Serogroups, and drug resistance of nontyphoidal Salmonella in symptomatic patients with community-acquired diarrhea and chicken meat samples in Tehran.

BACKGROUND: Salmonella is considered as a main cause of community-acquired diarrhea in humans, however, sources of the multi-drug resistant (MDR) strains and their link with the disease are not well known. AIMS: This study aimed to investigate the frequency, serogroup diversity, and antimicrobial susceptibility patterns of Salmonella strains in poultry meat and stool samples of patients with community acquired diarrhea in Tehran. METHODS: We compared the frequency of non-typhoidal Salmonella serogroups, the similarities of their resistance patterns to 10 antimicrobial compounds, the prevalence of extended spectrum ß-lactamase (ESBL) and ampicillinase C (AmpC) genetic determinants, and class 1 and 2 integrons in 100 chicken meat and 400 stool samples of symptomatic patients in Tehran during June 2018 to March 2019. RESULTS: Salmonella was isolated from 75% and 5.5% of the chicken meats and human stool samples, respectively. The chicken meat isolates mainly belonged to serogroup C (88%, 66/75), while the human stool isolates were mainly related to serogroup D (59.1%, 13/22). The MDR phenotype and the most common rates of resistance to antibiotics, including tetracycline, trimethoprim/sulfamethoxazole (TS) and azithromycin, were detected in 4.5% and 45.3%, 59% and 13.6%, 43% and 9.1%, 42% and 9.1% of the human stool and chicken meat samples, respectively. Carriage of bla CTX, bla SHV, and bla PER genes in the meat isolate with ESBL resistance phenotype and bla ACC, bla FOX, and bla CMY-2 among the 7 meat strains with AmpC resistance phenotype was not confirmed using polymerase chain reaction (PCR). High prevalence of class 1 and 2 integrons was characterized and showed a correlation with resistance to TS and chloramphenicol. CONCLUSION: These findings showed a lack of association between chicken meats and human isolates due to discrepancy between the characterized serogroups and resistance phenotypes.

Quantification of Active and Latent Form of Human Cytomegalovirus Infection in Umbilical Cord Blood Donors by Real-Time PCR.

BACKGROUND: Umbilical cord blood (UCB) is believed to be a highly valuable source of hematopoietic stem cells for transplantation. Objective: To investigate the prevalence of active and latent human cytomegalovirus (CMV) infection in UCB donors in Iranian population. METHODS: A total of 825 UCB samples was collected under standard procedures and analyzed for the presence of CMV DNAs in buffy coat (latent infection) and plasma (active infection). DNA was extracted from buffy coat and plasma samples separately and tested with quantitative real-time PCR. All positive samples were checked by ELISA for IgG and IgM anti-CMV antibody. RESULTS: Latent CMV infection was detected in 17 (2%) buffy coat samples with a low level of viral load, which indicated the presence of latent viral infection in donors. None of the plasma samples were found positive for CMV DNA reflecting no active infection. In the 17 positive samples, CMV viral load was 91-104 (mean: 100) copies/mL. All samples positive for viral DNA were also found positive for CMV IgG antibody by ELISA. No CMV IgM antibody was detected in positive samples. CONCLUSION: CMV is still the most important virus that infects hematopoietic stem cells and could be dangerous, especially for immunocompromized transplant recipients. We therefore suggest using real-time PCR for the detection and quantification of the viral DNA in buffy coat and plasma of UCB donors. PCR of plasma for detection of CMV and antibody assay for CMV infection add no more sensitivity for the detection of latent CMV infection in UCB donors.

Quantitative polymerase chain reaction for detection of human herpesvirus-7 infection in umbilical cord blood donors.

OBJECTIVE: Umbilical cord blood (UCB) has been a reasonable alternative to granulocyte colony-stimulating factor-mobilized peripheral blood or bone marrow, as a source of hematopoietic stem cells with a lower risk of graft-versus-host disease. In immunocompromised hosts after transplantation, the risk of viral infection in adults, especially with beta-herpesviruses such as human herpesvirus-7 (HHV-7), may be increased. This virus in immunocompromised patients can be reactivated from latency and converted to an active phase. Therefore, light-upon-extension real-time polymerase chain reaction (PCR) was developed to assess the prevalence and load of HHV-7 in the plasma and buffy coat of donors. METHODS: About 825 UCB samples under standard protocol from donors were collected. Then, DNA from plasma and buffy coat was extracted and quantitative real-time PCR was performed with light-upon-extension primers. RESULTS: Overall, HHV-7 was detected in 3.64% (30/825) of UCB donors. HHV-7 DNA was detected in 26 (3.2%) buffy coat samples (latent infection), and only 4 (0.48%) of them were positive for HHV-7 DNA in plasma samples (active infection); the mean HHV-7 viral load was 1.31 × 10(1) copies/mL in latent infection, and 1.94 × 10(5) copies/mL in active infection. CONCLUSIONS: We suggest that real-time PCR in plasma and buffy coat could be a useful method to detect active and latent HHV-7 infection in UCB donors and determine its role in subsequent transmission events.

Microsatellite instability typing in serum and tissue of patients with colorectal cancer: comparing real time PCR with hybridization probe and high-performance liquid chromatography.

Allelic variation of BAT-25 (a 25-repeat quasimonomorphic poly T) and BAT-26 (a 26-repeat quasimonomorphic polyA) loci as two mononucleotide microsatellite markers, were analyzed with high-performance liquid chromatography (HPLC) compared with Real-Time PCR using hybridization probes. BAT-26 and BAT-25 markers were used to determine an appropriate screening technique with high sensitivity and specificity to diagnose microsatellite instability (MSI) status in patients with colorectal cancer (CRC). One of the pathways in colorectal tumor genesis is microsatellite instability (MSI+). MSI is detected in about 15% of all CRCs; 3% are of these are associated with Lynch syndrome and the other 12% are caused by sporadic. Colorectal tumors with MSI have distinctive features compared with microsatellite stable tumors. Due to the high percentage of MSI+ CRC in Iran, screening of this type of CRC is imperative. Two markers were analyzed in tissues and sera of 44 normal volunteers and tumor and matched normal mucosal tissues as well as sera of 44 patients with sporadic CRC. The sensitivity and specificity of BAT-26 with real time PCR method (Hybridization probe) were 100% in comparison with sequencing method as the gold standard, while HPLC had a lower sensitivity and specificity. According to HPLC data, BAT-26 was more sensitive than BAT-25 in identifying MSI tumors. Therefore, MSI typing using the BAT-26 hybridization probe method compared to HPLC could be considered as an accurate method for diagnosing MSI in CRC tumors but not in serum circulating DNAs.

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.

Challenges of implementing Iranian national laboratory standards.

After four years of publishing the Iranian National Laboratory Standard and following a strategic plan to implement its requirements, it was decided to review the taken actions, evaluating the achievements and the failures, as well as analyzing the gaps and planning the interventional activities to resolve the problems. A thorough evaluation revealed that the progress of implementation process varies considerably in different provinces, as well as in laboratories in different public and private sectors. Diversity and heterogeneousity of laboratories throughout the country is one of unresolvable problems. Although we encounter shortage of resources in the country, improper allocation or distribution of resources and budgets make the problems more complicated. Inadequacy of academic training in laboratory sciences has resulted in necessity of holding comprehensive post-graduate training courses. Revising academic curriculum of laboratory sciences could be mostly helpful, moreover there should be organized, training courses with pre-determined practical topics. providing specific technical guidelines, to clarify the required technical details could temporarily fill the training gaps of laboratory staff. Inadequate number of competent auditors was one of the difficulties in universities. Another important challenge returns to laboratory equipment, developing the national controlling system to manage the laboratory equipment in terms of quality and accessibility has been planned in RHL. At last cultural problems and resistance to change are main obstacles that have reduced the pace of standardization, it needs to rationalize the necessity of establishing laboratory standards for all stakeholders.

Molecular beacon probes-base multiplex NASBA Real-time for detection of HIV-1 and HCV.

BACKGROUND AND OBJECTIVES: Developed in 1991, nucleic acid sequence-based amplification (NASBA) has been introduced as a rapid molecular diagnostic technique, where it has been shown to give quicker results than PCR, and it can also be more sensitive. This paper describes the development of a molecular beacon-based multiplex NASBA assay for simultaneous detection of HIV-1 and HCV in plasma samples. MATERIALS AND METHODS: A well-conserved region in the HIV-1 pol gene and 5'-NCR of HCV genome were used for primers and molecular beacon design. The performance features of HCV/HIV-1 multiplex NASBA assay including analytical sensitivity and specificity, clinical sensitivity and clinical specificity were evaluated. RESULTS: The analysis of scalar concentrations of the samples indicated that the limit of quantification of the assay was <1000 copies/ml for HIV-1 and <500 copies/ml for HCV with 95% confidence interval. Multiplex NASBA assay showed a 98% sensitivity and 100% specificity. The analytical specificity study with BLAST software demonstrated that the primers do not attach to any other sequences except for that of HIV-1 or HCV. The primers and molecular beacon probes detected all HCV genotypes and all major variants of HIV-1. CONCLUSION: This method may represent a relatively inexpensive isothermal method for detection of HIV-1/HCV co-infection in monitoring of patients.

Excision of the primary tumour in patients with metastatic breast cancer: a clinical dilemma.

BACKGROUND: Approximately 10% of new breast cancer patients will present with overt synchronous metastatic disease. The optimal local management of those patients is controversial. Several series suggest that removal of the primary tumour is associated with a survival benefit, but the retrospective nature of those studies raises considerable methodologic challenges. We evaluated our clinical experience with the management of such patients and, more specifically, the impact of surgery in patients with synchronous metastasis. METHODS: We reviewed patients with primary breast cancer and concurrent distant metastases seen at our centre between 2005 and 2007. Demographic and treatment data were collected. Study endpoints included overall survival and symptomatic local progression rates. RESULTS: The 111 patients identified had a median follow-up of 40 months (range: 0.6-71 months). We allocated the patients to one ot two groups: a nonsurgical group (those who did not have breast surgery, n = 63) and a surgical group (those who did have surgery, n = 48, 29 of whom had surgery before the metastatic diagnosis). When compared with patients in the nonsurgical group, patients in the surgical group were less likely to present with T4 tumours (23% vs. 35%), N3 nodal disease (8% vs. 19%), and visceral metastasis (67% vs. 73%). Patients in the surgical group experienced longer overall survival (49 months vs. 33 months, p = 0.01) and lower rates of symptomatic local progression (14% vs. 44%, p < 0.001). CONCLUSIONS: In our study, improved overall survival and symptomatic local control were demonstrated in the surgically treated patients; however, this group had less aggressive disease at presentation. The optimal local management of patients with metastatic breast cancer remains unknown. An ongoing phase iii trial, E2108, has been designed to assess the effect of breast surgery in metastatic patients responding to first-line systemic therapy. If excision of the primary tumour is associated with a survival benefit, then the preselected subgroup of patients who have responded to initial systemic therapy is the desired population in which to put this hypothesis to the test.

Design and development of an in-house multiplex RT-PCR assay for simultaneous detection of HIV-1 and HCV in plasma samples.

BACKGROUND AND OBJECTIVES: HIV-1 and HCV infections are life threatening problems in patients who receive blood products. Serological methods have proven useful in detecting these infections, but there are setbacks that make it challenging to detect these infectious agents. By the advent of Nucleic Acid Testing (NAT) methods, especially in multiplex format, more precise detection is possible. MATERIALS AND METHODS: We have developed a multiplex RT-PCR assay for simultaneous detection of HIV-1 and HCV. Primers were designed for highly conserved region of genome of each virus. Using these primers and standard plasmids, we determined the limit of detection, clinical and analytical specificity and sensitivity of the assay. Monoplex and multiplex RT-PCR were performed. RESULTS: Analytical sensitivity was considered to be 100 and 200 copies/ml for HIV-1 and HCV, respectively. High concentration of one virus had no significant effect on the detection of the other one with low concentration. By analysis of 40 samples, clinical sensitivity of the assay was determined to be 97.5%. Using different viral and human genome samples, the specificity of the assay was evaluated to be 100%. CONCLUSIONS: The aim of this study was to develop a reliable, rapid and cost effective method to detect HIV-1 and HCV simultaneously. Results showed that this simple and rapid method is perfectly capable of detecting two viruses in clinical samples.

Fludarabine and busulfan as a myeloablative conditioning regimen for allogeneic stem cell transplantation in high- and standard-risk leukemic patients.

Busulfan and cyclophosphamide (BuCy) are currently the most widely used myeloablative regimen to treat malignancies with allogeneic stem cell transplantation. Fludarabine has considerable efficacy in both immunosuppression and tumor cells killing with a minimal extramedullary toxicity. We evaluated the efficacy of 40 mg/m(2) fludarabine i.v. for 5 days and busulfan 4 mg/kg/day p.o. for 4 days as myeloablative conditioning regimen in 70 patients (median age 24 years) with acute leukemia or chronic phase of myelogenous leukemia. They all had human leukocyte antigen-matched sibling donors. The patients received 10 mug/kg granulocyte colony stimulating factor (GCSF), 24 h after stem cell infusion until engraftment occurred. Graft-versus-host disease (GVHD) prophylaxis included 3 mg/kg cyclosporine-A i.v. from day -2 to +6 followed by 12 mg/kg p.o. until day +60. The median time of neutrophil recovery (>0.5 x 109/l) and platelet recovery (>20 x 109/l) were 10 and 12 days, respectively. Mucositis (93%) and hepatic toxicity (16%) resolved with conservative therapy. The incidence of acute GVHD grade I-II and III-IV were 38.6 and 15.7% respectively. Overall survival and disease-free survival were 71 and 64% respectively with 17 months median follow-up for surviving patients. We conclude that FluBu may be used as a substitute for BuCy with almost the same efficacy and with a lower transplant adverse effect but to increase anti-leukemic effects, especially in acute lymphoblastic leukemia patients, it needs some modifications.

Immunohistochemical analysis of p53, cyclinD1, RB1, c-fos and N-ras gene expression in hepatocellular carcinoma in Iran.

AIM: To study the effect of some genes especially those involved in cell cycle regulation on hepatocellular carcinoma. METHODS: Paraffin-embedded tissue samples of 25 patients (18 males and 7 females) with hepatocellular carcinoma were collected from 22 pathology centers in Tehran during 2000-2001, and stained using immunohistochemistry method (avidin-biotin-peroxidase) for detection of p53, cyclinD1, RB1, c-fos and N-ras proteins. RESULTS: Six (24%), 5 (20%), 12 (48%) and 2 samples (8%) were positive for p53, cyclinD1, C-fos and N-ras expression, respectively. Twenty-two (88%) samples had alterations in the G1 cell-cycle checkpoint protein expression (RB1 or cyclinD1). P53 positive samples showed a higher (9 times) risk of being positive for RB1 protein than p53 negative samples. Loss of expression of RB1 in association with p53 over-expression was observed in 4 (66.7%) of 6 samples. Loss of expression of RB1 was seen in all cyclinD1 positive, 20 (90.9%) N-ras negative, and 11 (50%) C-fos positive samples, respectively. CyclinD1 positive samples showed a higher (2.85 and 4.75 times) risk of being positive for c-fos and N-ras expression than cyclinD1 negative samples. CONCLUSION: The expression of p53, RB1 and c-fos genes appears to have a key role in the pathogenesis of hepatocellular carcinoma in Iran. Simultaneous overexpression of these genes is significantly associated with their loss of expression during development of hepatocellular carcinoma.

Genetic risk identifies multiple myeloma patients who do not benefit from autologous stem cell transplantation.

Genetic aberrations have emerged as major prognostic factors for patients with multiple myeloma (MM). We evaluated 126 MM patients for t(4;14) or t(11;14), 13q or p53 deletions and correlated the number of genetic aberrations with patient's clinical outcome following undergoing autologous stem cell transplantation. We demonstrate the significance of genetic-based risk classification that clearly segregate patients into low (no genetic abnormalities or only t(11;14)), intermediate (any one of the genetic abnormalities other than t(11;14)) and high-risk groups (any two or more of the genetic abnormalities other than t(11;14)). High-risk patients do not benefit from stem cell transplant and should be offered alternative therapies.

Cyclosporin A and mini short-term methotrexate vs cyclosporin A as graft-versus-host disease prophylaxis in patients with beta thalassemia major undergoing allogeneic blood and marrow transplantation.

We compared the effects of cyclosporin A (CsA) alone as graft-versus-host disease (GVHD) prophylaxis vs cyclosporine with short-course methotrexate (MTX) in patients with thalassemia. In all, 140 patients were enrolled in this study. The first group, of 50 patients, received CsA alone at 3 mg/kg i.v. from day -2 to +5 followed by 12.5 mg/kg p.o., which was tapered according to the patient's condition. The other group, of 90 patients, received the combination of CsA+MTX in which CsA was used with the above-mentioned dose and MTX was on 10 mg/m(2) day +1 and 6 mg/m(2) on days +3 and +6. Incidence of acute GVHD grade II-IV in the CsA group was 78% and in the CsA+MTX group was 52.2%, which was statistically significant (P=<0.001). There were no significant differences in the incidence of chronic GVHD between the two groups. The mean neutrophil engraftment to 0.5 x 10(9)/l was 14 and 23 days for CsA group and CsA+MTX group, respectively (P=<0.001). There were no significant differences for platelet recovery between the two groups. Graft failure in the CsA and CsA+MTX groups was seven (14%) and nine (10%) patients, respectively (P=0.58). Overall survival in the CsA and CsA+MTX groups was 77 and 85%, respectively. Disease-free survival in the CsA and CsA+MTX groups were 58 and 80%, respectively.