In silico characteristics for re-emerging possibility of Vibrio cholerae genotypes in Iran.

Epidemic cholera has been registered several times within recent years in Iran. The dominant genotype was Ogawa until 2011, but this gradually changed to Inaba. However, in 2015, the re-appearance of a previous Ogawa genotype was detected by the Iranian CDC. This raised worries because no evidence was found for its origin abroad. The aim of the present study was to identify clearly the source of this outbreak. Pulsed field gel electrophoresis (PFGE) was used to compare the recently detected Vibrio cholerae strains with those isolated from 2011 to 2015. We selected one strain per PFGE pattern, and compared the distinct patterns. BioNumerics software was applied, which enables interpretation of phenotypic and genotypic differences. In total, we studied 33 V. cholerae Ogawa strains. Analysis showed that strains could be discriminated on the basis of annual clusters but with a similarity of more than 80%. The highest homology was observed among those isolated each year from 2011 to 2014. In contrast, strains isolated in 2015 also exhibited close correlation with each other but were located in distinct clusters. The analysis also proved genetic variations among some strains. All 2015 strains showed differences with regard to previous genotypes despite some similarities. The new genotypes were probably imported into Iran from neighbouring countries such as Iraq by travellers or contaminated food sources since 2015. However, more investigations are required to identify the exact source of the 2015 outbreak.

Identification and molecular epidemiology of nosocomial outbreaks due to Burkholderia cepacia in cystic fibrosis patients of Masih Daneshvary Hospital, Iran.

INTRODUCTION: B. cepacia complex have emerged as an important opportunistic pathogen in hospitalized and immunocompromised patients. Small hospital outbreaks are frequent and are usually due to a single contaminated environmental source. In this study we were going to investigate the role of B.cepacia complex in those patients suspected to involve with cystic fibrosis and evaluate responsible types in Masih Daneshvary Hospital. METHODS: One hundred specimens were collected from all admitted patients who were suspected to cystic fibrosis to Masih Daneshvary hospital during one year April 2011 till end of March 2012. All were culture and identified standard procedure. All samples were checked by API system (API20NE) and by specific PCR method for genus Bulkhorderia and Bcc as well. Identified strains were finally tested by PFGE system to identifying specific involving pulse-types. RESULT: . Isolation and identification methods revealed 5 specimens were B.cepasia, The frequency of the cystic fibrosis detected at this study was lower than other similar study previously reported. All these isolates showed similar pattern by PFGE standard protocol that may have spread from a single source and could not be attributed to cross infections from patient to patients. DISCUSSION: Application of PFGE and identification of pulse-type is a potential tool to enhance the investigation of apparent nosocomial outbreaks of B.cepacia. However it needs to be adjusted with environmental findings. Implementation of educational programs and adherence to infection control policies are obviously the main element for complete elimination of an outbreak.

Quality assurance program for molecular medicine laboratories.

BACKGROUND: Molecular diagnostic methods have played and continuing to have a critical role in clinical laboratories in recent years. Therefore, standardization is an evolutionary process that needs to be upgrade with increasing scientific knowledge, improvement of the instruments and techniques. The aim of this study was to design a quality assurance program in order to have similar conditions for all medical laboratories engaging with molecular tests. METHODS: We had to design a plan for all four elements; required space conditions, equipments, training, and basic guidelines. Necessary guidelines was prepared and confirmed by the launched specific committee at the Health Reference Laboratory. RESULTS: Several workshops were also held for medical laboratories directors and staffs, quality control manager of molecular companies, directors and nominees from universities. Accreditation of equipments and molecular material was followed parallel with rest of program. Now we are going to accredit medical laboratories and to evaluate the success of the program. CONCLUSION: Accreditation of medical laboratory will be succeeding if its basic elements are provided in advance. Professional practice guidelines, holding training and performing accreditation the molecular materials and equipments ensured us that laboratories are aware of best practices, proper interpretation, limitations of techniques, and technical issues. Now, active external auditing can improve the applied laboratory conditions toward the defined standard level.

Genotyping Pattern among Iranian HCV Positive Patients.

BACKGROUND: Successful treatment to eliminate HCV RNA depends on the identified genotype. In the present study, we compared the frequency of different HCV genotypes, during four years study (2004 till 2008). METHODS: Sera specimens were received from 16 provinces of Iran. We used High Pure Viral Nucleic Acid Purification kit for extraction and samples were tested with improved form of RT-PCR technique. HCV genotypes were determined using Amplisense PCR kit and Amplicor HCV Monitoring Version 2 test utilized a reverse transcription (RT)-PCR approach to quantitative HCV RNA. Two hundreds six HCV positive specimens were entered to the study out of 389 tested samples. RESULTS: Type 3a was the most frequent type (46.6%), followed by type 1 (including 1a and 1b with 25.73% and 17.47% for each respectively) with 43.2%. Looking through collected results of the four years study confirmed the rate of HCV infection in those single genotypes 1b, 3a were slightly increased from 12.22% and 38.88% in the first year to 18.66 and 46.51% in the fourth year of the study period. CONCLUSION: The analyzed data proved that some patients were infected with two different types. High viral load was also more correlated to genotype 1 than other types.

Specific PCR Assay for Rapid and Direct Detection of Neisseria meningitidis in Cerebrospinal Fluid Specimens.

BACKGROUND: Neisseria meninigitidis is one of the most frequently encountered microorganisms associated with central nervous system infections. The aim of this study was to evaluate a PCR-based assay for specific and rapid detection of N. meninigitidis in CSF specimens. METHODS: Since April 2002 to July 2006, 130 CSF specimens were collected from patients suspected of having bacterial meningitis. Bacterial isolation and identification was carried out according to the standard bacteriological methods. The PCR was used to amplify a 101bp fragment of capsular transport gene A (ctrA) of N. meningitidis. RESULTS: PCR yielded an amplified product with the expected size of 101 base pair fragment. Sensitivity test proved 500 ng of N. meningitidis DNA as the final detection limit and specificity test revealed no cross-reaction for a wide range of respiratory pathogenic organisms. CONCLUSION: The PCR assay was more sensitive than the bacterial culturing. It might be possible to apply this procedure for rapid diagnosis of meningococci in clinical samples.

Evaluation of selective and nonselective media for isolation of Helicobacter pylori from gastric biopsy specimens.

The aim of the present study was to compare six media, three selective and three nonselective media, to determine the best combination of media for the primary isolation of Helicobacter pylori. Over a period of 8 months, mucosal antral biopsy specimens were obtained from 97 dyspeptic patients undergoing endoscopy. Biopsy samples were plated in parallel on all six media. Egg yolk emulsion agar (EYE), Skirrow's medium and modified Thayer-Martin medium were used as selective media; modified chocolate agar (MCHOC), Triptycase Soy Agar (TSA) and brain heart infusion agar were used as nonselective media. Overall, by using these six media, H. pylori were recovered from biopsy specimens from 48 of 97 patients, yielding an isolation rate of 49%. Comparison of all possible combinations of the six media showed that the highest rate of isolation of H. pylori was 100% (48 of 48) with EYE-MCHOC, followed by 97% (47 of 48) when EYE-SK was used. Conversely, it was found that none of the media used alone yielded a 100% rate of recovery (the maximum recovery rate was 92%, which was achieved with EYE). These results indicate that the association of EYE and MCHOC yielded the maximum recovery of H. pylori from gastric biopsy specimens. Therefore, the use of selective and nonselective media in parallel offers optimal recovery rates with only a slight increase in costs.

Influenza-like episodes in HIV-positive patients: the role of viral and 'atypical' infections.

OBJECTIVES: To document viral and 'atypical' infections in HIV-positive patients and association with influenza-like symptoms. PATIENTS AND METHODS: Monthly culture of urine, faeces and throat swabs in 63 HIV-positive patients (30 asymptomatic and 33 with AIDS-related complex/AIDS) over 5-27 months (with 1125 patient-months of follow-up), with further sample collections during influenza-like episodes. Standard viral detection methods were used. Throat swabs were assessed for Chlamydia sp. by culture and immunoblotting, and for Mycoplasma pneumoniae by polymerase chain reaction. RESULTS: Viruses were detected in 15 (50%) and M. pneumoniae in nine (30%) out of 30 HIV-positive patients during an influenza-like illness. A close temporal relationship with symptoms was observed in 12 (40%) patients: cytomegalovirus in six (20%), M. pneumoniae in three (10%), herpes simplex virus in three (10%), and enterovirus in one (4%). Influenza-like symptoms were more frequent in asymptomatic HIV infection than in AIDS-related complex/AIDS patients (actuarial risk at 1 year, 63 versus 26%; P=0.002), particularly in those with CD4 cell counts >300 x 10(6)/l at enrolment (P=0.002). At least 44% (four out of nine) M. pneumoniae infections were asymptomatic and 78% (seven out of nine) were associated with prolonged excretion (2-17 months). Chlamydia sp. were not detected. CONCLUSIONS: Influenza-like symptoms were more likely to be reported by HIV-positive patients at early stages of disease, possibly as a result of differences in immune responses to viral infection. There was a close association in 40% of cases between the development of symptoms and detection of cytomegalovirus, herpes simplex virus, enterovirus and M. pneumoniae (a previously unrecognized association).