Iranian Journal of Microbiology
Volume:8 Issue: 5, Oct 2016

The most common serotype of enterohaemorrhagic Esherichia coli group or Shiga-toxin-producing E. coli is O157:H7. Domestic and wild ruminants are regarded as the main natural reservoirs. O157:H7 serotype is the major cause of gastrointestinal infections in developed countries. In this study was conducted to survey on the toxigenic E. coli O157: H7 strains in milk of industrial dairy farms.
A total number of 150 milk samples were collected from dairy industry in Khuzestan, over a period of 6 months and were evaluated by cultivation in selective media (CT-SMAC) and multiplex PCR.
Two isolates were identified as E. coli using biochemical tests, none of them were toxigenic E. coli O157:H7 as determined by multiplex PCR. Using direct PCR on milk samples, 45 samples contained at least one gene of the studied genes in this investigation (rfb, flic, stx1, stx2). With direct PCR, 2 milk samples were positive for toxigenic O157:H7.
E. coli O157:H7 is present in this region and so the necessity for strict compliance of health standards is recommended. This is the first study on O157: H7 E. coli milk contamination in Khuzestan province. Based on these results, direct PCR is more accurate than indirect PCR.

The frequency of multi-drug resistant Acinetobacter spp. infections is increasing in Iran. Considering availability of limited therapeutic options, clinical response and outcome of ventilator-associated pneumonia due to multi-drug resistant A.baumannii were evaluated in critically ill patients.
In this prospective study, 29 patients with carbapenem resistance A. baumannii ventilator-associated pneumonia were enrolled. Endotracheal aspirate specimens were analyzed according to the clinical and laboratory standard institute instructions in the hospital’s microbiology laboratory. Demographics, clinical, microbiological and laboratory findings were collected for each patient during the treatment course. Therapeutic empirical regimen, change in antibiotic regimen following receiving antibiogram results, clinical and microbiological responses, duration of ICU stay and outcome were collected for each recruited individual.
All of A. baumanii isolates were resistant to pipracillin-tazobactam, ceftriaxon, amikacin and ciprofloxacin. The resistance rate of A. baumanii species was 41.4% for ampicillin/sulbactabm and 93.1% for meropenem. Patients received either meropenem/colistin (51.7%) or meropenem/ampicillin-sulbactam (48.3%) as the treatment regimens based on the antimicrobial susceptibility patterns of isolates. Ventilator-associated pneumonia clinical response, improvement and failure achieved in 15 (51.7%), 8 (27.6%) and 6 (20.7%) of the patients respectively. Microbiological eradication and intermediate status were observed in 9/29 (31%) and 11/29 (37.9%) of patients, respectively
The antibiotic regimens showed comparable efficacy in treatment of VAP due to MDR A. baumannii but mortality rate was high. Considering widespread and high mortality rates associated with MDR infections, applying infection control and antibiotic stewardship programs in hospitals are essential.

Strains of Shigella spp. can cause shigellosis, or bacillary dysentery.that is a public health problem worldwide. The aim of this study was to describe the population structure and genetic relatedness of multidrug resistant S. sonnei and S. flexneri isolated during a one year period from children with diarrhea in Tehran, Iran.
A total of 70 Shigella spp. were detected during the study period . Twenty MDR isolates of Shigella spp. were randomly selected and used in this study. Bacterial identification was performed by conventional biochemical and serological and confirmed by molecular method. After antimicrobial susceptibility testing, we used Multilocus sequence typing (MLST) for subtyping isolates.
We found 14 Shigella sonnei and 6 Shigella flexneri isolates. Results of MLST showed five sequence types (ST) (145, 152, 241, 245, 1502) and BURST analysis revealed the largest number of single locus variant (SLV) and highest frequency (FREQ) for ST152. ST 152 with nine members was predicted as the founder by BURST. Frequency for ST 1502 and ST 245 was four isolates and the least frequency was seen for ST 241 and 145 with one and two members, respectively. ST 145 and ST 245 were described as singletons in BURST. All isolates with ST145 and ST245 were identified as Shigella flexneri.
Annual Multi locus sequence typing of MDR Shigella would help us in better understanding of dominant species and comparing our results with the same studies in other countries especially our neighbor countries in source tracking purposes.

Antibacterial susceptibility testing of clinical bacterial isolates through disk diffusion method plays a major role in antibacterial treatment. One of the main factors affecting the result of these tests is the type, structure and quality of the disks. The main objective of this study was to compare the agreement of antibiotic disks originated from three companies on Quicolor and Mueller-Hinton agar.
Quicolor and Mueller-Hinton agar media were used in disk diffusion method. Seventy clinical isolates from Enterobacteriaceae family (21 Klebsiella spp., 36 Escherichia coli, 1 Enterobacter spp. and 12 Shigella spp.) were investigated in the study. After obtaining data, the results were interpreted as resistant, sensitive or intermediate. Kappa coefficient measured the agreement of two media. Coefficient of variation (CV) was also calculated for antibiotic disks.
The kappa agreement values for three types of antibiotic disks on Quicolor and Mueller-Hinton agar plates were good or excellent for all the examined antibiotics. CV values were also very satisfactory in the majority of cases.
Antibiotic disks from three manufacturers can successfully be used on both Quicolor and Mueller-Hinton agar plates.

Feline herpesvirus-1, feline calicivirus and Chlamydophila felis are the main causes of feline upper respiratory tract disease. This study was conducted to identify of FeHV-1, FCV and C. felis infections in domestic cat population and also to estimate the prevalence of each specific infection in Iran.
The ocular conjunctiva and oropharyngeal specimens obtained from 80 cats were examined using PCR and reverse transcription PCR.
FeHV-1 was detected in 23 (28.8%), FCV in 2 (2.5%) and C. felis in 16 (20%) cats. Twelve cats(15%) had co-infection with 2 or 3 of the mentioned pathogens. Ocular lesions were the most common clinical signs in the FeHV-1 and C. felis infections whereas respiratory lesions were more observed with the FCV infections. It seems that there is an age-related tendency in the infected cats, meaning that the age of the C. felis positive cats was less than those with FeHV-1 and FCV infections.
These results confirm the presence and show the prevalence of three major pathogens associated with upper respiratory tract disease for the first time in Iran.

Human coronaviruses (HCoVs) are one of the main causes of upper respiratory tract infections in humans. While more often responsible for mild illness, they have been associated with illnesses that require hospitalization.
270 Samples from patients hospitalized with the respiratory infection during the autumn season of 2015 were evaluated for the presence of four HCoVs (OC43, 229E, HUK1, and NL63) using an optimized SYBR green RT-PCR assay.
Fifteen HCoV-229E positive samples were identified (5.5 % positive). 85% of positive samples were male with the range of age between 12- 75 years old.
It is the first comprehensive study on determination of the role of human coronaviruses in respiratory infections in Iran. Our data provide a novel insight into the epidemiology of HCoVs in Iran. Further studies are needed and should include the isolation and molecular characterization of HCoVs in Iran.

Hepatitis C virus (HCV) infection is a worldwide concern and it is the major cause of liver disease. Several genotypes of the HCV have been reported from different regions of the world. The determination of the HCV genotypes is important for the prediction of response to antiviral treatment and clinical outcomes. So, HCV genotyping in each region is of great importance. This investigation was performed to determine the distribution of HCV genotypes in Arak city, Central province of Iran.
Patients & In this cross sectional study, 174 cases with chronic HCV infection from Arak city were enrolled. HCV infection was confirmed by positive results in HCV antibody (anti-HCV) and HCV-RNA tests. HCV genotypes were determined using a PCR based genotyping kit.
A total of 174 HCV infected patients with mean age of 37.5±10.24 years were enrolled. 97.7% of cases were male and 2.3% were female. The main route of HCV transmission was injection drug use (IDU) which was observed in 59.8% of cases. Genotyping results demonstrated that subtype 3a (52.9%) was the most prevalent HCV type in Arak, followed by subtype 1a (22.9%) and subtype 1ab (17.8%).
This study showed that HCV subtype 3a was the most prevalent HCV type, followed by subtype 1a and subtype 1ab in Arak, central province of Iran. Investigation of HCV genotypes in different parts of the country is needed to facilitate treatment options and preventive strategies.

Pneumocystis jiroveci is an important causative agent of Pneumocystis pneumonia. During childhood, exposure to Pneumocystis occurs and antibody was built in early childhood. The aim of this study was to describe the molecular epidemiology of P. jiroveci in children without any respiratory syndrome and survey the distribution of different mitochondrial large subunit, ribosomal ribonucleic acid (mtLSU- rRNA) genotypes.
Mini-bronchoalveolar lavage (mini-BAL) fluids from pediatric patients with no history of lung disorders were obtained during a 14-month period. P. jiroveci colonization was confirmed by immunofluorescence staining, nested PCR and sequencing. Genotypic characterization at the mitochondrial large subunit rRNA gene was performed by direct sequencing.
Of 172 BAL specimens from patients, with mean age of 4.9 years, the prevalence of P. jiroveci colonization was 3.5% (6 samples). The results of sequencing revealed the two polymorphisms; 85/A; 248/C in 3 cases, and 85/T; 248/C in other cases. One sample also showed a mutation replacement at position 258 (T-to-C change), which was not reported previously.
Colonized person as an environmental reservoir might play an important role in the progression of infection in immunocompromised patients. Diagnosis of the reservoir and genotyping can be essential for the prevention of nosocomial infections.

Toxoplasma gondii is an obligatory intracellular parasite which causes severe diseases in the fetus of pregnant women and immunocopmromised patients. Serological tests based on recombinant protein are one of the main diagnosis methods for the detection of specific antibodies in serum samples. Dense granule antigenic proteins derived from T. gondii (TgGRAs) are potential antigens for the development of diagnostic tools.
DNA was extracted from T. gondii (RH-strain) tachyzoites and PCR reaction was done using corresponding primers for GRA5 antigen. The PCR product was purified and ligated into pTG19-t vector and then subcloned into XhoI and BamHI digested pGEX6p-1 expression vector. Recombinant plasmid was transformed into E. coli (BL21 DE3) and induced by 1mM IPTG and analyzed by 15% SDS-PAGE. Expressed protein was confirmed by western blot analysis.
There was no difference among the sequences of T. gondii GRA5 gene from different isolates. The recombinant plasmid pGEX-6p-1/GRA5 induced by IPTG was expressed in E. coli. It was a GST fusion protein and could react with human positive sera analyzed by western blot.
The GRA5 gene of T. gondii isolates is highly conservative. This antigen as a recombinant protein was successfully expressed in E. coli, which showed high immunoreactivity.

Molecular typing methods are important and useful tools to assess the transmission, diversity of strains and differentiation between new infections and relapses which can effectively help in controlling infections. The aim of this study was to evaluate the molecular typing methods which have been used in Iran. By evaluating the results and discriminatory power of each method, we can assign appropriate weight to each technique and ultimately offer a common strategy for future epidemiological studies.
We searched several databases to identify studies addressing Mycobacterium tuberculosis molecular epidemiology in Iran. Hunter-Gaston discrimination index (HGDI) was used to evaluate the discriminatory power in each method. Relevant articles were selected and analyzed; HGDI index was calculated for each technique.
The most common genotyping methods used in the articles were RFLP, MIRU-VNTR, spoligotyping, PFGE and RAPD-PCR. The most frequently techniques were IS6110-RFLP, MIRU-VNTR and spoligotyping alone or in combination. The highest discrimination power (average HGDI: 0.9916) was obtained by RFLP followed by MIRU-VNTR (average HGDI: 0.9638) and spoligotyping (average HGDI: 0.9041) respectively.
Combination of MIRU-VNTR with spoligotyping can be recommended for large-scale genotyping in Iran. It seems appropriate to consider spoligotyping as the first technique for screening followed by other techniques with higher discrimination power such as MIRU-VNTR or IS6110-RFLP.

Pseudomonas aeruginosa is a Gram-negative, aerobic bacterium found in water and soil. It is a normal flora in skin and gastrointestinal tract of human beings. P. aeruginosa as an opportunistic pathogen involved in nosocomial infections having multiple pathogenic factors and shows high rate of resistance to different antibiotics. The aim of this study was to identify the most important native medicinal plants of Iran effective on P. aeruginosa.
All required information was obtained by searching keywords such as P. aeruginosa, medicinal plant extracts or essential oils in published articles in authentic scientific databases such as Science Direct, Wiley-Blackwell, Springer, Google scholar, Scientific Information Database (SID) and Magiran.
According to the literature review, our results showed 12 different native medicinal plants were effective against P. aeruginosa in Iran including Eucalyptus camadulensis, Marticaria chamomilla, Ferula gummosa Boiss, Lawsonia inermis, Ocimumgra tissimum, Allium sativum, Satureja hortensis L, Satureja bachtiarica Bunge, Satureja khuzestanica (Jamzad), Thymus daenensis Celak, Thymus carmanicus Jalals and Camellia sinensis.
Phytochemical analysis has shown that bioactive compounds of medicinal plants with their antioxidant and antimicrobial properties can be good alternatives for the synthetic medicines in food and drug industry.