Jundishapur Journal of Microbiology
Volume:11 Issue: 3, Mar 2018

Context: Research, development, and innovation are becoming increasingly important in the rapidly changing political, financial, and social landscape of the world. It is important to understand the landscape of research and development in developing courtiers, as research and development has been shown to improve developing countries’ economic growth. The aim of this study was to obtain a snap shot of a bibliometric analysis of the publications in the field of microbiology in sub - Saharan Africa (SSA). Among other questions, this study aimed at determining the most published authors, the most common areas of research, and institutes with the greatest number of publications in this field.
Evidence Acquisition: This study was conceptualised using 3 steps: creating a search strategy that encompasses the major fields of microbiology, creating and executing a search query, and analysing the results. Scopus was chosen as the search engine since it is the largest database of peer - reviewed literature and includes original articles, reviews, conferences, letters, editorials, and articles - in - press, etc.
Although at first glance it may seem that SSA contributed very little towards (less than 2%) the worlds microbiology literature, a closer examination of gross domestic product (GDP) spent on research proves that SSA countries are making inroads in publishing literature. Most literature published over the last 14 years has been journal articles in journals with an impact factor of 3.7. In 2014, most articles were published in journals with an average impact factor of 6.1. In terms of the number of publications by the top authors in the field, it seems as if they quantitatively match other international countries like Brazil and India.

Mucormycosis is an uncommon fungal infection in immunocompromised patients during the past decades. Identification of causative agents could play an important role in the management of infected patients.
The aim of the present study was the identification of etiologic agents of respiratory tract mucormycosis, based on sequencing methods.
Sinus tissue, bronchoalveolar lavage, and blood samples from the patients with suspected invasive fungal diseases were collected. Sinus tissue and bronchoalveolar lavage were examined by microscopic examination and cultured on Sabouraud dextrose agar. Blood samples were cultured on BACTEC medium. Semi-nested polymerase chain reaction (PCR) for diagnosis of mucormycosis was performed on samples, and products of positive PCR were sequenced and manually viewed with Chromas version 2.24 software. Pathology reports were collected from patients’ files.
Direct microscopic examinations, culture, and semi-nested PCR were positive in 11.7% (19/163), 6.7% (11/163), and 10.4% (17/163) of patients, respectively. None of the blood cultures were positive for Mucorales. The etiologic agents were Rhizopus oryzae (10 cases), R. microsporus (5 cases), and new species (2 cases). This new sequence (645 bp) was published in Gene bank and European Nucleotide archive of EMBL-EBI, and demonstrated 98% identity with Lichtheimia (Absidia) corymbifera genus.
Management of mucormycosis has an important role in the treatment and outcome of such infections. Molecular assay and DNA sequencing could be used in parallel with conventional mycology techniques to identify Mucorales and for best management of respective infections.

Microsporidiosis is considered as an opportunistic infection in immunodeficient patients.
Due to the increasing prevalence of parasitic infections and immunodeficiency diseases as well as the transmission risk of microsporidia from animals to human, the aim of this study was to evaluate molecular diagnosis of Enterocytozoon bieneusi and Encephalitozoon spp. by the multiplex/nested polymerase chain reaction (PCR) and staining methods in wild rats of Ahvaz city, southwest of Iran.
Initially, 160 stool samples were collected from wild rats in different parts of Ahvaz city. The samples were stained by the modified trichrome staining and explored microscopically. The DNA was extracted using the DNA stool kit and examined by multiplex/nested PCR. For differentiating the species of Encephalitozoon, the multiplex/nested PCR products were explored by the restriction fragment length polymorphism (RFLP) method using the restriction enzyme of Mnl1.
Of 160, 26 cases were suspected positive for microsporidia spore by the staining. Also, of 160, 18 cases were positive by the multiplex/nested PCR method, that 14 and 4 samples were detected as E. bieneusi and E. intestinalis, respectively. Of 14 E. bieneusi samples, 12 and 2 cases were detected as genotype D and M, respectively.
The findings revealed a relatively high prevalence of microsporidia infection in wild rats of the city and these animals can be a source of microsporidiosis. Due to the zoonotic potential of the microorganisms, high - risk individuals should be receiving the information about the risk of direct and indirect contact with the infected animals.

Production of extended-spectrum β-lactamase (ESBL) is one of the antibiotic resistance strategies in the bacteria. Extended spectrum β-lactamase producing Escherichia coli (E. coli) infections alarmingly increased in recent years in Turkey.
The current study aimed at determining antibiotic resistance and genotypic profiles of ESBL-positive E. coli isolates.
Forty-five ESBL-positive E. coli species were isolated from a variety of units both at the Mevlana University Foundation Hospital and the Mevlana University Medical Center at Konya province in Turkey from December 2013 to December 2014. Antibiotic resistance profile was determined by the Kirby-Bauer disk diffusion method. Genotypic profile was determined by pulsed-field gel electrophoresis (PFGE).
The rate of ESBL production in E. coli strains was 13.1%. The isolates were highly resistant to penicillins, cephalosporins, and monobactams, while very low resistant to carbapenems. Four PFGE profiles were identified: profile A (2%), profile B (2%), profile C (67%), and profile D (29%). Profile C, the most commonly identified profile, possessed 6 subprofiles (profiles C1 - C6) with more than 85% clonal similarity; Profile C2 was the commonest identified subprofile of profile C (27%).
Extended spectrum β-lactamase producing E. coli strains were highly resistant to β-lactam antibiotics.

Brucellosis is a zoonotic disease caused by Brucella species. Although brucellosis is considered as an occupational disease in adults, recently it has become an infectious disease affecting all age groups, including children. Molecular epidemiological studies are crucial for control and treatment of disease in children.
This study aimed at identifying Brucella species, to detect antibiotic susceptibilities and define transmission dynamics between the Brucella isolates in children.
A total of 77 Brucella isolates were identified by conventional and polymerase chain reaction methods. Anti - biotic susceptibilities were investigated by E - test strips. The isolates were genotyped by using multiple locus variable number tandem repeat analysis (MLVA) (MLVA - 16 Orsay), including 8 mini - satellite (panel 1) and 8 microsatellite (panel 2A and 2B) markers.
The mean age was 9.14 ± 3.4 years. All patients had been consuming unpasteurized milk. All isolates were Brucella melitensis biovar 3. Only 2 isolates were resistant to ceftriaxone, while the other isolates were susceptible to other antimicrobial agents. The MLVA - 16 typing revealed 42 MLVA profiles. Eighteen profiles included 2 or more isolates, indicating a clustering rate of 66.7%. Twenty - four isolates showed a unique profile. Single locus, double locus, and 3 locus variants were detected in 32, 26, and 15 isolates, respectively. Bruce 30, Bruce 16, Bruce 9, Bruce 7, and Bruce 4 were highly discriminatory loci, respectively. All strains were defined as genotype 122, according to MLVA - 11, and genotype 43 according to MLVA - 8, and were in the Eastern Mediterranean genotype.
High clustering rate revealed that brucellosis among the children mainly resulted from common sources. Controlling animal movements and avoiding contaminated milk products have an importance to interrupt spread of brucellosis in children.

Crimean-Congo hemorrhagic fever (CCHF) is asymptomatic in infected animals, yet the virus poses a serious threat to humans causing a symptomatic, hemorrhagic disease with a high case-fatality rate. Numerous genera of ticks serve as both vectors and reservoirs of the Crimean-Congo hemorrhagic fever virus (CCHFV).
The aim of the present study is to determine the CCHFV prevalence in ticks from northeast Iran to establish a phylogenetic relationship of the tick-derived CCHFV strains circulating in Iran.
During April to June 2015, a total of 93 hard ticks were collected from different animals in the Damghan district. The S-segment of positive samples was fully sequenced using the Sanger technique. A total of 142 CCHFV sequences comprised full-length of CCHFV sequences obtained in this study were aligned using the MAFFT algorithm, then phylogenetic tree was constructed using Geneious v 7.1.8.
The identified tick species included Hyalomma marginatum (6.5%), Hy. dromedarii (21.5%), Hy. anatolicum (15.1%), Hy. asiaticum (3.2%) and Hy. schulzei (2.2%), as well as Rhipicephalus sanguineus (47.3%). The CCHFV RNA was detected in 4 samples of 93 tick samples (4.3%) by RT-PCR. A total of 4 CCHFV sequences were obtained in this study clustered within clade IV (Asia-1 and Asia-2).
We demonstrated that 4 species of hard ticks could be a vector for CCHFV in Iran. In addition, our findings indicate the circulation of CCHFV clade IV strain in the northeast of Iran and provide a solid base for more targeted surveillance and prevention programs in Iran.

Saccharomyces boulardii, a non-pathogenic yeast, is effective on prevention and treatment of intestinal infections caused by bacterial pathogens and also affects the virulence factors of Candida albicans. SAP2, an important potential virulence factor of C. albicans is a suitable target for a new research.
The current study aimed at investigating the effect of S. boulardii extract on the expression of SAP2 gene and antifungal susceptibility of C. albicans isolates.
The current study investigated SAP2 relative expression and antifungal susceptibility patterns of C. albicans species isolated from oral lesions of HIV patients and the standard strain ATCC 10231 after exposure to S. boulardii extract. Susceptibility of C. albicans isolates to antifungal drugs was assessed according to those proposed in the clinical and laboratory standards institute (CLSI) M44-A2 reference method. The real-time polymerase chain reaction (PCR) was performed to evaluate SAP2 gene expression.
Saccharomyces boulardii extract 0.48 mg/mL changed the antifungal susceptibility pattern of C. albicans isolates to ketoconazole and itraconazole. Before exposure, 53.3% of the isolates were sensitive to ketoconazole, while it increased to 73.3% after exposure to S. boulardii extract. The sensitivity to itraconazole increased from 6.7% to 26.7% after exposure to S. boulardii extract. Although susceptibility of C. albicans isolates to other antibiotics (fluconazole, clotrimazole, nystatin, and amphotericin-B) did not change after exposure to S. boulardii extract, there was a significant difference in the average inhibitory zones of the isolates after exposure to S. boulardii extract.
The level of SAP2 expression significantly reduced in the isolates treated with 0.48 mg/mL S. boulardii extract. Comparison of SAP2 gene expression between ketoconazole-resistant and -intermediate isolates, and the ketoconazole-sensitive ones demonstrated the relative higher gene expression in resistant and intermediate isolates. Saccharomyces boulardii extract can be considered as a suitable probiotic candidate to prevent and treat C. albicans infections.

The antibiotic resistance of bacteria has increased in the last decade. The mecA gene plays an important role in the pathogenicity of Methicillin-Resistant Staphylococcus aureus (MRSA) by increasing antibiotics resistance. Recent studies have indicated that nanotechnology, as an antimicrobial agent, has had promising results.
The present study was conducted to determine the effect of Cu-BPDCA-Ty on antibacterial activity and mecA gene expression in clinical and standard strains of MRSA.
The phenotypic tests were used to identify MRSA strain and confirmed with molecular detection of mecA gene. Synthesized Cu-BPDCA-Ty was confirmed with different techniques such as XRD and SEM analysis. The minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) were determined by the micro broth dilution method. Real time PCR was used to investigate gene expression. Pta gene was considered as an endogenous control for normalization. Data were analyzed using one sample t test and paired t test in the SPSS software Version 22.
The findings indicated that the MIC and the MBC of Cu-BPDCA-Ty against the standard and clinical strains of MRSA were 0.5 mg/mL, 0.8 mg/mL, 0.46 ± 0.08 mg/mL, and 0.7 ± 0.1 mg/mL, respectively. Analysis of the real- time PCR indicated that all treated groups with Cu-BPDCA- Ty showed a significant decrease in the expression of the mecA gene compared to the control group (P Cu-BPDCA-Ty had an antibacterial effect on MRSA and induced downregulation of expression of the mecA gene.

Crimean - Congo hemorrhagic fever (CCHF) is a severe viral disease. Slaughterhouses are potentially high risk working environments for CCHF infection due to close contact of livestock and humans.
The current study aimed at conducting a serosurvey among abattoir workers and evaluating different factors affecting the transmission of CCHF.
A serosurvey was conducted to determine the frequency of Crimean-Congo haemorrhagic fever virus (CCHFV) IgG antibodies among abattoir workers in Mashhad, Northeastern Iran. Sera were collected from 136 slaughterhouse workers and assessed by the enzyme - linked immunosorbent assay (ELISA) for IgG CCHFV antibodies. In addition, a questionnaire was used to evaluate the risk factors involving in the transmission of the virus to the workers.
Serological evidence was observed in 39 out of 136 (29%) participants. The infection rate did not correlate with the work experience, type of livestock, and the permanent use of available personal protection equipment (PPE). However, standard hand disinfectants had a significant role in decreasing CCHFV IgG seropositivity (OR = 0.2, P = 0.004). Two out of 39 seropositive cases reported the history of hospitalization and CCHF infection diagnosis.
The results of the study demonstrated that almost one-third of the investigated slaughterhouse workers were exposed to CCHFV, though the clinical manifestations were less than those of nosocomial transmissions. The currently used PPE could not protect workers against CCHFV infection; therefore, the need for effective preventive strategies for workers in the livestock industry should be emphasized.

The opportunistic pathogen Klebsiella pneumoniae is one of the main causes of pediatric bacterial blood stream infections (BSI), which is complicated with sepsis and high mortality.
To identify atypical Klebsiella species affecting a sample of infected neonates with low antimicrobial response.
Multidrug resistant blood cultures for Klebsiella from a Neonatal Service, were submitted to molecular identification by sequencing analysis of 16S ribosomal RNA.
The mean age of the newborns was 14.7 ± 5.6 days. A total of 6 out of 8 cases were sepsis, 1 case of pneumonia, and 1 a catheter-related infection. The molecular identification showed 3 cases of K. pneumoniae subsp. ozaenae, 2 of K. pneumoniae and K. variicola, and 1 case of K. oxytoca. The highest antimicrobial resistance was against cephalosporins and Trimethoprim/sulfamethoxazole.
Klebsiella pneumoniae subsp. ozaenae was responsible for multidrug resistant strains of Klebsiella even in 37.5% of cases. In our clinical setting, the use of Amikacin and carbapenems are still useful to treat neonatal infections by Klebsiella even against K. variicola, which is the most resistant.