Background: There is a conserved portion in the 16S rRNA gene of bacteria which can be amplified by the universal PCR method. This fragment is 996 bp in length. In this method, only one set of universal primers is used for the amplification of the conserved region of the 16S rRNA gene, in common bacterial pathogens. Therefore, using the universal PCR method, these bacteria are detectable only by one set of primers; then for detection of the bacteria, the PCR products are digested by the restriction endonucleases. Since the restriction patterns of bacteria (RFLP) are expected to be different from each other, on that basis we can identify the bacteria.Methods: The conserved fragments of the 16S rRNA genes of the following bacteria were amplified by the universal PCR method: Streptococcus pyogenes, Escherichia coli, Pseudomonas aeruginosa and Neisseria gonorrhoeae. The PCR products were digested by BsuRI (Hae III) restriction endonucleases and were electrophoresed on agarose gel.Results: The restriction patterns of these bacteria were different. Thirty isolated E. coli and 28 isolated S. pyogenes from clinical samples were studied by this method. The size of PCR products and RFLP patterns of every bacterium were the same as standard strains. In comparison with culture method, the sensitivity of the universal PCR is 92.3 %. The sensitivity of this method was determined up to about 11 and 190 bacteria for gram negatives and gram positives respectively. Conclusion: These studies suggest that the universal PCR method accompanied with RFLP is a very useful and rapid method, for detection and identification of bacteria in body fluids.

Background: Recent studies suggest that bacteria may play a role in triggering rheumatoid arthritis. Considering the recent reports on viable but non-culturable cells (VBNC) in the synovial fluid and blood of patients, the role of bacteria has become more prominent. The present study aimed to use general and specific primers to detect microbiome in the blood of patients with rheumatoid arthritis. Methods: A general primer, called 16S rRNA was used in the present study to detect a wide range of bacteria in the blood of patients with rheumatoid arthritis. Specific primers were designed and used such as nuc and rfbE to trace Staphylococcus aureus and Escherichia coli in patients' blood. Examining 102 blood samples and performing the genomic extraction separately for each sample, PCR was then performed using general and specific primers, and the results were sequenced. The findings were analyzed using descriptive statistics.Results: According to the results, in 102 blood samples of rheumatoid arthritis patients, who were negative for bacteriological culture, there were 74 cases (72.54%) of 16S rRNA gene, and 54 cases (52.9%) of Staphylococcus aureus nuc gene, respectively. Moreover, a specific gene, rfbE, was traced in 12 samples. Conclusion: The findings of the present study indicated the presence of microbiome in the blood of patients with rheumatoid arthritis. Because the blast sequencing results of the PCR product showed a wide range of bacterial genomes. These findings may potentially improve the management of rheumatoid arthritis diagnosis and treatment.

Pasteurella multocida is known as an important heterogenic bacterial agent causes some severe diseases such as fowl cholera in poultry and haemorrhagic septicaemia in cattle and buffalo. A polymerase chain reaction (PCR) assay was developed using primers derived from conserved part of 16S-23S rRNA gene. The PCR amplified a fragment size of 0.7 kb using DNA from nine avian P. multocida isolates. Sequence alignment of the 16S-23S rRNA genes (ITS) revealed a considerable heterogenicity among the isolates. The percentage of similarity varied from 83.3 to 100% among the isolates. An interesting finding from this study was the presence of an inserted sequence (seven nucleotides) in the 16S-23S rRNA region in 55% of the isolates. According to phylogenic analysis based on ITS sequence alignment, the P. multocida isolates classified into 2 distinct clusters. The virulence of isolates in cluster II were higher than those in cluster I. Ribotyping of P. multocida by using 16S-23S rRNA gene PCR sequencing could be used as a marker in epidemiologic studies.