Genetic identification of members of the genus Corynebacterium at genus and species levels with 16S rDNA-targeted probes

Exploring the MALDI Biotyper for the Identification of Corynebacterium pseudotuberculosis biovar Ovis and Equi

Biochemical, serological, and molecular methods have been developed for the laboratory diagnosis of diseases caused by C. pseudotuberculosis (CP), but the identification of the pathogen and biovars differentiation may be time-consuming, expensive, and confusing compared with other bacteria. This study aimed to evaluate MALDI Biotyper and Overall Genome Relatedness Index (OGRI) analysis to optimize the identification and differentiation of biovars of C. pseudotuberculosis. Out of 230 strains isolated from several hosts and countries, 202 (87.8%) were precisely classified using MALDI Biotyper and the BioNumerics platform. The classification accuracies for the Ovis and Equi biovars were 80 (88.75%) and 82 (92.68%), respectively. When analyzing a sampling of these strains by Average Nucleotide Identity based on BLAST and TETRA analyses using genomic sequence data, it was possible to differentiate 100% of the strains in Equi and Ovis. Our data show that MALDI Biotyper and OGRI analysis help identify C. pseudotuberculosis at the species and biovar levels.

A PCR for dtxR gene: application to diagnosis of non-toxigenic and toxigenic Corynebacterium diphtheriae

The significant rise in the percentage of adults susceptible to diphtheria and the emergence of non-toxigenic Corynebacterium diphtheriae strains as the causative agent of endocarditis and other systemic infections emphasize the need for alternative laboratory diagnostic procedures. In this study, for the first time, the value of a species-specific PCR assay that targets the dtxR gene is documented as a procedure for differentiating C. diphtheriae from Corynebacterium-like colonies. The results of the PCR-dtxR were all positive for 91 C. diphtheriae (54 non-toxigenic and 37 toxigenic) strains. PCR-dtxR completely correlated with the standard biochemical and commercial identification for all C. diphtheriae strains tested. Conversely, the PCR-dtxR results were negative in 100% of the 111 non-diphtherial Gram-positive rod strains obtained during identification procedures in a hospital laboratory. Thus, the PCR-dtxR assay emerged as viable, cost-effective screening method for C. diphtheriae laboratory identification.

Rapid identification of clinically relevant Nocardia species using real-time PCR with SYBR Green and melting-curve analysis

The objective of this study was to develop and evaluate a rapid new method of identifying clinically relevant Nocardia species. DNA extracted from different Nocardia strains was used in a real-time PCR assay with SYBR Green and melting-curve analysis to identify Nocardia species. Ten control strains and four bacterial strains of closely related genera were employed, and samples from 28 patients were used. All Nocardia strains were identified correctly, and there was no cross-reaction with strains from genera closely related to Nocardia. The sensitivity and specificity of the method were 90 and 100 %, respectively. This method can be used to rapidly detect Nocardia species in culture, without cross-reaction with other closely related genera.

Rapid analysis of two food-borne microbial communities at the species level by Fourier-transform infrared microspectroscopy

The species composition of microbial communities in natural habitats may be extremely complex and therefore a quantitative analysis of the fraction each species contributes to the consortium has proven to be difficult. During recent years, the identification of bacterial pure cultures based on their infrared spectra has been established. Fourier-transform infrared microspectroscopy now proceeds a step further and allows identification of microorganisms directly plated from community dilutions. Infrared spectra of microcolonies of 70-250 microm in diameter can be recorded without producing a pure culture of the isolate. We have applied this novel technique for quantitative comparative analysis of two undefined, geographically separated food-borne smear cheese microbial consortia of limited complexity. Due to the high degree of automation, up to 200 microcolonies could be identified in 1 day and, in total, 3170 infrared spectra of microcolonies were recorded. The results obtained have been verified by Fourier-transform infrared macrospectroscopy and 16S rDNA sequencing. Interestingly, although the communities were unrelated, Staphylococcus equorum, Corynebacterium casei, Arthrobacter casei and Brevibacterium linens were found to be part of both consortia, however, with different incidence. In addition, Corynebacterium variabile, Microbacterium gubbeenense, Brachybacterium alimentarium, Enterococcus faecalis and an unknown species were detected in either one of the consortia.

Inter- and intraspecies variations of the 16S-23S rDNA intergenic spacer region of various streptococcal species

The 16S-23S rDNA intergenic spacer regions (ISR) of different streptococcal species and subspecies were amplified with primers derived from the highly conserved flanking regions of the 16S rRNA and 23S rRNA genes. The single sized amplicons showed a uniform pattern for S. agalactiae, S. dysgalactiae subsp. dysgalactiae (serogroup C), S. dysgalactiae subsp. equisimilis (serogroup G), S. dysgalactiae subsp. dysgalactiae (serogroup L), S. canis, S. phocae, S. uberis, S. parauberis, S. pyogenes and S. equi subsp. equi, respectively. The amplicons of S. equi subsp. zooepidemicus, S. porcinus and S. suis appeared with 3, 5 and 3 different sizes, respectively. ISR of selected strains of each species or subspecies investigated were sequenced and multiple aligned. This allowed a separation of ISR into regions, with 7 regions for S. agalactiae, S. dysgalactiae subsp. dysgalactiae (serogroup C), S. dysgalactiae subsp. equisimilis (serogroup G), S. dysgalactiae subsp. dysgalactiae (serogroup L), S. canis, S. phocae, S. pyogenes and S. suis, 8 regions for S. uberis and S. parauberis and mostly 9 regions for S. equi subsp. equi, S. equi subsp. zooepidemicus and S. porcinus. Region 4, encoding the transfer RNA for alanine (tRNA(Ala)), was present and identical for all isolates investigated. The size and sequence of ISR appears to be a unique marker for streptococci of various species and subspecies and could be used for bacterial identification. In addition the size and sequence variations of ISR of S. equi subsp. zooepidemicus, S. porcinus and S. suis allows a molecular typing of isolates of these species possibly useful in epidemiological aspects.

PCR and blot hybridization for rapid identification of Haloferax species

Based on the amplification of a 16S rDNA, a PCR assay for the identification of species of Haloferax to genus level was performed. Two variable regions of the 16S rDNA in Haloferax spp. were selected as genus-specific primers for the PCR assay and hybridization probe. Five genera of halophilic Archaea and Escherichia coli were examined as outside groups. Using this approach, all strains of Haloferax spp. were positive. In contrast, all species belonging to the most closely related genera, including Natrinema, Halorubrum, Halobacterium, and Haloarcula, were negative. In addition, the mass bloom of halophilic Archaea that develops in the El-Mallahet saltern of Alexandria City was positive using the same approach. This assay, which does not require pure cultures of microorganisms, is a specific and rapid method for identifying Haloferax spp. in hypersaline environments.

A Brevibacterium lactofermentum 16S rRNA gene used as target site for homologous recombination

Genes for rRNA are highly conserved and present in multiple copies in most prokaryotic organisms increasing the number of theoretical sites for homologous recombination. They might be targets for integration events between unrelated microorganisms providing that an efficient genetic transfer is present. We have used a plasmid containing a portion of the 16S rRNA gene from the rrnD operon of Brevibacterium lactofermentum to transform the same strain resulting in non-essential inactivation of various rrn operons. Integration of the transforming DNA occurs in all cases. The system may be used to test possible gene transfer at least among closely related strains and is of great interest for integration of foreign DNA and for mapping.

Design of cluster-specific 16S rDNA oligonucleotide probes to identify bacteria of the Bacteroides subgroup harbored in human feces

To develop a new simple method for identification of bacteria in the Bacteroides subgroup isolated from human feces, we designed a panel of four 16S rDNA-targeted oligonucleotide probes specific for each cluster of the Bacteroides subgroup. The probes Bac and bacvul were targeted to the Bacteroides cluster, and the probes Pre and Por have their target regions characteristic to those of the Prevotella cluster and the Porphyromonas cluster, respectively. The probes presented in this work were constructed to be specific for reference strains in each cluster of the Bacteroides subgroup and were not cross-hybridized with other major intestinal bacteria. The use of combination of these four probes will faciliate the identification of the clusters of the Bacteroides subgroup harbored in the intestine as compared to biological and biochemical testings.

Rapid identification of clinically relevant Nocardia species to genus level by 16S rRNA gene PCR

Two regions of the gene coding for 16S rRNA in Nocardia species were selected as genus-specific primer sequences for a PCR assay. The PCR protocol was tested with 60 strains of clinically relevant Nocardia isolates and type strains. It gave positive results for all strains tested. Conversely, the PCR assay was negative for all tested species belonging to the most closely related genera, including Dietzia, Gordona, Mycobacterium, Rhodococcus, Streptomyces, and Tsukamurella. Besides, unlike the latter group of isolates, all Nocardia strains exhibited one MlnI recognition site but no SacI restriction site. This assay offers a specific and rapid alternative to chemotaxonomic methods for the identification of Nocardia spp. isolated from pathogenic samples.