http://ijm.tums.ac.ir/index.php/ijm/issue/feed Iranian Journal of Microbiology 2018-10-08T22:14:07+0330 IJM Office ijm@tums.ac.ir Open Journal Systems http://ijm.tums.ac.ir/index.php/ijm/article/view/1638 Bacteriological profile of intra-abdominal infections in a tertiary care hospital 2018-10-07T00:08:02+0330 Sukanya Sudhaharan sukanyavimala@gmail.com Padmaja Kanne kannepadmaja@gmail.com Lakshmi Vemu lakshmivemu57@gmail.com Padmasri Chavali cpadmasri24@gmail.com Shanker Rao Desmukha shamkerdesmukha@gmail.com Bheerappa Nagari nbheerappa@gmail.com <p><strong>Background and Objectives:</strong> Intra-abdominal infections (IAIs) include a wide spectrum of pathological conditions, ranging from uncomplicated appendicitis to fecal peritonitis .The resulting infections should be diagnosed early and treated based on the organism isolated and its susceptibility. In this study the bacteriological profile and antimicrobial resistance pattern of intra-abdominal infections was analyzed.</p> <p><br><strong>Materials and Methods:</strong> A retrospective analysis of samples received from 119 cases of intra-abdominal infections in our Institute from January 2015 to December 2017 was analyzed. Patients with primary peritonitis from cirrhosis or ascites were not included in the study. The specimens were primarily processed, as per standard methods. Identification and antimicrobial susceptibility testing was done by the Vitek-2 system. Anaerobic culture was performed on 5% sheep blood agar plates and incubated in GEN bag anaerobic pouches.</p> <p><br><strong>Results:</strong> In our study perforative peritonitis 43/119 (36.1%) was predominant IAI followed by acute pancreatitis 14/119 (11.7%) and pancreatic necrosis 12/119 (10%). Microbial growth was observed in 66.3% (79/119) of the cases and combined infections were observed in14/119 (11.7%) of the cases. <em>Escherichia coli</em> was the predominant organism isolated in 58/119 (40.8%), out of which 41/58 (70.6%) were ESBL producers and 16 /58 (27.5%) were multi drug resistant isolates. <em>Klebsiella pneumoniae</em> was isolated from 11/119 (9.2%) cases out of which 8/11 (72.7%) were ESBL and 3/11 (27.2%) were multidrug resistant isolates. Post-operative complications was observed in 12/119 (10%) patients with mortality in 15/119 (12.6%) patients.</p> <p><br><strong>Conclusion:</strong> Early diagnosis and appropriate management of the infections will help to prevent the morbidity and mortality associated with these infections.</p> 2018-10-06T23:37:57+0330 ##submission.copyrightStatement## http://ijm.tums.ac.ir/index.php/ijm/article/view/1579 Detection of methicillin-resistant Staphylococcus aureus (MRSA) in clinical samples of patients with external ocular infection 2018-10-07T19:39:15+0330 Ashkan Faridi D.kalantar@kmu.ac.ir Amir Tavakoli Kareshk D.kalantar@kmu.ac.ir Mehdi Fatahi-Bafghi D.kalantar@kmu.ac.ir Mahsa Ziasistani D.kalantar@kmu.ac.ir Mohammad Reza Kandehkar Ghahraman D.kalantar@kmu.ac.ir Seyedeh Zeinab Seyyed-Yousefi D.kalantar@kmu.ac.ir Noshin Shakeri D.kalantar@kmu.ac.ir Davood Kalantar-Neyestanaki D.kalantar@kmu.ac.ir <p><strong>Background and Objectives:</strong> <em>Staphylococcus aureus</em> is the main Gram-positive bacteria isolated from patients with ocular infections. Herein, we describe the pattern of antibiotic resistance, presence of resistance genes including <em>ermA, ermB, ermC, msrA, mecA</em> and the <em>pvl</em> cytotoxin gene in <em>S. aureus</em> isolates collected from patients with external ocular infection.</p> <p><br><strong>Materials and Methods:</strong> In this study, 8 <em>S. aureus</em> isolates were collected from 81 patients that suffered from eye damage. Antibacterial susceptibility of isolates was determined using the Kirby-Bauer disk diffusion method. Resistance genes including <em>ermA, ermB, ermC, msrA, mecA</em> and the <em>pvl</em> virulence gene were detected by PCR method. Staphylococcal cassette chromosome <em>mec</em> (SCC<em>mec</em>) in MRSA isolates were detected by the multiplex-PCR method.</p> <p><br><strong>Results:</strong> Three isolates were resistant to cefoxitin which is considered MRSA. The <em>mecA</em> gene was identified in MRSA isolates. SCC<em>mec</em> type IV and the <em>pvl</em> gene were detected in one of the MRSA isolates that was recovered from a diabetic patient.</p> <p><br><strong>Conclusion:</strong> The emergence of <em>S. aureus</em> isolates belonging to SCC<em>mec</em> type IV and pvl gene among patients with ocular infection is very serious; therefore, identify genetic characterization of MRSA isolates for empirical therapy and infection control is very important.</p> 2018-10-06T23:40:32+0330 ##submission.copyrightStatement## http://ijm.tums.ac.ir/index.php/ijm/article/view/1715 Prevalence of Coxiella burnetii in unpasteurized dairy products using nested PCR assay 2018-10-07T00:08:03+0330 Fargol Abdali f.abdalli69@gmail.com Saeid Hosseinzadeh hosseinzadeh@shirazu.ac.ir Enayat Berizi enayat.berizi@gmail.com Siamak Shams shams_siamak@yahoo.com <p><strong>Background and objectives:</strong> Q fever is a worldwide disease which is common between human and livestock. This disease is created by an obligate intracellular Rickettsia called <em>Coxiella burnetii (C. burnetii)</em>. Cattle, goats and sheep are among the main reservoirs of the disease in humans. The most common routs of transmitting the infection to humans are inhalation of contaminated aerosols and drinking milk and non-pasteurized dairy products. This study was aimed to determine the prevalence of <em>C. burnetii</em> in non-pasteurized dairy products in Shiraz.</p> <p><strong>Materials and Methods:</strong> In this study (from summer 2016 to winter 2016), 238 non-pasteurized dairy products, (48 raw milk, 48 yogurt, 46 cheeses, 48 dough and 48 ice cream samples) were collected from the retail market and analyzed using a nested PCR assay.</p> <p><strong>Results:</strong> This study showed that 20 samples (8.4%) of 238 non-pasteurized dairy products were reported positive for <em>C. burnetii</em> (13 of 48 (27.08%) raw milk, 3 of 48 (6.25%) yogurt, 2 of 46 (4.35%) cheese, 2 of 48 (4.16%) dough and 0 of 48 ice cream samples).</p> <p><strong>Conclusions:</strong> The present study suggests that non-pasteurized dairy as main sources of <em>C. burnetii</em> in Shiraz, Southern Iran; thus, the consumption of pasteurized milk and dairy products is a valuable method to prevent the disease in human.</p> 2018-10-06T23:43:48+0330 ##submission.copyrightStatement## http://ijm.tums.ac.ir/index.php/ijm/article/view/1734 Prevalence of dengue and leptospirosis co-infection in a tertiary care hospital in south India 2018-10-07T00:08:03+0330 Arun Sachu varunn27@gmail.com Anitha Madhavan anitha_anoop@yahoo.co.in Anu Vasudevan anitha_anoop@yahoo.co.in Jayalakshmi Vasudevapanicker anitha_anoop@yahoo.co.in <p><strong>Background and Objectives:</strong> Dengue and Leptospirosis were often discussed separately with rash being more common in dengue and jaundice in leptospirosis. But with increasing reports of co-infection, the situation has become worse. The main objective of this study was to look for the presence of both Dengue and Leptospira IgM antibodies in serum samples of patients, presenting with acute febrile illness. Medical records of the co-infected patients were examined to analyse the clinical features and laboratory findings.</p> <p><br><strong>Materials and Methods:</strong> Serum samples of patients presenting with acute febrile illness were screened for the presence of Dengue IgM antibodies and Leptospira antibodies. Clinical features and laboratory parameters of patients with co-infection were compared with patients having dengue alone. Rainfall data was obtained to look for an association between rainfall and Dengue, leptospirosis and co-infected cases.</p> <p><br><strong>Results:</strong> Co-infection was seen in 33 (3.4%) samples. There was a statistically significant association between clinical features like rashes, bleeding gums and co-infection. There was a statistically significant association between various laboratory parameters like thrombocytopenia and co-infection. There was positive correlation between rainfall and development of dengue, leptospirosis, and co-infection but it was not statistically significant.</p> <p><br><strong>Conclusion:</strong> The overall prevalence of co-infection was 3.4%. This study re-emphasizes the fact that dengue and leptospirosis are widely prevalent in south India and clinicians should be aware that co-infection with dengue and leptospirosis is not uncommon.</p> 2018-10-06T23:46:13+0330 ##submission.copyrightStatement## http://ijm.tums.ac.ir/index.php/ijm/article/view/1516 Molecular diagnosis of genital tract infections among HIV-positive women in Iran 2018-10-07T00:08:03+0330 Mohammad Amin Behzadi ma.behzadi@mssm.edu Mohammad Ali Davarpanah madavarpanah1380@gmail.com Mandana Namayandeh mandananamayandeh@yahoo.com Bahman Pourabbas bpourmicrobiology@gmail.com Soheyla Allahyari sohayari@gmail.com Mazyar Ziyaeyan ziyaeyanm@sums.ac.ir <p><strong>Background and Objectives:</strong> Human immunodeficiency virus (HIV)-infected women are usually at a higher risk of sexually transmitted infections (STIs) than others. The objective of this study was to characterize the prevalence of human papilloma virus (HPV), herpes simplex virus (HSV), <em>Chlamydia trachomatis</em> (CT), and <em>Neisseria gonorrhoeae</em> (NG), and associated risk factors among HIV-infected women in Fars province, Iran.</p> <p><br><strong>Materials and Methods:</strong> In this cross-sectional study, cervical swab samples were collected from 71 HIV-infected women, aged 17-45 years (mean ± standard deviation: 31.11 ± 6.58 years), and tested for HPV, HSV, CT, and NG using PCR assays.</p> <p><br><strong>Results:</strong> Overall, 77.5% of patients were positive for the tested STIs with the following distribution: 36 (50.7%) HPV, 7 (9.9%) HSV, 4 (5.6%) NG, and 27 (38%) CT. From those, 39 (55%) were positive for only one infection, while 16 (22.5%) were positive for multiple infections. We observed that the prevalence of all tested STIs increased by age, except for HSV which showed a slight decrease, although not statistically significant. Socio-economic factors such as low educational level, multiple sex partners, and being a sex worker significantly correlated with higher positive prevalence of STIs in the studied population.</p> <p><br><strong>Conclusion:</strong> A high prevalence of STIs was observed among HIV-infected women in this region. These data might prompt policy makers and STI experts to focus on providing a comprehensive sex education, including participation in screening programs for STIs among high-risk groups.</p> 2018-10-06T23:48:03+0330 ##submission.copyrightStatement## http://ijm.tums.ac.ir/index.php/ijm/article/view/1679 Characterization of gyrA and parC mutations in ciprofloxacin-resistant Pseudomonas aeruginosa isolates from Tehran hospitals in Iran 2018-10-07T19:33:21+0330 Rosetta Moshirian Farahi rosamoshirian@gmail.com Ahya Abdi Ali abdialya@alzahra.ac.ir Sara Gharavi sgharavi@alzahra.ac.ir <p>&nbsp;</p> <p><strong>Background and Objectives:</strong><em> Pseudomonas aeruginosa</em>, a major cause of several infectious diseases, has become a hazardous resistant pathogen. One of the factors contributing to quinolone resistance in <em>P. aeruginosa</em> is mutations occurring in <em>gyrA</em> and <em>parC</em> genes encoding the A subunits of type II and IV topoisomerases, respectively, in quinolone resistance determining regions (QRDR) of the bacterial chromosome.</p> <p><br><strong>Materials and Methods:</strong> Thirty seven isolates from patients with burn wounds and 20 isolates from blood, urine and sputum specimen were collected. Minimum Inhibitory Concentrations (MICs) of ciprofloxacin were determined by agar diffusion assay. Subsequently, QRDRs regions of <em>gyrA</em> and <em>parC</em> were amplified from resistant isolates and were assessed for mutations involved in ciprofloxacin resistance after sequencing.</p> <p><br><strong>Results:</strong> Nine isolates with MIC≥8 µg/ml had a mutation in <em>gyrA</em> (Thr83→Ile). Amongst these, seven isolates also had a mutation in <em>parC</em> (Ser87→ Leu or Trp) indicating that the prevalent mutation in <em>gyrA</em> is Thr83Ile and Ser87Leu/Trp in <em>parC</em>. No single <em>parC</em> mutation was observed.</p> <p><br><strong>Conclusion:</strong> It seems that mutations in <em>gyrA</em> are concomitant with mutations in <em>parC</em> which might lead to high-level ciprofloxacin resistance in <em>P. aeruginosa</em> isolates from patients with burn wounds and urinary tract infections.</p> 2018-10-06T23:50:02+0330 ##submission.copyrightStatement## http://ijm.tums.ac.ir/index.php/ijm/article/view/1529 The antibacterial effect of aquatic and methanolic extract of Myrtus communis on Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis and Prevotella intermedia 2018-10-07T00:08:04+0330 Leila Rahimvand lili.am69@ymail.com Mohammad Niakan niakan@shahed.ac.ir Noushin Jalayer Naderi jalayer@shahed.ac.ir <p class="a"><strong>Background and Objectives:</strong> Anaerobic Gram negative bacteria are the main cause of periodontal destruction. It has been shown that <em>Myrtus communis</em> have anti-bacterial activity on Gram positive and Gram negative bacteria. The aim of this study was to determine the antibacterial effect of aquatic and methanolic extract of <em>Myrtus communis</em> on some of the oral Gram-negative bacteria.</p> <p class="a"><br><strong>Materials and Methods:</strong> The antibacterial effect of aquatic and methanolic extracts of <em>Myrtus communis</em> was determined using disk diffusion method at different concentrations from 10 to 500 mg/ml. The diameter of inhibition zones were determined. The MIC was defined using the standard broth macrodilution method. The results of the study were reported descriptively.</p> <p class="a"><br><strong>Results:</strong> The aquatic extract of <em>Myrtus communis</em> from 20 to 500 mg/ml had antibacterial effect on <em>Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis</em> and <em>Prev</em>otella intermedia. The methanolic extract from 10 to 500 mg/ml had antibacterial effect on <em>A. actinomycetemcomitans, P. gingivalis</em> and <em>P. intermediate</em>. The MIC was achieved at 10 mg/ml, 10 mg/ml and 10 mg/ml for aquatic and methanolic extracts of <em>Myrtus communis</em> on <em>A. Actinomycetemcomitans, P. Gingivalis</em> and <em>P. Intermediate</em>, respectively.</p> <p class="a"><br><strong>Conclusion:</strong> Aquatic and methanolic extracts of <em>Myrtus communis</em> had antibacterial effect on <em>P. gingivalis, A. actinomycetemcomitans</em> and <em>P. intermediate</em>. Most concentrations of aqueous extract were effective on bacteria, so, providing an alcoholic extract, that is a time consuming and costly method, does not seem necessary.</p> 2018-10-06T23:54:10+0330 ##submission.copyrightStatement## http://ijm.tums.ac.ir/index.php/ijm/article/view/1497 Echovirus 30 and coxsackievirus A9 infection among young neonates with sepsis in Iran 2018-10-08T22:10:41+0330 Abdolnabi Shabani abdolnabi.shabani@gmail.com Manoochehr Makvandi manoochehrmakvandi29@yahoo.com Alireza Samarbafzadeh samarbaf5@gmail.com Ali Teimoori teimoori_ali@yahoo.com Mojtaba Rasti mojtabarasti@yahoo.com Chiman Karami chkarami.chiman@gmail.com Nasteran Rastegarvand bord_peto@yahoo.com Roya Nikfar nikfarroya@yahoo.com Ahmad Shamsizadeh shamsizadeh-a@hotmail.com Azam Salehi azam.salhi436@gmail.com Kambiz Ahmadi Angali kzfir@yahoo.com <p><strong>Background and Objectives:</strong> Human enteroviruses (EV) are the most common causes of neonatal sepsis-like disease. The frequencies of EV including coxsackievirus A, coxsackievirus B and Echovirus serotypes have been studied in young infants (younger than three months) with sepsis. So far, the role of enteroviruses among neonates with sepsis was not determined in Ahvaz, Iran. Therefore, this study was aimed to evaluate the frequency of EV among hospitalized young infants with clinical signs and symptoms of sepsis in Ahvaz.</p> <p><br><strong>Materials and Methods:</strong> Blood specimens from 128 neonates (younger than 90 days), including 56 (43.75%) girls and 72 (56.25%) boys, were collected from hospitalized neonates with clinical signs and symptoms of sepsis-like symptoms. All blood samples were negative for bacterial culture. RNA was extracted from all sera and tested for detection of 5'UTR (Untranslated Region) of the EV by RT-PCR. To determine specific strains of EV, positive 5ˊUTR samples were further tested for detection of the VP1 region of EV by RT-PCR.</p> <p><br><strong>Results:</strong> Overall, 50/128 (39.06%) specimens, including 24 (48%) girls and 26 (52%) boys, were positive for EV. 21/ 50 (42%) specimens were positive for the VP1 region. Randomly, 8 positive VP1 were selected and sequenced. Analysis of sequencing data showed 7/21 (33.33%) samples were positive for Echovirus 30 and 1/21 (4.76%) samples were positive for CVA9.</p> <p><br><strong>Conclusion:</strong> The results of this survey indicate high prevalence of 39.06% of EV among young neonates with sepsis. A high prevalence of 33.3% Echoviruses 30 and a low rate of 4.76% coxsackievirus A9 infection has been observed in neonatal patients with viral sepsis. This outbreak is probably one of the first Enterovirus outbreaks to be reported in Ahvaz, Iran. The results of this survey will help to minimize unneeded use of antimicrobial drugs and reduce unnecessary hospitalization.</p> 2018-10-06T23:58:13+0330 ##submission.copyrightStatement## http://ijm.tums.ac.ir/index.php/ijm/article/view/1688 Detection of JC Polyomavirus tumor antigen in gastric carcinoma: a report from Iran 2018-10-08T22:14:07+0330 Samira Izi zahediaf@mums.ac.ir Masoud Youssefi zahediaf@mums.ac.ir Farzad Rahmani zahediaf@mums.ac.ir Nema Mohammadian Roshan zahediaf@mums.ac.ir Atefeh Yari zahediaf@mums.ac.ir Farnaz Zahedi Avval zahediaf@mums.ac.ir <p><strong>Background and Objectives:</strong> Factors contributing to development of gastric cancer are still under investigation. The JC Virus (JCV), as an oncogenic virus, has been indicated to play a possible role in gastric carcinogenesis. Theoretically, tumor antigen (T-Ag), the viral transforming protein, is capable of binding and inactivating tumor suppressor proteins p53 and pRb, there by promoting cancer development although such a role in gastric cancer is still controversial and additional data is needed to reach a definite conclusion. The prevalence of the virus varies in different geographic regions, therefore, we aimed to investigate JCV presence in cancerous gastric tissues of Iranian patients.</p> <p><br><strong>Materials and Methods:</strong> Thirty-one paired samples were included in this study (total of 62 samples). T-Ag sequences were investigated using real-time PCR in formalin fixed paraffin embedded (FFPE) tissue samples from the tumor site and relevant adjacent non-cancerous tissues (ANCT). In positive samples, JCV copy number (viral load) was also measured using real-time PCR. To evaluate T-Ag protein expression, immunohistochemistry examination was performed using an anti-T-Ag specific antibody.</p> <p><br><strong>Results:</strong> JCV sequences were detected in 17 out of 31 gastric cancer tissue samples (54.84%) and in 10 out of 31 of the non-cancerous adjacent gastric mucosa (32.25%) (Odds ratio of 2.4). Viral load in tumoral and adjacent tissue samples was not statistically different (p=0.88). Immunohistochemical study confirmed presence of JC T-Ag in the nuclear compartment.</p> <p><br><strong>Conclusion:</strong> We showed the presence of the JC virus in gastric carcinoma tissue samples in our geographic region. This finding provides supportive data for a possible contribution of JCV in gastric cell transformation to malignancy. However, we highly recommend additional investigations to further explore JC virus and gastric cancer in order to reach a conclusion.</p> 2018-10-07T00:04:02+0330 ##submission.copyrightStatement## http://ijm.tums.ac.ir/index.php/ijm/article/view/1826 A case report of human tularemia from Iran 2018-10-08T22:07:19+0330 Mahdi Rohani mostafavi@pasteur.ac.ir Behzad Mohsenpour mostafavi@pasteur.ac.ir Ahmad Ghasemi mostafavi@pasteur.ac.ir Saber Esmaeili mostafavi@pasteur.ac.ir Mohammad Karimi mostafavi@pasteur.ac.ir Heinrich Neubauer mostafavi@pasteur.ac.ir Herbert Tomaso mostafavi@pasteur.ac.ir Ehsan Mostafavi mostafaviehsan@gmail.com <p>Tularemia is one of the most contagious bacterial infections. Here, we report a human case of glandular tularemia in Iran following the first report in 1980. The patient was a 6-year-old girl who had consumed a hunted hare in Kurdistan Province in western Iran.</p> 2018-10-06T23:52:39+0330 ##submission.copyrightStatement##