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A study was performed to determine the prevalence and antimicrobial resistance of Shigella species and diarrheagenic Escherichia coli isolates cultured from patients with acute diarrhea in Tehran, Iran. Between May 2003 and May 2005, 1120 diarrheal specimens were collected and assayed for bacterial enteropathogens by conventional and molecular methods. Etiological agents were isolated from 564 (50.3%) specimens, and included 305 (54%) E coli, 157 (27.8%) Shigella species, and 102 (18%) from other genera of bacteria. The predominant E coli was Shiga toxin-producing E coli (105 isolates [34.5%]) and the predominant Shigella serotype was Shigella sonnei (88 isolates [56.1%]). A high rate of antibiotic resistance was observed among E coli, with 40 of 53 (75.5%) Shiga toxin-producing E coli isolates resistant to amoxicillin and tetra-cycline, and eight (5.2%) E coli isolates resistant to more than six antibiotics. Most Shigella isolates were resistant to tetracycline (95%) and trimethoprim-sulfamethoxazole (91.7%), with greatest antibiotic resistance observed among S sonnei (53 of 88 [60.2%] isolates). Antibiotic resistance is widespread in diarrheagenic E coli and Shigella in children with acute diarrhea in Tehran, Iran; hence, updated strategies for appropriate use of antimicrobial agents in Iran are needed.

Background and Aim There are geographical variations in Helicobacter pylori virulence genes; cagA, cagE, vacA and oipA. The present study compared the distribution of these genotypes in major ethnic groups residing in Tehran, Iran and their association with clinical outcomes. Methods A total of 124 H. pylori-positive patients living in Tehran were enrolled in this study. The ethnic distribution was 74 Persians, 33 Turks and 17 other ethnics including Kurds, Lurs, Afghanis and Arabs. The presence of the cagA, cagE and oipA genes and vacA alleles (signal [s] and middle [m] region) were determined by polymerase chain reaction (PCR) from H. pylori DNA. Results The cagA-positive status was predominant in all three ethnic groups (e.g. 65% in Persians and 73% in Turks). In contrast, the cagE-positive status was less than half in Persians (47%) and Turks (30%), whereas it was 77% in other ethnicities (P = 0.008). The predominant vacA genotypes were s1 and m1 in all three ethnic groups (e.g. 68% in Persians and 70% in Turks were s1). There was no significant association between cagA and cagE status or vacA genotypes and clinical outcomes. The oipA-positive strains were more common in non-ulcer dyspepsia (NUD) (63%) than in peptic ulcer patients (15%) (P = 0.001) in Persians, but the association was not observed in other ethnic groups. Conclusion There are some differences in the H. pylori genotypes among the ethnic groups in Iran. However, none of these markers seemed to be clinically helpful in predicting the clinical presentation of a H. pylori infection in Iran.

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Sulfidogenic biochemical reactors (BCRs) for metal removal that use complex organic carbon have been shown to be effective in laboratory studies, but their performance in the field is highly variable. Successful operation depends on the types of microorganisms supported by the organic matrix, and factors affecting the community composition are unknown. A molecular survey of a field-based BCR that had been removing zinc and arsenic for over 6 years revealed that the microbial community was dominated by methanogens related to Methanocorpusculum sp. and Methanosarcina sp., which co-occurred with Bacteroidetes environmental groups, such as Vadin HA17, in places where the organic matter was more degraded. The metabolic potential for organic matter decomposition by Ruminococcaceae was prevalent in samples with more pyrolyzable carbon. Rhodobium- and Hyphomicrobium-related genera within the Rhizobiales order that have the metabolic potential for dark hydrogen fermentation and methylotrophy, and unclassified Comamonadaceae were the dominant Proteobacteria. The unclassified environmental group Sh765B-TzT-29 was an important Delta-Proteobacteria group in this BCR that co-occurred with the dominant Rhizobiales operational taxonomic units. Organic matter degradation is one driver for shifting the microbial community composition and therefore possibly the performance of these bioreactors over time.

Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations.

Biochemical reactors (BCRs) using complex organics for bioremediation of mine-influenced water must operate successfully year round. In cold climates, where many mines in Canada are located, survival of the important microorganisms through the winter months is a concern. In this work, broad phylogenetic surveys, using metagenomics, of the microbial populations in pulp mill biosolids used to remediate metal leachate containing As, Zn, Cd and sulfate were performed to see if the types of microorganisms present changed over the seasons of one year (August 2008 to July 2009). Despite temperature variations between 0 and 17˝C the overall structure of the microbial population was fairly consistent. A cyclical pattern in relative abundance was detected in certain taxa. These included fermenter-related groups, which were out of phase with other taxa such as Desulfobulbus that represented potential consumers of fermentation byproducts. Sulfate-reducers in the BCR biosolids were closely related to psychrotolerant species. Temperature was not a factor that shaped the microbial population structure within the BCR biosolids. Kinetics of organic matter degradation by these microbes and the rate of supply of organic carbon to sulfate-reducers would likely affect the metal removal rates at different temperatures.

The geographical variation in Helicobacter pylori genotypes is an observed phenomenon. Cytotoxin associated genes A (cagA) and E (cagE), and vacuolating cytotoxin (vacA) genotypes of H. pylori are associated with peptic ulcer disease (PUD). This study compared the distribution of these genotypes in Iranian and Afghani isolates and their association with clinical outcomes. H. pylori infected patients, as proven by positive culture, were recruited prospectively. A total of 70 patients, 55 Iranian (26 men and 29 women, mean age 48 +/- 18 years) and 15 Afghani immigrants (13 men and 2 women, mean age 34.8 +/- 11 years) living in Tehran, Iran were enrolled in this study. DNA was extracted from isolated H. pylori and polymerase chain reaction was carried out to determine the cagA and cagE status and vacA alleles. The number of gastric cancer, peptic ulcer and gastritis cases was 11, 23 and 36, respectively. The cagA positive isolates were more common in Iranian (67%) than Afghani isolates (60%). cagE was positive in 53% of Afghani compared to 51% of Iranian isolates. The most common vacA s-region genotype was s1; 80% in Afghani and 67% in Iranian. The slml was a frequently observed genotype in Afghani strains (53%) while s1m2 (47%) was more common in strains isolated from Iranian patients. There is a difference in the H. pylori strains between Iranian and Afghani groups, for instance Iranian isolates were similar to European isolates while Afghani isolates were similar to isolates from India. However, there was no significant association between cagA, cagE and vacA genotypes and clinical outcomes in Iranian and Afghani patients.