Characterization of endemic Shigella boydii strains isolated in Iran by serotyping, antimicrobial resistance, plasmid profile, ribotyping and pulsed-field gel electrophoresis

Background: Shigellosis is one of the major causes of morbidity in children with diarrhea in Iran. The present study was undertaken to characterize apparently sporadic Shigella boydii strains isolated from pediatric patients in Iran. Findings: Ten S. boydii strains isolated from pediatric cases of gastroenteritis and acute diarrhea in Tehran between December 2002 and November 2003 were submitted to serotyping, antimicrobial susceptibility testing, plasmid profile analysis, ribotyping and pulsed field gel electrophoresis (PFGE). Seven isolates were attributed to serotype 2, whereas the remaining three belonged to serotypes 14, 18, 19, respectively. Six drug resistance phenotypes (R1 to R6) were defined with R4 - streptomycin (STR), ampicillin (AMP), sulfamethoxazole-trimethoprim (SXT) - being the most prevalent. Plasmid analysis resulted in seven different plasmid profiles with one to five DNA bands. All strains, but one, shared the same ribotype, but PFGE differentiated them in four groups. Conclusion: Based upon ribotyping and PFGE results, endemic circulation of S. boydii in Tehran, Iran, could be attributed to a few clones. Resistance pattern and plasmid profile analysis proved to be very effective in discriminating apparently unrelated strains of S. boydi

Prevalence of Enteropathogenic and Shiga Toxin-producing Escherichia coli Among Children With and Without Diarrhoea in Iran

The aim of the study was to determine the rates of detection of enteropathogenic Escherichia coli (EPEC) and Shiga toxin-producing E. coli (STEC) strains among children in two randomly-selected populations in Iran. In total, 1,292 randomly-selected faecal samples from children aged less than 10 years were screened for EPEC and STEC. Of the 1,292 cases participated in the study, 184 had diarrhoea, and 1,108 were healthy/asymptomatic children. The conventional culture method and slide agglutination with 12 different commercial EPEC antisera were used for the detection of EPEC. The colony sweep polymyxin- B extraction method, non-sorbitol fermentation (NSF) phenotype, and slide agglutination with O157: H7 antisera were used for the screening and detection of STEC. Of EPEC belonging to 11 different serogroups, O111 and O127 were most commonly found in 36.4% of the diarrhoeal cases and 7.2% of the asymptomatic children. A significant association (p<0.05) was found between isolation of EPEC and diarrhoea. 8.7% of the diarrhoeal cases and 2% of children without diarrhoea were infected with STEC, but none of the isolates belonged to the O157:H7 serotype. A significant association (p<0.05) was found between STEC and diarrhoeal cases. Based on these findings, it can be concluded that different EPEC serogroups may be agents of endemic infantile diarrhoea, and STEC strains are an important enteropathogen among young children

Increased Isolation and Characterization of Shigella sonnei Obtained from Hospitalized Children in Tehran, Iran

Shigella flexneri has been the most frequent cause of shigellosis in children in Iran. To evaluate the changes in frequency of serogroups, 302 Shigella species were isolated in 2003 from hospitalized children, aged less than 12 years, with acute diarrhoea in Tehran, Iran. The number of collected S. sonnei, S. flexneri, S. boydii, and S. dysenteriae isolates was 178 (58.9%), 110 (37.4%), 10 (3.3%), and 4 (1.3%) respectively. Most (94%) S. sonnei isolates were resistant to co-trimoxazole. They were, however, relatively or completely sensitive to 15 commonly-used antibiotics. The extracted plasmids showed 12 different profiles with two closely-related patterns constituting 70% of the total isolates. Ribotyping, using PvuII, HindIII or SalI restriction enzymes, generated a single pattern for all S. sonnei isolates. Data suggest that S. sonnei has become the predominant serogroup in children in the hospitals of Tehran

The influence of online resources on student–lecturer relationship in higher education: a comparison study

The internet has become a key resource for students’ higher education studies due to both its availability and currency. Previously within higher education, lectures, books and course materials were the only sources of information. This change, to more open access to information and more online materials being accessed outside of those provided by lecturers, and indeed institutions, is likely to accelerate and change the way students are learning. This study aims to help institutions understand better the impact of these changes on the student–lecturer relationship by exploring students’ perceptions of their studies in terms of power and students’ academic engagement in the classroom. The importance of the internet (online learning resources) to students’ achievements, the importance of lecturers and the student–lecturer relationship have all been widely investigated. However, limited research has been undertaken examining the impact of students’ use of the internet on the student–lecturer relationship, or comparing this across different countries and cultures. To address this, data were collected via semi- structured questionnaires distributed to undergraduate students from three countries: United Kingdom, Saudi Arabia and Kenya. Quantitative data were analysed using a simple statistical analysis approach and qualitative data were analysed using a thematic analysis approach. The results showed that students’ use of the internet has improved students’ academic self-confidence, academic self-reliance and student– lecturer connectedness, but students’ use of the internet has increased the gap in the student–lecturer expert relationship and referent relationship. The impact and rea- sons for this differed between the countries involved in this study

Sterol 14α-demethylase mutation leads to amphotericin B resistance in Leishmania mexicana

Amphotericin B has emerged as the therapy of choice for use against the leishmaniases. Administration of the drug in its liposomal formulation as a single injection is being promoted in a campaign to bring the leishmaniases under control. Understanding the risks and mechanisms of resistance is therefore of great importance. Here we select amphotericin B-resistant Leishmania mexicana parasites with relative ease. Metabolomic analysis demonstrated that ergosterol, the sterol known to bind the drug, is prevalent in wild-type cells, but diminished in the resistant line, where alternative sterols become prevalent. This indicates that the resistance phenotype is related to loss of drug binding. Comparing sequences of the parasites’ genomes revealed a plethora of single nucleotide polymorphisms that distinguish wild-type and resistant cells, but only one of these was found to be homozygous and associated with a gene encoding an enzyme in the sterol biosynthetic pathway, sterol 14α-demethylase (CYP51). The mutation, N176I, is found outside of the enzyme’s active site, consistent with the fact that the resistant line continues to produce the enzyme’s product. Expression of wild-type sterol 14α-demethylase in the resistant cells caused reversion to drug sensitivity and a restoration of ergosterol synthesis, showing that the mutation is indeed responsible for resistance. The amphotericin B resistant parasites become hypersensitive to pentamidine and also agents that induce oxidative stress. This work reveals the power of combining polyomics approaches, to discover the mechanism underlying drug resistance as well as offering novel insights into the selection of resistance to amphotericin B itself

Genomic insights into the 2016-2017 cholera epidemic in Yemen.

Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2-4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1-the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)-are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype

Molecular Structure and Transferability of Tn1546-Like Elements in Enterococcus faecium Isolates from Clinical, Sewage, and Surface Water Samples in Iran▿

The molecular structure and transferability of Tn1546 in 143 vancomycin-resistant Enterococcus faecium (VREF) isolates obtained from patients (n = 49), surface water (n = 28), and urban and hospital sewage (n = 66) in Tehran, Iran, were investigated. Molecular characterization of Tn1546 elements in vanA VREF was performed using a combination of restriction fragment length polymorphism analysis and DNA sequencing of the internal PCR fragments of vanA transposons. Long-PCR amplification showed that the molecular size of Tn1546 elements varied from 10.8 to 12.8 kb. The molecular analysis of Tn1546 showed that 45 isolates (31.5%) harbored a deletion/mutation upstream from nucleotide 170. No horizontal transfer of Tn1546 was observed following filter-mating conjugation with these isolates. Nevertheless, the rates of transferability for other isolates were 10−5 to 10−6 per donor. Insertion sequences IS1216V and IS1542 were present in 103 (72%) and 138 (96.5%) of the isolates, respectively. The molecular analysis of Tn1546 elements resulted in three genomic organizations. The genomic organization lineage 1 was dominated by the isolates from clinical samples (3.4%), lineage 2 was dominated mostly by sewage isolates (24.5%), and lineage 3 contained isolates obtained from all sources (72.1%). The genetic diversity determined using pulsed-field gel electrophoresis (PFGE) revealed a single E. faecium clone, designated 44, which was common to the samples obtained from clinical specimens and hospital and municipal sewage. Furthermore, the results suggest that lineage 3 Tn1546 was highly disseminated among our enterococcal isolates in different PFGE patterns

Prevalence of virulence factors and antibiotic resistance in vancomycin-resistant Enterococcus faecium isolated from sewage and clinical samples in Iran

Purpose: The purpose of the present study was to perform a molecular epidemiological survey by investigating the antibiotic resistance and the presence of known virulence factors in Enterococcus faecium isolates in Iran. The data collected from this study would allow us to control the spread and develop strategies for treatment of the enterococcal infections. Materials and Methods: In this study, 156 vancomycin-sensitive E. faecium (VSEF; 58) and vancomycin-resistant E. faecium (VREF; 98) samples were isolated from clinical specimen and sewage treatment plants (STPs). These isolates were screened for the presence of genes encoding for aggregation substance (asa1), cytolysin (cyl), enterococcal surface protein (esp), gelatinase (gelE) and hyaluronidase (hyl) by polymerase chain reaction (PCR). Results: Although significantly different, the results showed the presence of hyl and esp genes in both clinical (41 and 75%, respectively) and sewage (3.2 and 41%, respectively) isolates. Sensitivity of all isolates to seven antibiotics was examined. The results of the clinical isolates showed that the majority of esp positive isolates were also resistant to vancomycin, ciprofloxacin and erythromycin. Furthermore, cyl, gelE and asa1 were not found in either clinical or STP isolates. Finally, we determined the distinct types of isolates using Pulse Field Gel Electrophoresis (PFGE), which confirmed that most of the isolates were clonally unrelated. Conclusion: Our results demonstrated that higher number of the clinical E. faecium isolates carried virulence genes than the isolates from STP. Finally, the lack of the genes in clinical and STP isolates confirmed that these genes do not transfer horizontally

A rapid and reliable species-specific identification of clinical and environmental isolates of Vibrio cholerae using a three-test procedure and recA polymerase chain reaction

Purpose: Vibrio cholerae , the cause of cholera, is one of the leading causes of morbidity and mortality in many developing countries. Most laboratories initially rely on biochemical tests for a presumptive identification of these strains, followed by a polymerase chain reaction (PCR)-based method to confirm their identification. The aim of this study is to establish a rapid and reliable identification scheme for V. cholerae using a minimal, but highly specific number of biochemical tests and a PCR assay. Materials and Methods: We developed a species-specific PCR to identify V. cholerae, using a housekeeping gene recA, and used that to evaluate the sensitivity and specificity of 12 biochemical tests commonly used for screening and / or presumptive identification of V. cholerae in the clinical and environmental samples. Results: Here we introduced a combination of three biochemical tests, namely, sucrose fermentation, oxidase test, and growth in trypton broth containing 0% NaCl, as also the PCR of the recA gene, for rapid identification of V. cholerae isolates, with 100% sensitivity and specificity. The established method accurately identified a collection of 47 V. cholerae strains isolated from the clinical cases (n = 26) and surface waters (n = 21), while none of the 32 control strains belonging to different species were positive in this assay. Conclusion: The triple-test procedure introduced here is a simple and useful assay which can be adopted in cholera surveillance programs for efficient monitoring of V. cholerae in surface water and fecal samples