Iranian Journal of Microbiology
Volume:11 Issue: 2, Apr 2019

Global climate change leads to an increasing in the number and severity of weather events such as floods. Floods have been reported one-half of all weather-associated disasters with high impacts on countries. Global warming causes a different pattern of rainfall in Iran caused long-term drought since 30 years ago and recent heavy raining which lead to a massive flood in this country. It is predicted that health subsequences of Iran 2019 flood such as communicable diseases vary due to the geographical extent and different climates of flooded areas. However, observing long term and short term preventive measures can be effective to reduce the high impact of flood in Iran.

Floods are one of the natural disasters occurring worldwide which have a massive range of health impacts. In addition to immediate dangers such as drowning, floods can increase the transmission of some communicable diseases. Up to now there was no report of viral infection outbreaks after 2019 spring floods in Iran. This review explains the possible viral infections which may occur during or after floods.

The aim of this study was to determine the drug susceptibility pattern of the pathogens causing bacteraemia and fungemia in patients who have developed febrile neutropenia after chemotherapy. A total of 95 patients with suspected or proven malignancy (50 patients) were admitted to the adult haematology ward at Taleghani Hospital in Tehran. Blood samples were inoculated into the bottles of Bact/Alert blood culture system and sent to Payvand’s clinical and special laboratory immediately and then incubated at 35 ± 2°C. Culture from positive bottles were plated on appropriate media and incubated at 37°C and 30°C for bacterial and fungal isolation, respectively. A bacterial suspension with turbidity equal to 0.5 McFarland (1.5 × 108 CFU/mL) was prepared and used for the Vitec2 system (biomerioux). Statistical analysis using independent Fisher’s exact test was conducted and a p-value of < 0.05 was considered as significant. Among 50 patients with approved malignancy, Acute Lymphoblastic Leukaemia (ALL) and Acute Myeloid Leukaemia (AML) were the most common underlying diseases. This study showed, 20% (n: 10) of febrile neutropenic episodes established positive blood culture. Of them, 3 were Gram-negative (30%) and 5 were-Gram-positive bacteria (50%) and 2 patients (20%) showed fungemia with Fusarium spp. It is crucial to know about the likely pathogens and their local antibiotic and antifungal sensitivity patterns. Such local findings will show if any modifications to treatment guidelines are necessary.

Colonization of Pseudomonas aeruginosa in Cystic Fibrosis (CF) patients may lead to severe pulmonary disease and death. Different characteristics of P. aeruginosa from these patients were determined in the present study. Antimicrobial susceptibility and AmpC-overproduction were determined. The β-lactamase genes were detected by PCR and the oprD gene was sequenced in some of the carbapenem resistance isolates. Distribution of exo genes was determined by PCR. Cytotoxicity of Exo effector proteins was measured using A549 cells. Biofilm production was determined by microtiter plate assay. Random amplified polymorphic DNA (RAPD) –PCR was performed for molecular analysis. Polymyxin B, piperacillin/tazobactam and meropenem were the most active antibiotics and 9.6% of isolates were ampC overproducers. The prevalence of blaVEB, blaOXA, blaVIM, and blaPER genes were as follow: 22.7%, 3.75%, 6.25% and 3.75%, respectively. A high proportion (83.5%) of isolates was able to produce biofilm. The exoT gene was present in all isolates while exoU was present in about 35% of them. RAPD-PCR revealed 49 patterns among 78 tested isolates in which 34 patterns were detected once. Biofilm formation ability and relatively high frequency of exoS may contribute to the persistence of bacteria within lungs of CF patients. Some characteristics of isolates recovered from a single patient after several sampling procedures were similar, while others lacked resemblance.

Identification of yeasts provides helpful information for appropriate administration of anti-fungal treatments; however, few reports from the Vietnam have been published. This study has been performed to find the prevalence of Candida blood stream isolates from patients in two hospitals in Vietnam. Candida spp. were isolated from blood cultures in two hospitals, Vietnam between May 2013 and May 2015. Participating hospitals were 103 Military Hospital, Ha Noi city (550 beds) and Cho Ray Hospital, Ho Chi Minh city (1800 beds). All the bloodstream isolates were identified to species level by the germ tube test and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). In addition, unknown isolates were subjected to PCR sequencing. A total of 93 Candida isolates were isolated from blood cultures during the study period. The results of this study showed that C. tropicalis (n = 47, 50.54%) was the most common agent, followed by Candida albicans/dubliniensis (n = 18, 19.35%), C. parapsilosis (n = 16, 17.20%), C. glabrata (n = 6, 6.45%), C. mesorugosa (n = 5, 5.38%) and C. krusei (n = 1, 1.08%), respectively. The frequency of the non-albicans Candida species in blood is increasing, especially C. tropicalis. Additional investigations should be made to clarify the epidemiological profile of invasive Candida bloodstream in Vietnam.

Oral candidiasis is a serious problem for immunocompromised patients, especially patients with hematological malignancies. After becoming a systemic candidiasis it is difficult to diagnose, control and treat in individuals with hematological malignancies. The aim of this study was to diagnose candidiasis in the oral mucosa of patients with leukemias and lymphomas in a timely manner in order to prevent their progression to systemic candidiasis. In this cross sectional study, 50 clinical samples were collected from the mouth of patients with hematological malignancies undergoing chemotherapy from the oncology units of teaching hospitals in Kerman, Iran. Patients were from Kerman, Sistan-Baluchestan and Hormozgan in south-eastern Iran. Sampling was restricted to patients with diagnosed acute lymphoid leukemia (ALL); acute myeloid leukemia (AML); chronic lymphoid leukemia (CLL); chronic myeloid leukemia (CML); Hodgkin’s lymphoma (HL) and non-Hodgkin’s lymphoma (NHL). Presumptive species identification of fungi was performed using conventional methods like colony characteristics on CHROMagar Candida medium, germ tube production, and assessing the morphology fungi on corn meal agar. Confirmation of presumptive candida isolates was performed using PCR-RFLP. From a total of 50, 14 patients (28%) had positive oral candidiasis. Candida albicans (57.14%) was the most common species followed by Candida glabrata (14.28%), Candida parapsilosis (14.28%), Candida krusei (7.14%) and Candida kefyr (7.14%). Candida albicans had the highest rate of oral infection in ALL (35.71%) and then NHL (28.57%) patients. The results indicate that oral candidiasis is a prevalent fungal infection in the patients with hematologic malignancies with C. albicans being the main etiological agent. However, other species of Candida cause similar infections in these patients.

Bacterial agents are commonly accepted as the main etiology of endodontic infections. A significant proportion of oral bacteria cannot be cultured using existing methods. Since diversity and abundance of bacterial species are different in different populations, the present study was aimed to identify effective microorganisms in persistent endodontic infections in Iranian patients based on culture and molecular biology methods using sequence analysis of 16S rDNA gene.

Thirty patients with previous failure of endodontic treatment were enrolled in the study. After isolation and disinfection of the tooth surrounding area with 3% sodium hypochlorite and 30% hydrogen peroxide, sampling from the root canals was carried out using two sterile Hedstrom files and two sterile paper points, and then the specimens were transferred to the microbiology laboratory in thioglycolate transport medium so that they undergo aerobic-anaerobic culture, PCR, and 16S rDNA gene sequencing.

Of 30 patients (15 women and 15 men), 15 patients had radiographic lesions smaller than 5 mm and other 15 patients had radiographic lesions larger than 5 mm. The mean age of patients was 40.20 ± 13.76 years. A total of 26 patients were asymptomatic. Only four patients had clinical signs such as pain and percussion sensitivity and Tannerella forsythia was the most common bacterium found in this group of patients. 13 bacterial species were found in 11 different genus, one virus strain and one fungus strain. From 30 studied specimens, Enterococcus faecalis was the most common microorganism with prevalence rate of 63.63%.

This study showed the type and prevalence of effective bacteria in secondary/persistent endodontic infections in Iranian patients. E. faecalis is the most commonly found microorganism in Iranian patients.

Adenoviral keratoconjunctivitis is an extremely frequent ophthalmological disease caused by various serological subtypes of human adenovirus (HAdV) worldwide. Adenoviruses serotypes 8, 11, 19, 37 frequently cause epidemic keratoconjunctivitis (EKC). This study was conducted to evaluate the frequency of adenovirus serotypes in patients with EKC in Ahvaz , Iran. Eighty- eight ocular swabs were collected from patients with EKC. The specimens were analyzed for detection of adenovirus by standard PCR. The PCR products were further sequenced and analyzed to determine the serotypes. The study population consisted of 49/88 (55.7%) males and 39/88 (44.3%) females. Among them 25 (51.02%) males and 22 (56.41%) females were positive for HAdV serotype 8 (p= 0.488). Overall forty-seven (53.4%) samples were positive for AdV serotype 8 while forty- one patients (46.59%) were negative for the adenovirus serotypes. The results of this study revealed predominanance of HAdV 8 with high prevalence of 53.4% among patients with Keratoconjunctivitis. Forty- one patients (46.59%) were negative for adenovirus. Still, the role for other related viruses such as enteroviruses need to be investigated in patients with EKC.

HIV enteropathy may cause disruption of the intestinal barrier, leading to a loss of CD4+ T cells, increased intestinal permeability, and microbial translocation. Lactobacillus plantarum IS-10506 has the ability to improve gut barrier function. This study investigated the effect of L. plantarum IS-10506 on a number of biomarkers of enteropathy-related damage in HIV-infected paediatric patients undergoing antiretroviral therapy (ARV). A randomized, double-blind, placebo-controlled study was conducted on 2-18 year-old children, diagnosed as HIV infected according to the WHO 2007 criteria who had received ARV for ≥ 6 months. Subjects were excluded if ARV therapy was discontinued or the patients took probiotics ≥ 2 weeks prior to the study or during the study period. Subjects were randomized into a probiotic group and placebo group. The probiotic group received L. plantarum IS-10506 2.86 × 1010 cfu/day for 6 days. Blood lipopolysaccharide (LPS) level, serum CD4+ T cell count, serum CD8+ T cell count, CD4+/CD8+ T cell ratio, and faecal sIgA level were assessed as biomarkers. Twenty-one subjects completed this study. The blood LPS level decreased significantly in the probiotic group (p = 0.001). There was no significant difference in absolute CD4+ T cell count, percent CD4+ cells, absolute CD8+ T cell count, CD4+/CD8+ T cell ratio, or faecal sIgA. No serious adverse events were reported. The probiotic L. plantarum IS-10506 reduced the blood LPS level but showed no effect on the humoral mucosa and systemic immune response in HIV-infected children undergoing ARV therapy.

Microbial communities residing in the gut play a major role in the communication between the gut and the brain through neural, immune, and hormonal routes. Changes in abundance of beneficial intestinal bacteria can affect health of individuals. Conversely, drugs, disease, diet and other factors can alter the gut microbiome. However, there is limited information on the effect of exogenous factors on gut microbiota. In this study, we investigated whether a beneficial bacterium, the probiotic Lactobacillus plantarum IS-10506, can stimulate the gut–brain axis using Wistar rats. The animals were divided into two groups: one received L. plantarum IS strain 10506 supplementation, while the control group received no treatment. Activation of the gut–brain axis was evaluated by immunohistochemical analysis of intestinal and brain serotonin (5-HT) and brain neurotrophin (NT), serotonin transporter (5-HTT), and brain-derived neurotrophic factor (BDNF) levels. The results showed that BDNF (p< 0.000), NT (p< 0.000007), and 5-HTT (p< 0.000007) expression was upregulated in the brain along with intestinal 5-HT (p< 0.000) level in rats treated with L. plantarum strain IS-10506 relative to the control group. The probiotic L. plantarum IS-10506 stimulates the gut–brain axis and can potentially promote brain development and function.

Human β-defensin-2 (hBD-2) is an essential antibacterial peptide involved in innate immunity and is expressed in breast milk and intestinal mucosa. The aim of this study was to investigate fecal hBD-2 levels and gut microbiota in preterm neonates with different feeding patterns. This study was cross-sectionally designed and included 44 preterm neonates categorized into four groups as follows: breast milk only, breast milk predominant, formula milk predominant, formula milk only. The study was conducted at the Neonatology Ward, National Center Hospital Cipto Mangunkusumo, Jakarta from November 2016 to April 2017. hBD-2 levels were measured by ELISA. Intestinal bacteria were quantified by qPCR. hBD-2 levels were significantly different between groups (one-way ANOVA, p=0.004) and the highest value of hBD-2 was found in the formula milk predominant group (344.87±61.2 ng/mL). hBD-2 levels were positively correlated with feeding pattern (Spearman correlation test, p=0.009, r=0.391). There were no significant differences in the total number of specific intestinal microbiota (Bifidobacterium, Lactobacillus and Klebsiella) among groups (one-way ANOVA, p>0.05). Interestingly, the formula milk only group had the highest amount of Klebsiella compared with other groups. hBD-2 levels were not correlated with the quantity of Bifidobacterium, Lactobacillus and Klebsiella (Pearson correlation test, p>0.05). hBD-2 levels were significantly higher in the formula milk predominant group compared with the breast milk only group. Gut microbiota patterns showed that Bifidobacterium and Lactobacillus were higher in the breast milk only group, while Klebsiella was higher in formula milk group, although this difference was not statistically significant.

Probiotics are live microorganisms that, when administered in an adequate amount, confer a health benefit on the host through the gut. Saccharomyces cerevisiae is a widespread yeast found in nature. This microorganism has been used as a probiotic agent in recent years. In this study, the effect of microencapsulation on survival rate of S. cerevisiae var. boulardii in the simulated gastrointestinal tract medium and the impact of microencapsulated S. cerevisiae var. boulardii on some serum biochemical factors in a rat model was evaluated. 30 male wistar rats were divided into three groups (control, rats receiving microencapsulated S. cerevisiae var. boulardii, and rats receiving S. cerevisiae var. boulardii alone). The probiotic was gavaged at a dosage of 2 gr/kg BW for 8 weeks. Blood was collected from rats at the end of the treatment period and biochemical factors were measured using Mancompany kits. The results showed a significant increase in viability of microencapsulated S. cerevisiae var. boulardii in comparison with free S. cerevisiae var. boulardii (p<0.05). Weight of rats in probiotic treated groups was significantly higher in comparison with the control group (p<0.05). Moreover, probiotic treatment reduced mean levels of triglycerides, cholesterol, free blood sugar and liver enzymes in rats. Microencapsulation could increase the survival rate of yeast probiotics in the gastrointestinal tract; however, more studies are needed for better understanding of the exact effect of microencapsulation on probiotics’ function.

The aim of this study was to evaluate the antibacterial and antibiofilm activity of recombinant Azurin from Pseudomonas aeruginosa against different bacterial species. The azurin gene was cloned in the pET21a vector. The pET21a-azurin construct was transformed into Escherichia coli BL21. The recombinant Azurin was expressed and purified using affinity chromatography and confirmed by Western blotting. The cytotoxicity of rAzurin was assessed on peripheral blood mononuclear cells. Antibacterial and antibiofilm activity of rAzurin with different concentrations were determined by micro-broth dilution and crystal violet methods, respectively. The effect of rAzurin on bacterial species was statistically analyzed by t- test and spearman correlation. The identity of purified protein was confirmed by blotting and distinguished as a 14 kDa band on 15% SDS-PAGE. The IC50 of rAzurin on Peripheral Blood Mononuclear Cell (PBMC) was determined as 377.91±0.5 µg/mL in 24 h. Vibrio cholerae and Campilobacter jejuni displayed the most sensitivity to rAzurin (27.5 and 55 μg/mL, respectively) and the highest resistance (220 μg/mL) was displayed by P. aeruginosa and E. coli. The MIC for other species was 110 μg/mL. The Minimum Biofilm Inhibition Concentration (MBIC) was determined as 220 μg/mL for Salmonella enterica and V. cholerae, 300 μg/mL for Shigella sonnei, Shigella flexneri and P. aeruginosa and 440 μg/mL for the other species. The antimicrobial effect of rAzurin on bacterial species were significant (p value<0.05) and correlation coefficient was negative. The rAzurin appears to be an appropriate choice and a new strategy for prevention of bacterial infection. It inhibits bacterial growth and biofilm formation and candidates as antimicrobial peptides.

Chitosan, a polysaccharide derived from squid pens – the squid waste, is gaining considerable interests in biomedical engineering due to the biodegradability, biocompatibility, nontoxicity, and antibacterial activity. It is necessary to eradicate the bacteria from root canal in endodontic treatment, including Porphyromonas gingivalis. P. gingivalis is one of the most prevalently found bacteria in root canals and its presence can cause endodontic treatment failure. This study was conducted to find the antibacterial effect of chitosan from squid pen against P. gingivalis at a certain concentration. Chitosan 1.5% (w/v) was diluted in several tubes. The lowest concentration with no bacterial growth was considered to have antibacterial activity against P. gingivalis. There was no bacterial growth in nutrient agar media at the concentration of 10.75%. Chitosan that was made from squid pens has antibacterial activity against P. gingivalis.

Pfu DNA polymerase is an enzyme that exhibits the lowest error rate in the 3´ to 5´ exonuclease (proofreading) activity during DNA synthesis in Polymerase Chain Reactions (PCRs). This study was aimed to express and purify Pfu DNA polymerase in a bacterial expression system under a simple purification method. Pfu polymerase gene sequence, derived from Pyrocuccus furiosus (Pfu) genomic DNA, was cloned and overexpressed in E. coli BL21 (DE3) pLysS. Upon overexpression, bacterial lysate containing the Pfu DNA polymerase was heated at 94°C for 5 minutes. Pfu DNA polymerase having high thermal stability was retained while the other bacterial proteins were denatured. The resulting thermo stable Pfu DNA polymerase was separated from the other debris of the denatured proteins by simple centrifugation. The enzymatic activity of the resulting Pfu DNA polymerase was estimated by comparing with the commercial Pfu DNA Polymerases. An estimated 50000 units of functional Pfu DNA polymerase was produced from a 400 ml culture. The in-house produced Pfu DNA Polymerase could be used for routine amplification that requires high-fidelity such as cloning and DNA sequencing.

Septic arthritis (SA) remains to be a critical diagnosis for a swollen knee at the emergency department. Here, we report a rare case of bilateral knee arthritis in a 59-year-old diabetic woman who had been immobilized 5 months prior to admission. Her right knee swelling exacerbated in 10 days leading to left knee involvement. In 5 days the clear synovial tap in the first hospital turned purulent in the second hospital and empirical antibiotics get started with high WBC count, dominant neutrophils, and Gram-positive cocci in smear. Knee arthrotomy was performed after 6 days in the third hospital with the same smear results but negative blood and synovial cultures of both knees. When followed in retrograde, two positive blood cultures were reported for Streptococcus agalactiae in the second hospital. Vancomycin was changed to ampicillin and symptoms were resolved in 4 weeks. Despite improvement, mobility was not retained. Uncommon etiologic agents of knee arthritis should be in mind specifically in debilitated patients. Timely initiation of proper antibiotics hinders permanent sequels, hence clinicians should be suspicious of such organisms.