Iranian Journal of Microbiology
Volume:9 Issue: 6, Dec 2017

Tuberculosis (TB) is still responsible for a wide range of deaths worldwide. Beijing genotype is one of the most important and virulent strains in Mycobacterium tuberculosis. This study was designed for determination Beijing genotypes of M. tuberculosis in Golestan province, north of Iran.
In the current descriptive study, 238 clinical MTB isolates, obtained from patients with pulmonary and extra-pulmonary TB in north of Iran, were evaluated. Oligonucleotide primers for the Beijing and non-Beijing genotypes and specific probes for their detection by a real-time PCR method were employed. In addition, an association between the Beijing genotype and possible clinical and demographic factors was evaluated.
The method revealed that 33 cases (13.9%) were the Beijing lineage and 205 (86.1%) the non-Beijing genotype. The mean age of patients infected with the Beijing and non-Beijing strains was 37.27 ± 18.3 and 51 ± 21.2 years, respectively; the difference was statistically significant (P = 0.001). In addition, the prevalence of the Beijing strain decreased with age. Patients with a TB infection caused by the Beijing genotype were also more vulnerable to treatment failure. Based on the origin of the samples, the Beijing genotype was more often observed in extra-pulmonary samples compared with Pulmonary ones (P = 0.001).
The Beijing genotype of MTB is prevalent in our region especially among young people which could indicate the risk of further expansion in the future.

Acinetobacter baumannii bacteremia are grave because of the multi-resistance of the organism to antibiotics. This study aimed to determine the prevalence of A. baumannii isolated from blood cultures and to describe their antibiotic resistance patterns.
A retrospective longitudinal study was conducted on blood cultures between 2010 and 2014 from all Ibn Rochd University Hospital intensive care units; it was based on the exploitation of microbiology laboratory database (duplicates were excluded). Isolation and identification of A. baumannii were performed according to standard techniques of bacteriology and susceptibility testing as recommended by the CLSI. PCR was used to detect β-Lactamase genes,
blaOXA-51, blaOXA-23.
Among the 4232 samples received at the laboratory, 2402 (56.8%) were positive. Negative coagulase Staphylococcus was isolated in 21.6% of cases followed by A. baumannii (9.2%), and K. pneumoniae (9.1%). A. baumannii strains were resistant to most antibiotics tested: imipenem (75.7%), ceftazidim (85.4%), cefotaxim (98.6%), gentamicin (78.1%), amikacin (63.5%) and ciprofloxacin (88.2%). All A. baumannii strains, resistant to carbapenem, tested were positive for blaOXA-51 genes and 87.5% expressed the blaOXA-23 genes.
A. baumannii was the second germ frequently isolated from blood cultures in intensive care units. It was multi-resistant to antibiotics. The strengthening of hospital hygiene measures and surveillance of antibiotic resistance is needed to limit the spread of germs and to optimize the management of antibiotics.

Enterococcus faecalis is the leading cause of several human infections. This opportunist pathogen expresses surface components that have various functions in the infection process including bacterial adhesion, lytic activity, and induction of host immune responses. EF0737, a novel cell wall associated protein, may play an important role in pathogenesis of E. faecalis, based on our experiments. This study was conducted to clone and express EF0737 and demonstrate its interaction with biotinylated plasma proteins and patients’ sera.
The full length of ef0737 gene was cloned in pTZ57R/T cloning vector and subcloned in pET21a expression vector. Recombinant protein expressed in Escherichia coli Origami (DE3) was confirmed by western blot technique, using anti-His tagged monoclonal antibodies, and was then purified. Interaction of the recombinant protein with plasma proteins and patients’ sera were examined by western blot.
The ef0737 gene was successfully cloned and expressed in E. coli Origami host. Binding activity was observed between the purified EF0737 recombinant protein and fibrinogen and mucin among other plasma proteins. Moreover, reaction was also observed between the purified product and sera obtained from patients diagnosed with E. faecalis infection.
The observed reactions between EF0737 and fibrinogen, mucin and patients’ sera suggest that EF0737 may play important role in pathogenesis of infections caused by E. faecalis. However, more comprehensive characterization of this novel protein may provide better understanding of host pathogen interaction.

In the present study, the Lut Desert, Iran was chosen as one of the hottest places in the world (with the recorded temperature of 70.7°C during 2003-2009) to find out whether any heat-resistant microorganisms were present in the soil.
The samples were collected from surface and depth of three identified places of Gandom Beryan in the Lut Desert. Chemical analysis and enumeration of the total bacteria, yeasts and molds were performed. Four selective culture media were employed to isolate the filamentous actinomycetes. The suspected colonies were further confirmed using PCR assay. Then the culture cell-free-supernatants (CFS) of isolates were used to investigate their antimicrobial activity against Staphylococcus aureus, Bacillus cereus, Salmonella Typhimurium and Escherichia coli.
Chemical analysis of the samples included moisture (0.2-0.9%), ash (85-91%), organic materials (8.3-14.4%), pH (7.59-9.40) and electrical conductivity (380-2000 µS/cm). The number of isolated bacteria and molds varied from 0-20 to 0-40 CFU/g, respectively. Number of Actinomycetes isolated from the soil samples were between 0-12.2 CFU/g. Nine isolated colonies were identified as filamentous Actinomycetes. To determine the possibility of antimicrobial peptides, the CFS (cell-free supernatant) was firstly neutralized by NaOH and catalase. The results showed that none of the CFS of the isolates was effective against E. coli, S. Typhimurium and S. aureus, while the maximum inhibitory effect was investigated on B. cereus, which was 33.1%±1.19% (mean ± SD).
The results of the current study imply the presence of rare heat-resistant microorganisms in the soil of Gandom Beryan which may be further used to find out more about the function of natural bioactive compounds. Actinomycetes, as extremophile microorganisms, have shown the greatest genomic and metabolic diversity, as such the discovery of the novel Actinomycetes as a source of secondary metabolites is essential.

Acetic acid bacteria (AAB) are one of the major interests of researchers. Traditional vinegars are suitable sources of AAB because they are not undergone industrial process like filtering and adding preservatives. Komagataeibacter xylinus as a member of AAB is known as the main cellulose producer among other bacteria. The purpose of the current study was to isolate the bacteria from traditional vinegars and its molecular analyses.
Vinegar samples were collected. Well-organized bacteriological tests were carried out to differentiate isolated bacteria from other cellulose producers and to identify K. xylinus. NaOH treatment and Calcofluor white staining were used for detecting cellulose. Chromosomal DNA of each strain was extracted via three methods of boiling, phenol-chloroform and sonication. Molecular analyses were performed on the basis of 16S rRNA sequences and cellulose synthase catalytic subunit gene (bcsA) for further confirmation. Phylogenetic tree was constructed for more characterization. Two housekeeping genes were studied including phenylalanyl-tRNA synthase alpha subunit (pheS) and RNA polymerase alpha subunit (rpoA).
Of the 97 samples, 43 K. xylinus strains were isolated. They were identified via bacteriological and molecular techniques. 16S rDNA sequence showed 99% similarity with registered sequences of the bacteria. Biodiversity of the genome confirmed by analyzing bcsA, pheS and rpoA genes.
K. xylinus can be isolated from traditional vinegars. Screening tests ought to include the classical methods and molecular techniques. Different molecular techniques and more genomic research should be developed to expand our knowledge for distinguishing isolated bacteria especially in the fields of AAB.

Serratia marcescens, a potentially pathogenic bacterium, benefits from its swarming motility and resistance to antibiotic as two important virulence factors. Inappropriate use of antibiotics often results in drug resistance phenomenon in bacterial population. Use of probiotic bacteria has been recommended as partial replacement. In this study, we investigated the effects of some lactobacilli culture supernatant on swarming, motility and antibiotic resistance of S. marcescens.
Antimicrobial activity of lactobacilli supernatant and susceptibility testing carried out on S. marcescens isolates. Pretreatment effect of lactobacilli culture supernatant on antibiotic - resistance pattern in S. marcescens was determined by comparison of the MIC of bacteria before and after the treatment.
Our results showed that pretreatment with L. acidophilus ATCC 4356 supernatant can affect the resistance of Serratia strains against ceftriaxone, but it had no effect on the resistance to other antibiotics. Furthermore, culture supernatant of lactobacilli with concentrations greater than 2%, had an effect on the swarming ability of S. marcescens ATCC 13880 and inhibited it.
Probiotic bacteria and their metabolites have the ability to inhibit virulence factors such as antibiotic resistance and swarming motility and can be used as alternatives to antibiotics.

Because of importance of catalase in various industries, efforts have been made to find more suitable bacterial sources for catalase production. Kocuria is one of well-known catalase-producing genus. This is the first report about a new catalase-overproducing bacterial strain, Kocuria sp. ASB 107.
Kocuria sp. ASB 107 had been isolated from Abe-Siah Spring in Ramsar in our previous report. The bacterial biomass freezed, thawed and then lysed by three different operations separately: ultrasound, lysing buffer and enzymatic digestion. The crude extract was subjected to ammonium sulfate precipitation (40 and 60% saturation). Quality and quantity of the semi-purification was checked by electrophoresis and measuring specific activity, respectively.
Kocuria sp. ASB 107 can be lysed by a freeze-thaw stage followed by lysozyme digestion and not by lysing buffer and not by ultrasound. Surprisingly specific activity of catalase in crude extract from Kocuria sp. ASB 107 was measured to be 195, 370 U/mg protein which is too much higher than other bacterial strains. The bacterium showed a relatively long growth curve about 40 hours. Semi-purification using ammonium sulfate precipitation was led in an increased specific activity up to about 7×106 U/mg protein implying more than 3.6-fold purification.
We have showed natural catalase-overproducing ability of Kocuria sp. ASB 107. Yield and purity of catalase from Kocuria sp. ASB 107 showed great potential in industrial application suggesting the strain as good source for mass production of catalase for treatment of H2O2-containing wastewater in comparison to other bacterial sources.

Colonization of Candida species is common in pediatric patients admitted to hematology-oncology wards. The aim of this study was to identify colonized Candida species and their susceptibility patterns in hematologic pediatric patients.
Samples were collected from mouth, nose, urine and stool of the patients admitted to five university hospitals and cultured on sabouraud dextrose agar. The isolates were identified by API 20 C AUX system and their susceptibility patterns were evaluated by CLSI M27-A3 and S4.
From 650 patients, 320 (49.2%) were colonized with 387 Candida species. Candida albicans was the most prevalent isolated species, followed by Candida glabrata, Candida tropicalis, Candida famata, Candida kefyr and Candida kuresi. The epidemiological cut off value (ECV) for all Candida species to amphotericin B was ≤0.25 μg except C. krusei (4 μg). The resistance rate to fluconazole in this study in C. albicans was 4.9% with ECV 8 μg/ml, followed by C. tropicalis 8.8% with ECV 0.5 μg/ml. Voriconazole and posaconazole were effective antifungal agents for all Candida isolates. The ECV of C. albicans, Candida parapsilosis, C. tropicalis, C. glabrata and C. krusei for itraconazole were 0.5, 0.25, 0.5, 1 and 2 μg, respectively. The resistant and intermediate rates of Candida species to caspofungin in this study were 2.9%, 5.9%, 18.8%, 47.9%, 0.0% and 16.7% in C. tropicalis, C. glabrata and C. parapsilosis respectively.
C. albicans was the most prevalent species in pediatric colonized patients. New azole agents like voriconazole and posaconazole are effective against non- albicans Candida species. Increase in intermediate species is alarming to future emerging resistant species.

Sheeppox virus causes systemic disease in sheep that is often associated with high morbidity and mortality. Protection against sheep pox is mainly based on medical prophylaxis, vaccination being the only way. In Morocco, and up to now, there is no available information about local challenge strain to use for controlling the efficiency of vaccines produced against sheep pox. Hence, the objective of the present study was to evaluate and compare the pathogenicity of seven Sheeppox virus (SPVs) isolates from 1993-1995 in Morocco.
These seven SPV isolates have undergone various tests to evaluate their pathogenicity: Passages and titration on cell culture, Experimental inoculation on sheep, Virus-neutralization, In vivo titration and viral re-isolation by real-time PCR assay.
All infected lambs showed severe clinical signs, while most of them have been reproduced on 5 dpi and persisted until 21 dpi. The lambs infected by Oj1P4, Oj2P4 and BerP5 appeared lethargic, reluctant to move compared to those infected by other isolates. The results also revealed that all isolates were able to induce serological response. Virus isolation from infected organs and blood and amplification of the viral DNA by real-time PCR proved the presence of the virus in tissues and blood of infected lambs. These Moroccan SPVs demonstrated that the three isolates Oj1P4, Oj2P4 and BerP5 have a high pathogenicity; especially the BerP5 isolate which has an important infectious titer.
These results demonstrate that the Berkane isolate is the most pathogenic of the tested isolates and it can be an excellent challenge strain for the control of the efficiency of vaccines against sheep pox produced in Morocco.

Despite the availability of relatively effective vaccines, Streptococcus pneumoniae still causes widespread morbidity and mortality. Current vaccines contain free polysaccharides or protein-polysaccharide conjugates, but do not induce protection against serotypes that are not included in the vaccines. Therefore, developing alternative vaccines is of high priority and importance. Several investigators have identified protective antigens common to pneumococci of many or all serotypes. Malley et al. in their study, have recommended unencapsulated whole cells, as an alternative vaccine, a number of such antigens unoccluded by capsule were presented in a native configuration in 2001. This review aimed at presenting this candidate of pneumococcal vaccine and results in an animal model.