible differences could be detected by analysis of outer membrane proteins. A small 6.4-kb plasmid, pIMVS2, was detected in all Australian isolates from chickens but not in the Israeli isolates. Restriction fragment length polymorphism studies with cosmid clones as probes provided the most discrimination among isolates, allowing us to divide them into seven groups. This technique revealed that significant differences exist between Australian and Israeli isolates and provided additional insights into the epidemiology of these Salmonella isolates.     

Characterization of Phytophthora cinnamomi populations from ornamental plants in South Carolina,USA

Abstract

Fifty-one isolates of Phytophthora cinnamomi isolated from ornamental plants in South Carolina, USA, between 1995 and 2000 were characterized by sporangium morphology, mating type, sensitivity to the fungicide mefenoxam, fatty acid methyl ester (FAME) profile analysis, and amplified fragment length polymorphism (AFLP) analysis. Sporangium shapes were predominantly ovoid to ellipsoid, and size averaged 65.5×40.3 μm (length×breadth) with average length/breadth ratio of 1.6. Forty-nine isolates were the A2 mating type with only two A1 isolates found. This is the first report of the A1 mating type of P. cinnamomi in South Carolina. All isolates were sensitive to mefenoxam and EC₅₀ values for all isolates were less than 0.2 μg ml^?1. FAMEs of each isolate were analysed by gas chromatography and revealed five major fatty acids: myristic (14:0), palmitic (16:0), linoleic (18:2ω6c), oleic (18:1ω9c), and eicosapentaenoic (20:5ω3c) acids. These five fatty acids accounted for more than 80% of FAME profiles. Cluster analysis of FAME profiles showed that individual isolates had unique pattern that could be divided into four major clusters. AFLP analysis based on 200 informative loci also separated isolates into four major clusters. A1 isolates were different from all A2 isolates. The percentage of polymorphic loci (10.5%) and Nei's gene diversity (0.0435) were much higher for the two A1 isolates than for any cluster of A2 isolates even though A2 isolates had more isolates within a cluster. A2 isolates exhibited relatively little genetic variation overall, which suggests that these isolates may have come from a common source.     

Molecular and phenotypic characterization of Pseudomonas spp. isolated from milk

Putative Pseudomonas spp. isolated predominantly from raw and processed milk were characterized by automated ribotyping and by biochemical reactions. Isolates were biochemically profiled using the Biolog system and API 20 NE and by determining the production of proteases, lipases, and lecithinases for each isolate. Isolates grouped into five coherent clusters, predominated by the species P. putida (cluster A), P. fluorescens (cluster B), P. fragi (as identified by Biolog) or P. fluorescens (as identified by API 20 NE) (cluster C), P. fragi (as identified by Biolog) or P. putida (as identified by API 20 NE) (cluster D), and P. fluorescens (cluster E). Isolates within each cluster also displayed similar enzyme activities. Isolates in clusters A, C, and D were generally negative for all three enzyme activities; isolates in cluster B were predominantly positive for all three enzyme activities; and isolates in cluster E were negative for lecithinase but predominantly positive for protease and lipase activities. Thus, only isolates from clusters B and E produced enzyme activities associated with dairy product flavor defects. Thirty-eight ribogroups were differentiated among the 70 isolates. Ribotyping was highly discriminatory for dairy Pseudomonas isolates, with a Simpson's index of discrimination of 0.955. Isolates of the same ribotype were never classified into different clusters, and ribotypes within a given cluster generally showed similar ribotype patterns; thus, specific ribotype fragments may be useful markers for tracking the sources of pseudomonads in dairy production systems. Our results suggest that ribogroups are generally homogeneous with respect to nomenspecies and biovars, confirming the identification potential of ribotyping for Pseudomonas spp.     

Biochemical and biological characterization of four isolates of Spodoptera exigua nuclear polyhedrosis virus

Biological and biochemical properties of four nuclear polyhedrosis virus isolates from beet armyworm, Spodoptera exigua, were investigated. The isolates originated from the United States (SeNPV‐US), Thailand (SeNPV‐TH) and from two locations in Spain (SeNPV‐SP1 and SeNPV‐SP2). Restriction endonuclease analysis of the viral genomes revealed limited restriction fragment length polymorphism and indicated that these viruses contained distinct, but closely related, genotypes (variants). One BglII fragment from each isolate can serve as a restriction fragment length polymorphism marker for the identification of each isolate. The estimated genome size of the SeNPVs is approximately 134 kilobase pairs. The mobility profiles of the occluded virion polypeptides and polyhedrins of the four SeNPV isolates were very similar. Staphylococcus aureus V8 digestion of polyhedrin suggested that the polyhedrin from SeNPV‐US is distinct from the polyhedrins of the other isolates. Bioassays of the isolates in second‐instar S. exigua larvae showed that the SeNPV‐TH was the most potent SeNPV for beet armyworm with an LD₅₀ value of only 1.5 polyhedra per second‐instar larva.     

Random amplified polymorphic DNA (RAPD) profiling of Legionella pneumophila

Random amplified polymorphic DNA (RAPD) profiling of Legionella pneumophila by PCR can be used to provide a simple and efficient comparison of clinical and environmental isolates. RAPD profiling is quicker and cheaper to perform than restriction fragment length polymorphism (RFLP) typing, eliminating the need for blotting, hybridization and detection. For some isolates, RAPD profiling is more discriminatory than RFLP typing, being able to distinguish between isolates with identical RFLP types.