Detection of Genes Related to Linezolid Resistance (poxtA, cfr, and optrA) in Clinical Isolates of Enterococcus spp. from Humans: A First Report from Iran

Background

Enterococci may develop resistance to linezolid through chromosomal mutations that involve specific linezolid resistance genes, such as cfr, optrA, and poxtA. The objective of this study was to evaluate the antibiotic susceptibility of enterococcal isolates and identify cfr, optrA, and poxtA genes in MDR isolates.

Materials and Methods

Enterococcal isolates were collected from various clinical specimens at Al-Zahra, Amin, and Khorshid Hospitals in Isfahan. The Enterococcus isolates were identified as belonging to the E. faecalis and E. faecium species by using specific gene (D alanine D alanine ligase ddl) sets in PCR. To detect cfr, optrA, and poxtA genes among the species, a multiplex-PCR assay was performed.

Results

Out of 175 isolates, E. faecalis predominated 129/175 (73.7%). Furthermore, the prevalence of vancomycin-resistant Enterococci (VRE) and linezolid-resistant Enterococci (LRE) was 29.7% and 4%, respectively. The overall prevalence of MDR was 91.1%, 68.9%, and 66.6% of E. faecium, E. faecalis, and other Enterococcus spp., respectively. Interestingly, the frequency of optrA (71.4%) in E. faecium and poxtA and crf (42.8%) in E. faecalis were detected among LRE species. A statistically significant relationship (P < 0.05) was found between the presence of the three genes and the occurrence of LRE.

Conclusion

This is the first study to report the detection of linezolid resistance genes (cfr, optrA, and poxtA) in clinical Enterococcus spp. isolates from Iran, conducted at Isfahan University of Medical Sciences hospitals. The emergence of enterococcal strains that resist linezolid is concerning as it can lead to the spread of resistant strains among patients, resulting in treatment failure.

Evolutionary trajectories of beta-lactamase NDM and DLST cluster in Pseudomonas aeruginosa: finding the putative ancestor

Pseudomonas aeruginosa has different antibiotic resistance pathways, such as broad-spectrum lactamases and metallo-β-lactamases (MBL), penicillin-binding protein (PBP) alteration, and active efflux pumps. Polymerase chain reaction (PCR) and sequencing methods were applied for double-locus sequence typing (DLST) and New Delhi metallo-β-lactamase (NDM) typing. We deduced the evolutionary pathways for DLST and NDM genes of P. aeruginosa using phylogenetic network. Among the analyzed isolates, 62.50% of the P. aeruginosa isolates were phenotypically carbapenem resistance (CARBR) isolates. Characterization of isolates revealed that the prevalence of bla_NDM, bla_VIM, bla_IMP, undetermined carbapenemase, and MexAB-OprM were 27.5%, 2%, 2.5%, 12.5%, and 15%, respectively. The three largest clusters found were DLST t20-105, DLST t32-39, and DLST t32-52. The network phylogenic tree revealed that DLST t26-46 was a hypothetical ancestor for other DLSTs, and NDM-1 was as a hypothetical ancestor for NDMs. The combination of the NDM and DLST phylogenic trees revealed that DLST t32-39 and DLST tN2-N3 with NDM-4 potentially derived from DLST t26-46 along with NDM-1. Similarly, DLST t5-91 with NDM-5 diversified from DLST tN2-N3 with NDM-4. This is the first study in which DLST and NDM evolutionary routes were performed to investigate the origin of P. aeruginosa isolates. Our study showed that the utilization of medical equipment common to two centers, staff members common to two centers, limitations in treatment options, and prescription of unnecessary high levels of meropenem are the main agents that generate new types of resistant bacteria and spread resistance among hospitals.

In vitro antimicrobial effects of green tea, microwaving, cold boiled water, and chlorhexidine on Streptococcus mutans and Candida albicans on silicone pacifiers

Background

This study aimed to compare the antimicrobial effects of green tea, microwaving, cold boiled water, and chlorhexidine (CHX) on Streptococcus mutans and Candida albicans on silicone pacifiers.

Materials and Methods

In this in vitro experimental study, 60 equal-size samples of silicone pacifiers were cut, ultraviolet sterilized, and randomly divided into two groups (n = 30) for immersion in 0.5 McFarland standard suspension of S. mutans and C. albicans. The samples in each group were then randomly divided into five subgroups (n = 6) for disinfection with 0.12% CHX, cold boiled water, green tea, microwaving for 7 min, and distilled water. The sample suspensions were cultured on blood agar (for S. mutans) and Sabouraud dextrose agar (for C. albicans) and incubated. The number of colonies was counted after 24 and 48 h. Data were analyzed using the Kruskal-Wallis and Mann-Whitney tests (P < 0.05).

Results

At 24 and 48 h, the S. mutans colony count was the lowest in CHX and green tea subgroups followed by microwave, cold boiled water, and distilled water subgroups (P < 0.05).

Conclusion

CHX and green tea can significantly decrease the S. mutans and C. albicans colony count on silicone pacifiers.

Discovery of potential inhibitors against New Delhi metallo-β-lactamase-1 from natural compounds: in silico-based methods

New Delhi metallo-β-lactamase variants and different types of metallo-β-lactamases have attracted enormous consideration for hydrolyzing almost all β-lactam antibiotics, which leads to multi drug resistance bacteria. Metallo-β-lactamases genes have disseminated in hospitals and all parts of the world and became a public health concern. There is no inhibitor for New Delhi metallo-β-lactamase-1 and other metallo-β-lactamases classes, so metallo-β-lactamases inhibitor drugs became an urgent need. In this study, multi-steps virtual screening was done over the NPASS database with 35,032 natural compounds. At first Captopril was extracted from 4EXS PDB code and use as a template for the first structural screening and 500 compounds obtained as hit compounds by molecular docking. Then the best ligand, i.e. NPC120633 was used as templet and 800 similar compounds were obtained. As a final point, ten compounds i.e. NPC171932, NPC100251, NPC18185, NPC98583, NPC112380, NPC471403, NPC471404, NPC472454, NPC473010 and NPC300657 had proper docking scores, and a 50 ns molecular dynamics simulation was performed for calculation binding free energy of each compound with New Delhi metallo-β-lactamase. Protein sequence alignment, 3D conformational alignment, pharmacophore modeling on all New Delhi metallo-β-lactamase variants and all types of metallo-β-lactamases were done. Quantum chemical perspective based on the fragment molecular orbital (FMO) method was performed to discover conserved and crucial residues in the catalytic activity of metallo-β-lactamases. These residues had similar 3D coordinates of spatial location in the 3D conformational alignment. So it is posibble that all types of metallo-β-lactamases can inhibit by these ten compounds. Therefore, these compounds were proper to mostly inhibit all metallo-β-lactamases in experimental studies.

Investigation of carbapenem resistant Acinetobacter baumannii ST2 in Iran

This study investigated carbapenem resistance among Acinetobacter baumannii isolated from respiratory specimens. Epidemiological relationship of the isolates was also evaluated. In this study, 81 respiratory specimens of A. baumannii from AL Zahra Hospital were confirmed by phenotypic and genotypic methods. Antimicrobial susceptibility was performed by disc diffusion method. Carbapenem resistance genes were identified by PCR. The isolates were typed by RAPD-PCR and multilocus sequence typing (MLST) methods. All isolates were resistant to imipenem and 80 isolates to meropenem. Frequency of oxacillinase genes was as follows: blaOXA-23 gene was positive in 74 (91.3%), blaOXA-24 gene in 50 (61.7%) and blaOXA-58 was not found in any isolates. On the other hand 22 (27.2%) isolates contained blaIMP-1, 3 (3.7%) isolates contained blaIMP-2 gene, 5 (6.2%) isolates contained blaVIM-1, 4 (5%) isolates had blaVIM-2 and none of the isolates had blaSIM-1 gene. RAPD-PCR typing identified 16 different patterns, with one pattern being the most frequent one in 26 isolates. In MLST 6 different sequence types were identified, the most predominant being ST2 belonging to clonal complex 2. The results of this study showed high resistance to carbapenems as well as high abundance of oxacillinase genes.

The Occurrence of Type I, II, and III Integrons in Multi-drug Resistance and Methicillin-Resistant Staphylococcus aureus Isolates in Iran

Integrons are mobilizable platforms-DNA elements with impacts on moving antibiotic resistance genes among bacteria and capable of spreading multi-drug resistance (MDR) in pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) strains are the main cause of community-acquired and nosocomial infections with high mortality and morbidity rates worldwide. This work is mainly aimed at calculating the frequency of Type I, II, and III integrons within multi-drug resistance and Methicillin-resistant S. aureus Isolates in Iran. In this cross-sectional study, 230 clinical isolates of S. aureus were gathered from patients of educational hospitals in the provinces of Iran. These isolates were verified utilizing particular biochemical examinations and then assessed for antibiotic susceptibility through disk diffusion technique and standard procedures were done. Genomic and plasmid DNA of all isolates were extracted using Extraction Kit and PCR assay was used for the detection of Type I, II and III integrons genes. Out of the 230 S. aureus isolates, 136 (59.1%) isolates were MRSA and 141 (61.3%) isolates exhibited the MDR pattern. PCR and sequencing showed that 57 (24.8%) of tested isolates carry Type I integron. Among the isolates investigated, MRSA and MDR isolates showed frequencies of 56.1% and 57.9%, respectively. Type II and III integrons were found in none of 230 isolates. The IntI I gene was present in approximately one-quarter of this study isolates. The great prevalence rate of MDR and MRSA isolates and concurrently the existence of Type I integron among those isolates have been considered an important concern in medical society.

High rate of carbapenem-resistant Klebsiella pneumoniae detected from hospital equipments in Iran

The objective of this study was to assess the prevalence, antibiogram, and related genes of carbapenem-resistant Klebsiella pneumoniae (CRKP) among hospital environment samples. A total of 250 samples were taken from different surfaces and medical devices of three hospitals in Isfahan, Iran. All samples were cultured and K. pneumoniae strains were identified by conventional microbiological methods and polymerase chain reaction (PCR). Antibiogram of isolates was performed by disk diffusion method and production of carbapenemases and metallo-β-lactamases (MBLs) was confirmed using modified Hodge test and E-test, respectively. Molecular detection of the related genes was carried out by PCR. Overall, 37 (14.8%) K. pneumoniae strains were isolated, of which 34 (91.9%) strains were resistant to carbapenems. Twenty-eight (82.4%) isolates were positive for carbapenemases and seven (20.6%) isolates were phenotypically MBL producers. The results of PCR showed that the prevalence of bla_OXA-48, bla_NDM, bla_IMP, bla_SHV, bla_CTX-M, bla_TEM, and class 1 integron among CRKP isolates was 70.6%, 52.9%, 2.9%, 100%, 82.4%, 55.9%, and 76.5%, respectively. However, bla_KPC, bla_GES, bla_IMI, bla_VIM, and class 2 integron were not detected in any of the isolates. This study showed that the environment of our hospitals is contaminated with CRKP and it emphasizes the importance of using standard methods for infection control.

Investigation of antimicrobial susceptibility, class I and II integrons among Pseudomonas aeruginosa isolates from hospitalized patients in Isfahan, Iran

Objectives

The role of integrons in the transfer of antibiotic resistance is one of the important issues, therefore, this study is aimed to investigate antibiotic resistance pattern and prevalence of class 1 and 2 integrons in P. aeruginosa isolated.

Results

Out of 72 confirmed P. aeruginosa isolates, 50% were from ICU patients. Antibacterial susceptibility pattern showed that isolates were most resistant to ceftazidime (76.4%) and colistin was the most effective antibiotic (100%) and molecular analysis of class I and II integrons showed 55.5% and 29.1% of isolates were positive, respectively and the proportions of MDR isolates were significantly higher among integron-positive isolates with 73.6% compared to negative isolates with 22.9%. Our results showed that there was a correlation among class 1 and 2 integrons with MDR P. aeruginosa isolates. According to the importance of integrons in acquisition and dissemination of antibiotics resistance genes, the performance of antibiotic surveillance programs and investigating the role of integrons is recommended to control the spreading of antibiotics resistance genes.

First Report of the Isolation of Nocardia thailandica from the Bronchoalveolar Lavage of a Patient in Iran

Nocardiae are Gram-positive, filamentous, aerobic, relatively slow-growing, and weakly acid-fast bacteria which cause nocardiosis in humans. We describe a 53-year-old patient with chronic bronchitis referred to Al-Zahra Hospital, Isfahan. A bronchial washing sample was taken from the patient. A Nocardia-like microorganism was detected in microscopic evaluation. Based on the phenotypic and 16S rRNA gene sequencing, the isolate was identified as Nocardia thailandica. The patient was treated with trimethoprim-sulfamethoxazole and linezolid. This is the first report of the isolation of Nocardia thailandica from Iran.

The emergence of blaOXA-48 and blaNDM among ESBL-producing Klebsiella pneumoniae in clinical isolates of a tertiary hospital in Iran

The aim of this study was to investigate the prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKP) and the most common types of carbapenemases, metallo-beta-lactamases (MBLs), and extended-spectrum beta-lactamases (ESBLs) among CRKP isolates in a tertiary hospital in Isfahan, Iran. Eighty non-repetitive clinical isolates of K. pneumoniae were obtained from different clinical specimens. Antibiotic resistance pattern of isolates was determined by disk diffusion method and production of carbapenemases and MBLs was confirmed using modified Hodge test and E-test, respectively. Molecular detection of the antibiotic resistance genes was performed using PCR. Fifty-one (63.8%) isolates have decreased susceptibility to carbapenems, of which 46 (90.2%) isolates were as carbapenemase producer and four (7.8%) isolates were positive for MBLs, phenotypically. The results of PCR showed that the prevalence of bla_OXA-48, bla_NDM, bla_SHV, bla_CTX-M, and bla_TEM genes among CRKP isolates were 90.2%, 15.7%, 98%, 96.1%, and 90.2%, respectively. No isolates carrying the bla_KPC, bla_GES, bla_IMI, bla_VIM, and bla_IMP genes were detected. This study showed that the production of OXA-48 is one of the main mechanisms of resistance to carbapenems in CRKP isolates in Isfahan. In addition, the dissemination of NDM-producing CRKP isolates is a potential risk for the health care system of this area in the near future.

Prevalence of metallo‑beta‑lactamase producing Acinetobacter baumannii isolated from intensive care unit in tertiary care hospitals

INTRODUCTION

The emergence of Metallo-beta-lactamase (MBL)-producing Acinetobacter baumannii has become a global concern in nosocomial infections. The aim of this study is to determine the prevalence of MBL producing genes among clinical isolates of A. baumannii from hospitalized patients.

METHODS

This study was performed from October 2015 to October 2016 at three teaching hospitals located in Isfahan, Iran. Totally, 100 A-baumannii isolates were collected from clinical specimens and identified as A-baumannii using standard microbiological methods. Antimicrobial susceptibility test was determined by disc diffusion method according to the CLSI. Furthermore, the determination of bla _IMP-1, bla _IMP-2, bla _VIM-1, bla _VIM-2and bla _SIM-1 was detected by PCR.

RESULTS

Totally, Sixty-eight percent (68%) of isolates of A. baumannii were recovered from tracheal aspirate. According to the antibiotic susceptibility pattern, the highest level of resistance was against ciprofloxacin (99%), while among tested antibiotics amikacin (10%) was found to be the most effective. 21%, 4%, 7% and 6% isolates carried bla _IMP-1, bla _IMP-2, bla _VIM-1 and bla _VIM-2 genes, respectively. Also, bla _SIM-1 was not detected in any of the isolates.

CONCLUSION

The results of this study showed high rate of the MBL producing A-baumannii isolates in our region and displayed that MBLs producing A-baumannii strains are emerging threats to ICUs.

Prevalence of CTX-M and TEM β-lactamases in Klebsiella pneumoniae Isolates from Patients with Urinary Tract Infection, Al-Zahra Hospital, Isfahan, Iran

Background:

Extended-spectrum β-lactamase (ESBL)-producing is a significant resistant mechanism to β-lactams in Enterobacteriaceae, especially in Klebsiella pneumoniae. The main objectives of this study were to genetically characterize urinary clinical isolates of K. pneumoniae through the investigating of blaTEM, blaCTX-M and using molecular typing by Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) method. We also determined the frequency of antibiotic resistance of K. pneumoniae strains to characterize the β-lactamases included.

Materials and Methods:

A cross-sectional study was carried out to evaluate 98 strains of K. pneumoniae isolated from urine culture of outpatients referred to Al-Zahra Hospital, Isfahan, Iran. Antibiotic susceptibility testing was performed using Kirby–Bauer's method. Screening of ESBLs was carried out using double-disk screening test. PCR technique was performed to detect TEM and CTX-M genes. The total DNA of each strain was tested by ERIC-PCR.

Results:

In 98 K. pneumoniae studied clinical isolates, 25.5% were ESBL producing and 44.9% multidrug-resistant (MDR). From 25 ESBL isolates, 23 (92%) cases showed MDR phenotype. In ESBL producing isolates, 23 (92%) were blaCTX-M and 19 (76%) blaTEM positive. The antimicrobial drug susceptibilities of ESBL isolates indicated high resistant rates for cefotaxime and ceftazidime. All 25 ESBL producing isolates were resistant to cefotaxime. Complex patterns of fingerprints isolates showed that 36% of the isolates were belonged to the cluster no 5.

Conclusion:

This study revealed high antimicrobial resistance rates among ESBL isolates which can lead to various health difficulties. Epidemiological data collection from patients is recommended to develop the strategies to manage antibiotic resistance.

Investigation of Class I, II, and III Integrons Among Acinetobacter Baumannii Isolates from Hospitalized Patients in Isfahan, Iran

Objectives

This study aimed to determine the prevalence of class I, II, and III integrons among clinical Acinetobacter baumannii isolates collected from hospitalized patients.

Methods

This cross-sectional study was conducted at two teaching hospitals in Isfahan, Iran, from October 2015 to October 2016. A total of 147 non-duplicate A. baumannii isolates were collected from clinical specimens and identified as A. baumannii using standard microbiological methods and confirmed by genotyping. Antimicrobial susceptibility was determined using disc diffusion method, and the presence of integron genes was performed using the polymerase chain reaction.

Results

Out of 147 confirmed A. baumannii isolates, 97.3% of isolates were extensive drug-resistant (XDR) and 2.7% were multidrug-resistant (MDR). Class I and II integrons were detected in 63.9% and 78.2% of the A. baumannii, respectively. Class III integron was not detected in any of the isolates.

Conclusion

Our results show a high prevalence of classes I and II integrons which may play a key role in the acquisition of MDR and XDR phenotype among A. baumannii isolates in our region. Therefore, use of appropriate infection control in clinical settings and implementation of treatment strategies is necessary for our hospitals.

High prevalence of multidrug-resistance uropathogenic Escherichia coli strains, Isfahan, Iran

BACKGROUND AND OBJECTIVES

Urinary tract infection (UTI) is one of the most frequent infectious diseases and can occur in all age groups. Escherichia coli is the main cause of this infection. Multiple resistances to antimicrobial agents are increasing quickly in E. coli isolates and may complicate therapeutic strategies for UTI. The aim of this study was to determine the antibiotic resistance pattern and the multidrug-resistance (MDR) phenotypes in uropathogenic E. coli (UPEC).

MATERIALS AND METHODS

A total of 135 UPEC isolates were collected from both outpatients (91 isolates) and inpatients (44 isolates) between September, 2012 and February, 2013. In order to determine the MDR among UPEC isolates, we have tested 15 antimicrobial agents and antibiotic susceptibility was done by Kirby-Bauer disk diffusion method.

RESULTS

The percentage of MDR isolates (resistant to at least three drug classes such as aminoglycosides, fluoroquinolones, penicillins, cephalosporins, or carbapenems) was 68% in the inpatients and 61% in the outpatients. Antibiotic resistance to ampicillin, ceftazidim, nalidixic acid, and trimethoprim/sulfamethoxazole were higher than 50%. Amikacin, nitrofurantoin, and gentamicin showed markedly greater activity (89.1%, 85.9%, and 82.4% sensitivity, respectively) than other antimicrobial agents. Resistance to meropenem did show either in outpatients or in inpatients.

INTERPRETATION AND CONCLUSIONS

The high prevalence of drug resistance among UTI patients calls for continuous monitoring of the incidence of drug resistance for appropriate empiric selection of antibiotic therapy. Empirical treatment of UTIs should be relied on susceptibility patterns from local studies.

Production of IFN-γ and IL-4 Against Intact Catalase and Constructed Catalase Epitopes of Helicobacter pylori From T-Cells

Background:

Helicobacter pylori infection is highly prevalent in the developing countries. It causes gastritis, peptic ulcer disease, and gastrocarcinoma. Treatment with drugs and antibiotics is problematic due to the following reasons: cost, resistance to antibiotics, prolonged treatment and using multiple drugs. Catalase is highly conserved among the Helicobacter species and is important to the survival of the organism. It is expressed in high amounts and is exposed to the surface of this bacterium; therefore it represents a suitable candidate vaccine antigen.

Objectives:

A suitable approach in H. pylori vaccinology is the administration of epitope based vaccines. Therefore the responses of T-cells (IFN-γ and IL-4 production) against the catalase of H. pylori were determined. Then the quality of the immune responses against intact catalase and three epitopes of catalase were compared.

Materials and Methods:

In this study, a composition of three epitopes of the H. pylori catalase was selected based on Propred software. The effect of catalase epitopes on T-cells were assayed and immune responses identified.

Results:

The results of IFN-γ, IL-4 production against antigens, epitopes, and recombinant catalase by T-cells were compared for better understanding of epitope efficiency.

Conclusions:

The current research demonstrated that epitope sequence stimulates cellular immune responses effectively. In addition, increased safety and potency as well as a reduction in time and cost were advantages of this method. Authors are going to use this sequence as a suitable vaccine candidate for further research on animal models and humans in future.

Antibiotic Resistance Patterns and Genetic Diversity in Clinical Isolates of Pseudomonas aeruginosa Isolated From Patients of a Referral Hospital, Isfahan, Iran

Background:

Pseudomonas aeruginosa is a well-known opportunistic pathogen, which affects hospitalized patients in different wards due to its natural resistance to drugs.

Objectives:

The purpose of the current study was to determine the antibiotic susceptibility profiles and genetic relatedness in P. aeruginosa isolated from patients admitted to a referral hospital in Isfahan, Iran.

Materials and Methods:

Out of 150 analyzed samples, 54 P. aeruginosa isolates were recovered and were subjected to antibiotic resistance patterns and genetic diversity determination by Kirby-Bauer’s disk diffusion method and RAPD-PCR, respectively.

Results:

The highest percentage of resistance was observed against ceftazidime and imipenem with 30 (55.6%) isolates; meanwhile all isolates were sensitive to polymyxin B. Twenty-eight (51.8%) isolates revealed resistance to all applied antibiotics. RAPD-PCR (Random Amplified Polymorphic DNA- Polymerase Chain Reaction) results showed 54 unique genotypes, which were divided into 39 clusters.

Conclusions:

Although different source of P. aeruginosa may involve in patient colonization, genetically related strains were isolated from different wards and or the same ward of the hospital. Our results pointed to the restriction of currently used antibiotics in studied hospital. We hope that our results cast light on the control and transmission of the infection in the investigated hospital.

Molecular detection of metallo-β-lactamase gene blaVIM-1 in imipenem-resistant Pseudomonas aeruginosa strains isolated from hospitalized patients in the hospitals of Isfahan

BACKGROUND

Pseudomonas aeruginosa is an opportunistic human pathogen that causes serious problems, especially in people, who have immunodeficiency. In recent times, metallo-β-lactamase (MBLs) resistance in this bacterium has led to some difficulties in treating bacterial infections. The metallo-beta-lactamase family of genes, including blaVIM-1, is being reported with increasing frequency worldwide. The aim of this study is the detection of the metallo-β-lactamase gene blaVIM-1 in imipenem-resistant P. aeruginosa (IRPA) strains isolated from hospitalized patients.

MATERIALS AND METHODS

In this study, 106 P. aeruginosa samples were isolated from various nosocomial infections. The isolates were identified, tested for susceptibility to various antimicrobial agents by the Kirby-Bauer disk diffusion method, and all the imipenem-resistant isolates were screened for the presence of MBLs by using the combined disk (IMP-EDTA). The minimal inhibitory concentration (MIC) of imipenem was determined by E-test on the Mueller-Hinton agar. To detect the blaVIM-1 gene, the isolates were subjected to a polymerase chain reaction (PCR).

RESULTS

Of all the P. aeruginosa isolates, 62 (58.5%) were found to be imipenem-resistant P. aeruginosa (MIC ≥32 μg/ml). Twenty-six (42%) of the imipenem-resistant isolates were MBL positive. None of these isolates carried the blaVIM-1 gene using the PCR assay.

CONCLUSION

The results demonstrated the serious therapeutic threat of the MBL-producing P. aeruginosa populations. The rate of imipenem resistance due to MBL was increased dramatically. Early detection and infection-control practices are the best antimicrobial strategies for this organism. None of MBL-producing isolates in this study carry the blaVIM-1 gene; therefore, another gene in the MBL family should be investigated.

Epidemiology of VIM-1-imipenem resistant Pseudomonas aeruginosa in Iran: A systematic review and meta-analysis

BACKGROUND

Pseudomonas aeruginosa is an opportunistic human pathogen which causes serious problems, especially in people who have immunodeficiency. Metallo beta-lactamase (MBL) resistance in this bacterium has led some difficulties in treating bacterial infections. MBLs are being reported with increasing frequency worldwide. The aim of the present systematic review and meta-analysis was to collect data about the relative frequency (RF) of VIM-1-imipenem resistant P. aeruginosa (VIM-1-IRPA) in different regions of Iran and report an overall prevalence if possible.

MATERIALS AND METHODS

PubMed, ISI web of science, Scopus and Google Scholar were searched using following key terms: "P. aeruginosa," "imipenem," "VIM-1" and "Iran" were. Articles/abstracts, which used clinical specimens and had done polymerase chain reaction to detect the VIM-1 gene of MBL genes, were included in this review. STATA SE version 11.2 (StataCorp, College Station, TX, USA) was used for statistical analysis.

RESULTS

Out of 5457 results found, 10 articles were eligible to be included in our systematic review and meta-analysis. These studies were carried out in Tehran, Isfahan, Kurdistan, Ahvaz, Markazi and Northwest of Iran (Orumieh and Tabriz). Pooled estimation of 1972 P. aeruginosa samples showed that 13% (95% confidence interval = 10.5-16.5%]) of strains were VIM-1 positive. VIM-1-IRPA RF in different studies varied from 0% to 19.5% in Isfahan and Markazi provinces, respectively. We found a moderate heterogeneity (Chochran Q-test, P = 0.032, I-squared = 50.7%) of VIM-1-IRPA RF among studies.

CONCLUSION

According to the results of this study VIM-1-IRPA RF in Iran is in low-level Prevention strategies to reduce the prevalence rates of VIM-1 positive strains in Iran are needed.

Comparison of three phenotypic and deoxyribonucleic acid extraction methods for isolation and Identification of Nocardia spp

BACKGROUND

The aerobic Actinomycetes are a large group of soil-indwelling bacteria that are distributed in world-wide. These Gram-positive bacteria are most commonly associated with opportunistic infections in both immunocompromised and immunocompetent hosts.

MATERIALS AND METHODS

In this study, three phenotypic and deoxyribonucleic acid (DNA) extraction methods for isolation and identification of Nocardia genus were compared. Samples were taken in five different locations of Isfahan's suburb from hospitals area, parks, agricultural lands, gardens, arid lands with different soil temperature and pH.

RESULTS

In this study, showed that slip-buried-method was better than two other phenotypic methods; 14 out of 70 soil samples (20%) were positive for Nocardia spp. DNA of positive samples were extracted with three techniques and DNA extraction by microwave technique was better than others. This technique was confirmed with observation of DNA bands on 1% agarose gel.

CONCLUSIONS

These bacteria are important in immune deficient patients such as cancer patients, transplant recipients, tuberculosis; acquired immunodeficiency syndrome etc., Their affluence is unsteady in different zones of the world. In this study, among the three phenotypic methods for the isolation of Nocardia slip-buried method was better than other methods. Among DNA extraction techniques, DNA extraction by microwave method would be selective method for DNA extraction of Nocardia spp. compared with others techniques.

Efflux pump regulatory genes mutations in multidrug resistance Pseudomonas aeruginosa isolated from wound infections in Isfahan hospitals

BACKGROUND

Multidrug resistance Pseudomonas aeruginosa (MDR-P. aeruginosa) is a worldwide threat for public health. Hyperexpression of efflux pump systems (MexAB-OprM and MexCD-OprJ), which is a well-known mechanisms for MDR emerging, is controlled by regulatory genes, mexR and nfxB, respectively. The aim of this study was to evaluate point mutations in mexR and nfxB genes in MDR- P. aeruginosa isolated from wound infections.

MATERIALS AND METHODS

A total of 34 P. aeruginosa cultures obtained from wound infections were analyzed. Among them eight isolates identified as MDR-P. aeruginosa and were subjected to determination of mutations in mexR and nfxB genes.

RESULTS

We detected eight-point mutations in mexR and 12-point mutations in nfxB. The most common mutations were common G327-A (eight isolates), G384-A (eight isolates), G411-A (eight isolates). Mutations in A371-C and A372-C were the predominant substitution which was seen in nfxB. Amino acid substitutions were also found at position 124 and 126 for NfxB and MexR, respectively.

CONCLUSIONS

P. aeruginosa isolates with mutation in efflux pump regulatory genes such as mexR and nfxB could be a main factor contributed to antibiotic resistance and must be considered in antibiotic treatment.

The study of mutation in 23S rRNA resistance gene of Helicobacter pylori to clarithromycin in patients with gastrointestinal disorders in Isfahan - Iran

Background:

Helicobacter pylori antimicrobial resistance is an important factor responsible for treatment failure. The purpose of this study was evaluating the prevalence of point mutations in clarithromycin-resistant clinical isolates of H. pylori in Isfahan city of Iran.

Materials and Methods:

Thirty isolates of H. pylori from 130 biopsy specimens were isolated by culture and confirmed by biochemical and PCR tests. The MIC of clarithromycin antibiotic for 30 clinical isolates of H. pylori was determined by E-test method. The point mutations in the 288 bp of 23S rRNA gene of H. pylori were investigated in four clarithromycin-resistant clinical isolates by PCR followed by sequencing.

Results:

Among 30 isolates of H. pylori, 4 cases were resistant to clarithromycin. One point mutation was found at position T2243C in the 23S rRNA gene in all resistance isolates.

Conclusions:

In our study, H. pylori resistance to clarithromycin associated with point mutation at position 2243 (T2243C).

Morphological and Bactericidal Effects of Different Antibiotics on Helicobacter pylori

Background:

Helicobacter pylori (H. pylori) is a spiral Gram negative bacteria that can transform to the coccoid form in adverse conditions.

Objectives:

The aim of this study was to determine the in vitro morphological and bactericidal effects of metronidazole, amoxicillin and clarithromycin on H. pylori.

Materials and Methods:

The standard strain 26695 of H. pylori was cultured on Brucella agar (BA) and the minimum inhibitory concentrations (MICs) of three antibiotics were determined by E-test method. The bacteria were exposed to antibiotics at 1/2 MIC, MIC and 2X MIC concentrations in Brucella broth (BB). Induced coccoid forms were confirmed by Gram staining and light microscopy. The viability of cells as well as the susceptibility of viable coccoids to antibiotics were examined using the flow cytometry method.

Results:

All of the three antibiotics at sub-MIC induced coccoid forms. The highest rates of coccoids (> 90%) were induced at 0.008 μg/mL concentration (1/2 MIC) of amoxicillin, 72 hours postexposure. Metronidazole and clarithromycin with 1/2 MIC (0.5 and 0.125 µg/mL respectively) induced lower rates of coccoid forms (60% and 40% respectively). Potent bactericidal effects on coccoids were observed with Metronidazole at 2X MIC and clarithromycin at MIC (0.25 µg/mL) (80 - 90%). Amoxicillin with MIC and 2X MIC had no bactericidal effect on coccoid forms.

Conclusions:

Despite the good in vitro bactericidal effect of amoxicillin on spiral forms of H. pylori, this antibiotic has little effect on induced coccoids that may develop after the inappropriate in vivo antibacterial treatment. Hence, for successful therapy, it is essential not only to eradicate the spiral forms, but to eliminate the viable coccoids.

Resistance pattern of Helicobacter pylori strains to clarithromycin, metronidazole, and amoxicillin in Isfahan, Iran

BACKGROUND

Helicobacter pylori (H. pylori) resistance to antibiotics has become a global problem and is an important factor in determining the outcome of treatment of infected patients. The purpose of this study was to determine the H. pylori resistance to clarithromycin, metronidazole, and amoxicillin in gastrointestinal disorders patients.

MATERIALS AND METHODS

In this study, a total of 260 gastric antrum biopsy specimens were collected from patients with gastrointestinal disorders who referred to Endoscopy Section of the Isfahan Hospitals. The E-test and Modified Disk Diffusion Method (MDDM) were used to verify the prevalence of antibiotic resistance in 78 H. pylori isolates to the clarithromycin, metronidazole, and amoxicillin.

RESULTS

H. pylori resistance to clarithromycin, metronidazole, and amoxicillin were 15.3, 55.1, and 6.4%, respectively. In this study, we had one multidrug resistance (MDR) isolates from patient with gastritis and peptic ulcer disease.

CONCLUSION

Information on antibiotic susceptibility profile plays an important role in empiric antibiotic treatment and management of refractive cases. According to the results obtained in this study, H. pylori resistance to clarithromycin and metronidazole was relatively high. MDR strains are emerging and will have an effect on the combination therapy.

A new multiplex polymerase chain reaction assay for the identification a panel of bacteria involved in bacteremia

Background:

Throughout the world, bloodstream infections (BSI_s) are associated with high rates of morbidity and mortality. Rapid pathogens identification is central significance for the outcome of the patient than culture techniques for microbial identification. To develop an end point multiplex PCR to identify a group of bacteria including Enterococcus spp., Pseudomons aeruginosa, Staphylococcus spp., Acinetobacter baumannii, 16S rDNA, and Drosophila Melanogaster were used as internal control (IC).

Materials and Methods:

Design of primers was done using Mega4, Allel ID6, Oligo6 and Oligo analyzer softwares. Genetic targets for primer designing and identification of genus Enterococcus spp., Staphylococcus spp., and species of Acinetobacter baumannii, Pseudomons aeruginosa, included the rpoB, rpoB and gyrA, sss respectively. Then PCR and multiplex PCR were performed

Results:

The intended specificity was obtained for the bacteria, which used in this study and there wasn't seen any unspecific amplification by the multiplex PCR. The test showed a sensitivity ranging from 1 to 100 target copies per reaction depending on the bacterial species.

Conclusions:

The presented multiplex PCR offers a rapid and accurate molecular diagnostic tool for simultaneous detection of some pathogenic microorganisms. The IC exists in the multiplex PCR accompanied by other primers in the system, can serve as a simple, cost- effective internal control for the multiplex PCR assay.

Assessment of cagE and babA mRNA expression during morphological conversion of Helicobacter pylori from spiral to coccoid

Helicobacter pylori (H. Pylori) is an actively dividing spiral bacterium that changes to coccoid morphology under stressful environments. The infectivity of the coccoids is still controversial. The aim of this study was to determine the viability and expression of two important virulence genes (babA and cagE), in antibiotic-induced coccoid forms. Three strains of H. pylori, the standard 26695 and two clinical isolates (p1, p2) were converted to coccoid form by amoxicillin. Coccoids were identified according to Gram-staining and microscopic morphology. The viability of the cells was analyzed by flow cytometry. The expression of cagE and babA in coccoid forms were evaluated and compared to the spirals by quantitative PCR assay. The coccoid forms were developed after 72 h exposure of H. pylori to ½ MIC of amoxicillin, and the conversion form was completed (100 %) at 144 h in all of three isolates. Flow cytometry analyses showed that the majority of the induced coccoids (90-99.9 %) were viable. Expression of cagE and babA was seen in coccoids; however, in lower rate (cagE, ~3-fold and babA, ~10-fold) than these in spiral forms. Coccoid forms of two clinical isolates significantly expressed higher rate of cagE and babA than standard 26695 strain (P = 0.01). These results suggest that the induced coccoid form of H. pylori is not a passive entity but can actively infect the human by expression of the virulence genes for long time in stomach and probably play a role in chronic and severe disease.

Identification of Nontuberculous Mycobacteria Species Isolated from Water Samples Using Phenotypic and Molecular Methods and Determination of their Antibiotic Resistance Patterns by E- Test Method, in Isfahan, Iran

INTRODUCTION

Many studies have shown epidemiological links between strains isolated in tap water, and those isolated from patients. Molecular methods linked to PCR are more reliable and faster for identification of non- tuberculous mycobacteria (NTM). In this study molecular methods were used for identification and typing of NTM.

MATERIALS AND METHODS

Five hundred ml of 85 water samples was passed through 0.45 μm filters. The filters were transferred directly onto 7H10 Middle Brook solid media, containing 15% OADC. PCR for 16S rRNA was done and the PCR product (1500 bp) was sequenced. PRA of the hsp65 gene was investigated to identify the species of isolates. For evaluation of susceptibility of NTM to antimycobacterial agents, E-test method was used.

RESULT

The genus of 26 isolated NTM was confirmed by 16s rRNA sequence based method. Nineteen isolates of Mycobacteria were differentiated using hsp65 genes PRA. The dominant isolates were M. fortuitum (26.7%), M. chelonae like organism (13.3%) and M. mucogenicum (13.3%). Seventy one percent of NTM species were resistant to isoniazid, 64% to rifampin, 57% to ethambutol, 35% to tetracycline, 14 % to azithromycin and 7.1 % to amikacin.

CONCLUSION

The results showed that E-test method is not a proper technique for antimycobacterial assay because some NTM species are slow in growing and have no growth on Muller Hinton agar. Regarding the 16S rRNA sequence analysis, the identification of isolates was restricted to the genus level, because 99% similarity within 16S rRNA of two isolates may or may not determine the same species.

Development of PCR-based method for detection of Enterobacteriaceae in septicemia

OBJECTIVE

Sepsis is a systemic inflammatory response associated with high mortality rates in the clinical setting. A multiplex endpoint polymerase chain reaction (PCR) based assay for rapid detection of enterobacteriaceae involved in septicemia, which included Internal Control (IC) and 16S rDNA, is presented here. To develop a panel of primers for DNA fragments of 16S rDNA, enterobacteriaceae, IC, and evaluate analytical sensitivity and specificity of the test.

MATERIALS AND METHODS

Primers for amplification of enterobacteriaceae, IC, and16S rDNA were designed, and then PCR was performed. Minimal analytical sensitivity was determined by cloning and colony PCR, and specificity was tested on the basis of their respective standard strains. This study is a cross-sectional Model.

RESULTS

Our results showed the rpoB gene as the most promising target for detection of enterobacteriaceae by PCR amplification. Specificity and sensitivity of endpoint PCR were 100%, 100%, and 100%, and 10, 1, and 100 copies/reaction for enterobacteriaceae, IC, and 16S rDNA, respectively.

CONCLUSION

The molecular panel presented offers the advantage of an easy, reliable, and cost-effective system when compared to other molecular detection methods. However, further evaluation is needed. Our assay holds promising for more rapid pathogens related in clinical sepsis.

Molecular Characterization of Environmental Non-Tuberculous Mycobacteria Using PCR- RFLP Analysis of 441 Bp Heat Shock Protein 65 Fragments

BACKGROUND

Non- Tuberculous Mycobacteria are environmental opportunistic pathogens that can be found in various terrestrial and aquatic habitats. There are an epidemiological links between species isolated in tap water and those isolated from patients. hsp65 gene has more variability in its sequences, compared to the some more conserved genes in NTM, for identification of mycobacteria to species level. In this study, the prevalence of NTM in Isfahan City water samples was determined using culture, biochemical tests and PCR-RFLP analyses of hsp65 gene.

METHODS

Eighty-five water samples were collected and cultured. The mycobacterial isolates were identified by conventional biochemical tests. A 441 bp fragment of hsp65 genes was amplified and digested by two restriction enzymes, BstEII and HaeII. Digested products were analyzed using polyacrilamid gel electrophoresis (PAGE).

RESULTS

25.9% of the water samples contained different species of NTM. Dominant isolates were M. fortuitum (26.7%), M. chelonae like organism (13.3%) and M. mucogenicum (13.3%). Nineteen isolates of Mycobacteria were differentiated using hsp65 genes PCR-RFLP. Three isolates could not be identified at the species level because their RFLP patterns were different from other known PCR-RFLP profiles. There were different hsp65 gene PCR-RFLP profiles produced by digestion with BstEII and HaeIII.

CONCLUSION

This study showed that PCR-RFLP of hsp65 gene in mycobacteria is more reliable method for identification of NTM at the specie level than conventional phenotypic methods (P<0.05). In comparing of RFLP patterns of this study to other investigation, some minor differences were negligible.

Two Dimensional Structural Analysis and Expression of a New Staphylococcus aureus Adhesin Based Fusion Protein

OBJECTIVES

Staphylococcus aureus is a foremost source of numerous nosocomial and community acquired infections. Antibiotic therapy for vancomycin resistant S. aureus (VRSA) can not promise the eradication of infections. Since adhesion is the major route of infections, adhesin based vaccine could suppress S. aureus infections. Fibronectin binding protein A (FnBPA) and clumping factor A (ClfA) are major responsible adhesions involved in S. aureus infections, so they could be candidate vaccine molecules against an extensive range of infections. This project intended to express a new fusion protein construct and analysis of biological activity regarding binding activity.

MATERIALS AND METHODS

pfnbA- ClfA construct was transformed to Escherichia coli BL21 (DE3). Transformant E. coli were grown in LB broth and induced with IPTG and cellular extracts were separated on SDS-PAGE. RT-PCR was performed to verify expression. Binding activity of fusion protein was studied using human gingival fibroblast (HGF) cell line. D1-D3 protein from unpublished study was used as control.

RESULTS

The expected fusion protein fragment showed by SDS-PAGE. RT-PCR verified the existence of mRNA relating to expressed fusion protein. Binding activity of S. aureus decreased after treatment of HGF cells with fusion protein.

CONCLUSION

In total, binding activity of fusion protein was approximately two fold lesser than D1-D3 protein. It is supposed that the fusion protein could not be attached to its ligand easily and would be more accessible to antigen presenting cells and consequently protective antibodies will be produced. This project is pending for in vivo infection study in animal model.

Prevalence of Genes Encoding Bi-Component Leukocidins among Clinical Isolates of Methicillin Resistant Staphylococcus aureus

BACKGROUND

Staphylococcus aureus has been recognized as a major human pathogen and is the major cause of nosocomial infections. Gamma-toxin, leukocidin and other bi-component toxins are a family of proteins encoded by the hlg and luk-PV, respectively. Panton-Valentine leukocidin (PVL) is an example of these toxins and causes leukocyte destruction and tissue necrosis. The aim of this study was to determine the prevalence of bi-component leukocidin in Methicillin Resistant Staphylococcus aureus (MRSA) isolates in staphylococcal infections.

METHODS

Collectively, 143 isolates of S. aureus were obtained from Tehran University of Medical Sciences hospitals and confirmed with biochemical tests. Then polymerase chain reaction was used to detect luk-PV loci and luk-E/D. Coagulase gene was used as internal control. The antibiotic susceptibility patterns of isolates were determined using disk diffusion method.

RESULTS

Out of 149 S. aureus isolates 24.2% were luk-PV positive and 73.8% were luk-E/D positive.

CONCLUSION

There was PVL positive MRSA isolates with high prevalence in evaluated hospitals. The diseases from these bacteria are with extensive necrosis, leucopenia and even death. We desire that, prevent from progress and death by diagnosis and right treatment.

Prevalence of Porphyromonas gingivalis and Bacteroides forsythus in chronic periodontitis by multiplex PCR

The present research decided to study prevalence of Porphyromonas gingivalis and Bacteroides forsythus in chronic periodontitis patient by use of Multiplex PCR. The subgingival plaque samples from 61 patients suffering from chronic periodontitis with probing depth PD > or = 6 and 40 healthy controls were collected by sterile curette. In this study we used two species-specific Forward primers in combination with a single Reverse primer. These primers target variable and conserved region of 16S rRNA gene, respectively. The study included 61 patients (34 women, 27 men; 24-69 years of age; mean 43) and 40 periodontally healthy controls (22 Women, 18 men, 21-69 years in age; mean 41.35%). Porphyromonas gingivalis was detected in 51 samples (83.61%) and 16 samples (40%) of chronic periodontitis patients and healthy subjects, respectively and Bacteroides forsythus was detected in 32 samples (52.50%) of chronic periodontitis patients and was not detected in any sample from healthy persons. We set up Multiplex PCR in order to detect P. gingivalis and B. forsythus simultaneously. The present data suggest that P. gingivalis is a more important cofactor in etiology of chronic periodontitis. Further studies are needed to determine spectrum of pathogenicity of the disease and effective management of diagnosis and treatment in order to decrease the risk of periodontic complicates such as systemic infection.