Pathogen In Iran Research Articles

Assessing the diversity of zoonotic bacterial agents in rodents and small mammals in Iran.

The purpose of this study was to assess the prevalence of zoonotic bacteria, including Coxiella burnetii, Bartonella spp., Rickettsia spp., Brucella spp., Borrelia spp., and Ehrlichia spp., among small mammalian in Iran. We examined 618 small mammals collected between 2016 and 2020 from different parts of Iran. We extracted DNA from spleen samples and used quantitative real-time PCR to identify specific genes. We found 559 (90.45%) samples infected with at least one of the analyzed pathogens. Among the studied specimens, 86.08% tested positive for Bartonella spp., 2.42% for Ehrlichia spp., 0.80% for Borrelia spp., 0.64% for C. burnetii, 0.48% for Brucella spp., and 0% for Rickettsia spp. Bartonella krasnovii (25.81%) and Bartonella taylorii (25.81%) were the most prevalent among the Bartonella species. This study identified a rodent infected with Brucella abortus. Among the Borrelia-positive samples, four out of five were identified as Borrelia duttonii. Among the positive cases in the Ehrlichia genus, Ehrlichia canis, Candidatus Ehrlichia shimanensis, and Neoehrlichia mikurensis were identified. Meriones persicus was the most prevalent captured rodent with 315 specimens (51.22%). Our study revealed that a large proportion of the small mammals analyzed were infected with one or more of the targeted pathogens. M. persicus exhibited significant infection rates with C. burnetii, Bartonella spp., Ehrlichia spp., Brucella spp., and Borrelia spp. This suggests that this rodent species could serve as a crucial reservoir for zoonotic pathogens in Iran.

An Autochthonous Susceptible Candida auris Clade I Otomycosis Case in Iran.

Candida auris is a newly emerging multidrug-resistant fungal pathogen considered to be a serious global health threat. Due to diagnostic challenges, there is no precise estimate for the prevalence rate of this pathogen in Iran. Since 2019, only six culture-proven C. auris cases have been reported from Iran, of which, five belonged to clade V and one to clade I. Herein, we report a case of otomycosis due to C. auris from 2017 in a 78-year-old man with diabetes mellitus type II without an epidemiological link to other cases or travel history. Short tandem repeat genotyping and whole genome sequencing (WGS) analysis revealed that this isolate belonged to clade I of C. auris (South Asian Clade). The WGS single nucleotide polymorphism calling demonstrated that the C. auris isolate from 2017 is not related to a previously reported clade I isolate from Iran. The presence of this retrospectively recognized clade I isolate also suggests an early introduction from other regions or an autochthonous presence. Although the majority of reported C. auris isolates worldwide are resistant to fluconazole and, to a lesser extent, to echinocandins and amphotericin B, the reported clade I isolate from Iran was susceptible to all antifungal drugs.

Budget impact analysis of temocillin insurance coverage for urinary tract infections caused by ESBL-producing pathogens in Iran.

One of the most prevalent infections with a significant disease burden is urinary tract infections (UTIs), which occurs in approximately 50% of women at least once in their lifetime. Antimicrobial resistance to pathogens causing UTIs is expanding worldwide and has been associated with increased use of broad-spectrum antibiotics, including carbapenems, leading to significant costs for insurance and healthcare systems. The emergence of resistance to carbapenems has led to an increasing need for and interest in carbapenem-sparing strategies, including the use of narrow-spectrum antibiotics, such as temocillin. Temocillin has a strong bactericidal effect, along with high tolerability and a good safety profile. It is also stable toward most extended-spectrum beta-lactamases (ESBL). The purpose of our study was to design a budget impact analysis (BIA) model and estimate the budget impact of temocillin insurance coverage for the treatment of UTIs caused by ESBL-producing bacteria from the perspective of the payer. The BIA model with insurance payer perspective was used to estimate the impact of temocillin insurance coverage on the treatment of UTIs caused by ESBL-producing bacteria over a 1-year time horizon in Iran. Direct medicine costs, hospitalization and paraclinical costs, and side effect costs were considered in this model. To assess the impact of uncertainty on the model inputs, 1-way sensitivity analyses were performed. The model demonstrates that inclusion of temocillin in insurance coverage, decreasing treatment costs from $36 million to $34 million, will result in overall savings of > $1.9 million and lead to > $9 million savings in insurance costs for antimicrobial resistance. The inclusion of temocillin in the insurance coverage in Iran for patients developing UTIs caused by ESBL-producing bacteria would be cost-saving for insurance and decrease the risk associated with emerging antimicrobial resistance.

Prevalence and Antimicrobial Resistance Patterns in ESKAPE Pathogens in Iran

Background: The spread of resistant bacteria has caused serious concern worldwide. The spread of multidrug-resistant (MDR) and extensive drug-resistant (XDR) limits the choice of antibiotics, making available antibiotics less effective. Objectives: This study aimed to investigate resistance patterns to seven global threatening organisms announced by the Centers for Disease Control and Prevention (CDC) for one year in Iran, called ESKAPE bacteria (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.). Methods: Clinical isolates were collected from 10 selective hospitals in nine provinces. Antibiotic susceptibility testing was performed according to the Clinical and Laboratory Standards Institute for each bacterium. Results: A total of 5522 bacterial species were considered, of which 30% were ESKAPE. Multidrug-resistant A. baumannii and Staphylococcus aureus methicillin-resistant Staphylococcus aureus (MRSA) were the most identified in Gram-negative and -positive bacteria, with the frequency of 44% and 39%, respectively. The remaining bacteria, including E. coli, K. pneumoniae, Enterobacter spp. P. aeruginosa, and Enterococcus spp., had the frequency of 30%, 32%, 21%, 20%, and 22%, respectively. Conclusions: The determined patterns for the antibiotic resistance of the ESKAPE bacteria can help determine antibiotic stewardship. Also, the high rates of the ESKAPE bacteria in Iran could be alarming for healthcare centers not to misuse broad-spectrum antibiotics.

Tick-borne pathogens in Iran

Objective: Different studies have been performed on the prevalence of tick-borne pathogens in different areas of Iran; however, as far as our knowledge, there is no regional meta-analysis available for consideration and estimation of tick species infected with different pathogens in Iran. Methods: In this review, among different databases, a total of 95 publications were included, and the infection of different tick species to different tick-borne pathogens was determined; furthermore, presence of pathogens (with 95% confidence intervals) in tick vectors was calculated separately for each province, using Comprehensive Meta-Analysis version 2 (Biostat, USA). Results: Totally, among all 95 studies, 5 673 out of 33 521 investigated ticks were positive according to different detection methods. Overall estimated presence of pathogens in tick vectors in Iran was 8.6% (95% CI 7.0%-10.6%, P<0.001). Of all 46 species of ticks in 10 genera in Iran, 28 species in 9 genera, including Alveonasus, Argas, Boophilus, Dermacentor, Haemaphysalis, Hyalomma, Ixodes, Ornithodoros, and Rhipicephalus were infected with at least 20 pathogens in 10 genera including Aegyptianella, Anaplasma, Babesia, Borrelia, Brucella, Orthonairovirus [Crimean- Congo hemorrhagic fever virus (CCHFV)], Coxiella, Ehrlichia, Rickettsia and Theileria in 26 provinces of Iran. The presence of pathogens in ticks collected in western Iran was more than other regions. Hyalomma anatolicum (20.35%), Rhipicephalus sanguineus (15.00%), and Rhipicephalus bursa (14.08%) were the most prevalent infected ticks for different pathogens. In addition, most literatures were related to CCHFV and Theileria/Babesia spp. Conclusions: Public health and veterinary professionals should be aware of diagnosing possible diseases or outbreaks in vertebrates.

Genetic variation, vegetative compatibility, and aggressiveness diversity of Diplodia bulgarica isolates from apple orchards in West Azarbaijan province of Iran

AbstractThis study investigated inter‐simple sequence repeat (ISSR), vegetative compatibility, and aggressiveness diversity in 101 isolates of Diplodia bulgarica recovered from apple trees displaying symptoms of canker and decline in West Azarbaijan province of Iran. Marker analyses revealed high within population diversity, low genetic differentiation, high gene flow, and sharing of multilocus genotypes (MLGs) among geographic populations. Moreover, clustering and multivariate analyses identified two highly differentiated genetic clusters with limited admixture between them. These findings may suggest that the pathogen has been introduced from two genetically divergent sources and has been moved within the region through infected materials. The large number of MLGs, low clonal fraction, and absence of a widely distributed dominant genotype may explain the occurrence of recombination in this pathogen. However, significant linkage disequilibrium in the populations and limited admixture between genetic clusters may indicate the rare occurrence of recombination in D. bulgarica populations in West Azarbaijan, and that the pathogen has not been in the province long enough to reach equilibrium. Vegetative compatibility analyses revealed the occurrence of anastomosis between nonself pairings and high vegetative compatibility group diversity within populations. All studied MLGs produced necrotic lesions on detached shoots of Red Delicious apple but differed in their aggressiveness levels. Our results provide new insights into genetic and phenotypic variation of D. bulgarica that can assist in developing management strategies. Our findings also highlight the vital need for quarantine measures and the production of healthy plant materials to prevent the introduction and spread of the pathogen in Iran.

Prevalence and molecular epidemiology of ceftaroline non-susceptible methicillin-resistant Staphylococcus aureus isolates, first clinical report from Iran.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the major pathogens in Iran with a high prevalence and a high level of antibiotic resistance. Ceftaroline is a fifth generation cephalosporin binding and inhibiting penicillin binding protein (PBP2a). In the present study, 228 clinical MRSA isolates were collected from four cities of Iran and their susceptibility to ceftaroline was evaluated by E-test and the disk diffusion method. Our results showed a high susceptibility rate (97.3%) to ceftaroline in MRSA strains from Iran. Six isolates were found to be ceftaroline non-susceptible (CPT-NS) with Minimum inhibitory concentration (MIC) ≥2 µg/mL. All CPT-NS isolates were isolated from blood and tracheal aspirate and belonged to SCCmec type III as well as agr type I and were all susceptible to vancomycin. Out of six isolates, three, two and one belonged to spa type t030, t4864, and t969, respectively. Vancomycin, quinupristin/dalfopristin, linezolid, chloramphenicol, and tigecycline were the most active agents against CPT-NS isolates. Due to the broad-spectrum activity and low toxicity of ceftaroline as well as the increased rate of vancomycin resistance among MRSA strains in recent years, ceftaroline can be considered as a novel approach to treat MRSA-induced infections.

Microbial antagonists against plant pathogens in Iran: A review

Abstract The purpose of this article was to give a comprehensive review of the published research works on biological control of different fungal, bacterial, and nematode plant diseases in Iran from 1992 to 2018. Plant pathogens cause economical loss in many agricultural products in Iran. In an attempt to prevent these serious losses, chemical control measures have usually been applied to reduce diseases in farms, gardens, and greenhouses. In recent decades, using the biological control against plant diseases has been considered as a beneficial and alternative method to chemical control due to its potential in integrated plant disease management as well as the increasing yield in an eco-friendly manner. Based on the reported studies, various species of Trichoderma, Pseudomonas, and Bacillus were the most common biocontrol agents with the ability to control the wide range of plant pathogens in Iran from lab to the greenhouse and field conditions.

Drug Susceptibility Testing of Mycobacterium Simiae: An Emerging Pathogen in Iran.

Mycobacterium simiae is an emerging pathogen in Iran and little is known about drug susceptibility patterns of this pathogen. Twenty-five clinical isolates of M. simiae from 80 patients with confirmed NTM pulmonary disease were included in this study. For drug susceptibility testing (DST), proportional and broth microdilution methods were used according to the clinical and laboratory standards institute (CLSI) guideline. All clinical isolates of M. simiae were resistant to isoniazid, rifampicin, ethambutol, streptomycin, amikacin, kanamycin, ciprofloxacin, and clarithromycin. They also were highly resistant to ofloxacin (80%). Susceptibility to ofloxacin was only noted in the 5 isolates. Clinical isolates of M. simiae were multidrug-resistant, and had different drug susceptibility patterns than previously published studies. DST results can assist in selecting more appropriate treatment regimens. Newer drugs with proven clinical efficacy correlating with in vitro susceptibility should be substituted with first- and second-line anti-TB drug testing.

Molecular Epidemiology of OXA-48 and NDM-1 Producing Enterobacterales Species at a University Hospital in Tehran, Iran, Between 2015 and 2016.

Carbapenem-resistant Enterobacterales (CRE) is an increasing problem worldwide. Here, we examined the clonal relatedness of 71 non-repetitive CRE isolates collected in a university hospital in Tehran, Iran, between February 2015 and March 2016. Pulsed-field gel electrophoresis (PFGE) and MLST were used for epidemiological analysis. Screening for antibiotic resistance genes, PCR-based replicon typing, conjugation experiments, and optical DNA mapping were also performed. Among all 71 isolates, 47 isolates of Klebsiella pneumoniae (66.2%), eight Escherichia coli (11.2%), five Serratia marcescens (7%), and two Enterobacter cloacae (2.8%) harbored blaNDM–1 and blaOXA–48 genes together or alone. PFGE analysis revealed that most of the OXA-48- and NDM-1-producing K. pneumoniae and all of OXA-48-producing S. marcescens were clonally related, while all eight E. coli and two E. cloacae isolates were clonally unrelated. The predominant clones of carbapenemase-producing K. pneumoniae associated with outbreaks within the hospital were ST147 (n = 13) and ST893 (n = 10). Plasmids carrying blaNDM–1 and blaOXA–48 were successfully transferred to an E. coli K12-recipient strain. The blaOXA–48 gene was located on an IncL/M conjugative plasmid, while the blaNDM–1 gene was located on both IncFII ∼86-kb to ∼140-kb and IncA/C conjugative plasmids. Our findings provide novel epidemiologic data on carbapenemase-producing Enterobacterales (CPE) in Iran and highlight the importance of horizontal gene transfer in the dissemination of blaNDM–1 and blaOXA–48 genes. The occurrence and transmission of distinct K. pneumoniae clones call for improved infection control to prevent further spread of these pathogens in Iran.

Fungal pathogens associated with branch and trunk cankers of nut crops in Iran

Branch and trunk canker diseases have become prevalent on nut crops in Iran. During 2015 to 2018, extensive field surveys were conducted on 58 almond, 43 pistachio and 80 walnut orchards in Iran to study fungal pathogens associated with symptomatic trees. One hundred and fifty-six representative fungal isolates were selected and identified based on morphological characteristics and by phylogenetic comparison of DNA sequence data. Fungal species found were Collophorina hispanica, Pleurostoma richardsiae, nine species of Phaeoacremonium (namely P. angustius, P. cinereum, P. italicum, P. fraxinopennsylvanicum, P. minimum, P. parasiticum, P. scolyti, P. tuscanum and P. viticola), 11 species of Botryosphaeriaceae (namely Botryosphaeria dothidea, Diplodia gallae, D. mutila, D. seriata, Dothiorella plurivora, Do. sarmentorum, Do. viticola, Lasiodiplodia citricola, L. mahajangana, L. theobromae and Neofusicoccum parvum), four species of Diatrypaceae (namely Cryptosphaeria pullmanensis, Diatrype whitmanensis, Eutypella citricola and E. vitis) and two non-identified Eutypella spp. (Eutypella sp. 1 and Eutypella sp. 2). Some of these species represent new reports in Iran and/or are reported for the first time in their respective hosts. Pathogenicity tests demonstrated that most of these fungi were pathogenic to inoculated almond, pistachio and walnut shoots. Therefore, more importance should be given to fungal trunk pathogens in Iran, and specific management strategies should be included within the nut crops IPM management programs, with the aim of improving their sustainability.

Multiple Introductions of Tomato Pathogen Clavibacter michiganensis subsp. michiganensis into Iran as Revealed by a Global-Scale Phylogeographic Analysis.

Tomato bacterial canker caused by Clavibacter michiganensis subsp. michiganensis is one of the most important seed-borne tomato diseases around the globe. The disease was initially reported in 1993 in Iran, and it became a rising threat for the multibillion dollar tomato industry of the country during the last decade. In this study, using phylogeographic analyses, we determined genetic diversity and geographic distribution of C. michiganensis subsp. michiganensis in Iran. Our field surveys showed that the pathogen is expanding into the southern and eastern areas of the country. Furthermore, multilocus sequence analysis and typing (MLSA/MLST) using the sequences of five housekeeping genes (atpD, gyrB, ppk, recA, and rpoB) revealed that 37 C. michiganensis subsp. michiganensis strains isolated in Iran had high genetic diversity and placed in 15 sequence types (STs), while all the available 184 worldwide C. michiganensis subsp. michiganensis sequences were placed in 43 STs. MLSA divided the worldwide C. michiganensis subsp. michiganensis strains into two phylogroups (I and II). Among the 37 strains isolated in Iran, 30 strains clustered in phylogroup I, while 7 strains clustered in phylogroup II. Phylogeographic data inferred from the allelic profile of the five housekeeping genes suggested multiple introductions of C. michiganensis subsp. michiganensis inoculum into Iran, while the geographic origin of the Iranian C. michiganensis subsp. michiganensis strains remains undetermined. Further analyses using higher numbers of strains are warranted to decipher the evolutionary history of C. michiganensis subsp. michiganensis in Iran. Additionally, stricter seed/transplant inspections are recommended to reduce the risk of pathogen expansion to areas with no history of the disease.IMPORTANCEClavibacter michiganensis subsp. michiganensis, the causal agent of tomato bacterial canker disease, is one of the economically important pathogens of solanaceous crops (e.g., eggplant, pepper, and tomato) around the world. The disease occurs in many countries, with a particular importance in regions characterized by high precipitation and humid environmental conditions. As a seed-borne pathogen, C. michiganensis subsp. michiganensis is included in the A2 (high risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Bacterial canker disease was reported for the first time in 1993 in Iran, while the geographic distribution, genetic diversity, and phylogenetic position of the causal agent remain undetermined. In this study, using the multilocus sequence analysis and typing (MLSA/MLST) approach, we provided a phylogeographic scheme for the C. michiganensis subsp. michiganensis strains isolated in Iran. Furthermore, global-scale phylogenetic analyses led to determination of phylogenetic position of Iranian C. michiganensis subsp. michiganensis strains among worldwide population of the pathogen. Based on diversity parameters and population structure, we suggest relatively higher genetic diversity of the bacterial canker pathogen in Iran than has so far been observed in the other areas of the world. Results obtained in this study provide a novel insight into the genetic diversity and population structure of the bacterial canker pathogen on a global scale.

Molecular Typing Reveals High Genetic Diversity of Xanthomonas translucens Strains Infecting Small-Grain Cereals in Iran.

This study provides a phylogeographic insight into the population diversity of Xanthomonas translucens strains causing bacterial leaf streak disease of small-grain cereals in Iran. Among the 65 bacterial strains isolated from wheat, barley, and gramineous weeds in eight Iranian provinces, multilocus sequence analysis and typing (MLSA and MLST) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD), identified 57 strains as X. translucens pv. undulosa, while eight strains were identified as X. translucens pv. translucens. Although the pathogenicity patterns on oat and ryegrass weed species varied among the strains, all X. translucens pv. undulosa strains were pathogenic on barley, Harding's grass, rye (except for XtKm35) and wheat, and all X. translucens pv. translucens strains were pathogenic on barley and Harding's grass, while none of the latter group was pathogenic on rye or wheat (except for XtKm18). MLST using the 65 strains isolated in Iran, as well as the sequences of the four genes from 112 strains of worldwide origin retrieved from the GenBank database, revealed higher genetic diversity (i.e., haplotype frequency, haplotype diversity, and percentage of polymorphic sites) among the Iranian population of X. translucens than among the North American strains of the pathogen. High genetic diversity of the BLS pathogen in Iran was in congruence with the fact that the Iranian Plateau is considered the center of origin of cultivated wheat. However, further studies using larger collections of strains are warranted to precisely elucidate the global population diversity and center of origin of the pathogen.IMPORTANCE Bacterial leaf streak (BLS) of small-grain cereals (i.e., wheat and barley) is one of the economically important diseases of gramineous crops worldwide. The disease occurs in many countries across the globe, with particular importance in regions characterized by high levels of precipitation. Two genetically distinct xanthomonads-namely, Xanthomonas translucens pv. undulosa and X. translucens pv. translucens-have been reported to cause BLS disease on small-grain cereals. As seed-borne pathogens, the causal agents are included in the A2 list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Despite its global distribution and high economic importance, the population structure, genetic diversity, and phylogeography of X. translucens remain undetermined. This study, using MLSA and MLST, provides a global-scale phylogeography of X. translucens strains infecting small-grain cereals. Based on the diversity parameters, neutrality indices, and population structure, we observe higher genetic diversity of the BLS pathogen in Iran, which is geographically close to the center of origin of common wheat, than has so far been observed in other areas of the world, including North America. The results obtained in this study provide a novel insight into the genetic diversity and population structure of the BLS pathogen of small-grain cereals on a global scale.

Host-feeding patterns of Culex mosquitoes in Iran

BackgroundDifferent mosquito-borne pathogens are circulating in Iran including Sindbis virus, West Nile virus, filarioid worms and malaria parasites. However, the local transmission cycles of these pathogenic agents are poorly understood, especially because ecological data on vector species are scarce and there is limited knowledge about the host range; this understanding could help to direct species-specific vector control measurements or to prioritize research.MethodsIn the summers of 2015 and 2016, blood-fed mosquitoes were collected at 13 trapping sites on the coast of the Caspian Sea in northern Iran and at an additional trapping site in western Iran. Mosquitoes were generally collected with either a Biogents Sentinel trap or a Heavy Duty Encephalitis Vector Survey trap installed outside. A handheld aspirator was used at the trapping site in western Iran, in addition to a few samplings around the other trapping sites. On average, eight trapping periods were conducted per trapping site. The sources of blood meals were identified using a DNA barcoding approach targeting the cytochrome b or 16S rRNA gene fragment.ResultsThe source of blood meals for 580 blood-fed mosquito specimens of 20 different taxa were determined, resulting in the identification of 13 different host species (9 mammals including humans, 3 birds and 1 reptile), whereby no mixed blood meals were detected. Five mosquito species represented more than 85.8% of all collected blood-fed specimens: Culex pipiens pipiens form pipiens (305 specimens, 55.7% of all mosquito specimens), Cx. theileri (60, 10.9%), Cx. sitiens (51, 9.3%), Cx. perexiguus (29, 5.3%) and Anopheles superpictus (25, 4.6%). The most commonly detected hosts of the four most abundant mosquito species were humans (Homo sapiens; 224 mosquito specimens, 40.9% of all mosquito specimens), cattle (Bos taurus; 171, 31.2%) and ducks (Anas spp.; 75, 13.7%). These four mosquito species had similar host-feeding patterns. The only exceptions were a relatively high proportion of birds for Cx. pipiens pipiens f. pipiens (23.2% of detected blood meal sources) and a high proportion of non-human mammals for Cx. theileri (73.4%). Trapping month, surrounding area, or trapping method had no statistically significant impact on the observed host-feeding patterns of Cx. pipiens pipiens f. pipiens.ConclusionsDue to the diverse and overlapping host-feeding patterns, several mosquito species must be considered as potential enzootic and bridge vectors for diverse mosquito-borne pathogens in Iran. Most species can potentially transmit pathogens between mammals as well as between mammals and birds, which might be the result of a similar host selection or a high dependence on the host availability.

Isolation and sequencing of Dashli virus, a novel Sicilian-like virus in sandflies from Iran; genetic and phylogenetic evidence for the creation of one novel species within the Phlebovirus genus in the Phenuiviridae family.

Phlebotomine sandflies are vectors of phleboviruses that cause sandfly fever or meningitis with significant implications for public health. Although several strains of these viruses had been isolated in Iran in the late 1970's, there was no recent data about the present situation at the outset of this study. Entomological investigations performed in 2009 and 2011 in Iran collected 4,770 sandflies from 10 different regions. Based on morphological identification, they were sorted into 315 pools according to species, sex, trapping station and date of capture. A phlebovirus, provisionally named Dashli virus (DASHV), was isolated from one pool of Sergentomyia spp, and subsequently DASHV RNA was detected in a second pool of Phlebotomus papatasi. Genetic and phylogenetic analyses based on complete coding genomic sequences indicated that (i) DASHV is most closely related to the Iranian isolates of Sandfly fever Sicilian virus [SFSV], (ii) there is a common ancestor to DASHV, Sandfly fever Sicilian- (SFS) and SFS-like viruses isolated in Italy, India, Turkey, and Cyprus (lineage I), (iii) DASHV is more distantly related with Corfou and Toros viruses (lineage II) although common ancestry is supported with 100% bootstrap, (iii) lineage I can be subdivided into sublineage Ia including all SFSV, SFCV and SFTV except those isolated in Iran which forms sublineage Ib (DASHV). Accordingly, we suggest to approve Sandfly fever Sicilian virus species consisting of the all aforementioned viruses. Owing that most of these viruses have been identified in human patients with febrile illness, DASHV should be considered as a potential human pathogen in Iran.

Virulence genes, Shiga toxin subtypes, major O-serogroups, and phylogenetic background of Shiga toxin-producing Escherichia coli strains isolated from cattle in Iran.

The aim of this study was to investigate the virulence potential of the isolated bovine STEC for humans in Iran. In this study a collection of STEC strains (n=50) had been provided via four stages, including sampling from feces of cattle, E.coli isolation, molecular screening of Shiga toxin (stx) genes, and saving the STEC strains from various geographical areas in Iran. The STEC isolates were subjected to stx-subtyping, O-serogrouping, and phylo-grouping by conventional polymerase chain reaction (PCR). Occurrence of stx1 (52%) and stx2 (64%) was not significantly different (p=0.1), and 16% of isolates carried both stx1 and stx2, simultaneously. In addition, 36% and 80% of the isolates were positive for eae and ehxA, respectively. Molecular subtyping showed that stx1a (52%), stx2a (44%), stx2c (44%), and stx2d (30%) were the most prevalent subtypes; two combinations stx2a/stx2c and stx2c/stx2d coexisted in 18% and 10% of STEC strains, respectively. Three important non-O157 serogroups, including O113 (20%), O26 (12%), and O111 (10%), were predominant, and none of the isolates belonged to O157. Importantly, one O26 isolate carried stx1, stx2, eae and ehxA and revealed highly virulent stx subtypes. Moreover, all the 21 serogrouped strains belonged to the B1 phylo-type. Our study highlights the significance of non-O157 STEC strains carrying highly pathogenic virulence genes in cattle population as the source of this pathogen in Iran. Since non-O157 STEC strains are not routinely tried in most diagnostic laboratories, majority of the STEC-associated human infections appear to be overlooked in the clinical settings.

Occurrence and characterization of a new red-pigmented variant of Curtobacterium flaccumfaciens, the causal agent of bacterial wilt of edible dry beans in Iran

A number of crop diseases are emerging at an alarming rate worldwide. Bacterial wilt of dry beans, caused by Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff), is one of them. In Iran, this disease was first reported in 2012, which, since then, has rapidly spread across the major dry bean growing areas of the country causing severe yield losses. Previously, only two colony variants (yellow and orange) of the pathogen had been described from Iran in association with bacterial wilt of dry beans. In this study, we describe a new red-pigmented variant of Cff, isolated from dry bean seeds stored in seed banks of Khomein Bean Research Station, the major seed supplier in the region. Because Cff is a quarantine pathogen in Iran and elsewhere, with a potential threat for dry bean productions, more knowledge about the biology of this pathogen and epidemiology of the disease it causes are a prerequisite for the development of effective disease management strategies. Within this framework, we performed phenotypic and genetic characterization of the red-pigmented variant of the pathogen, in comparison with previously isolated yellow and orange variants, including pathogenicity, host range, bacteriocin production and genetic diversity. Our results showed a similar host range of different Cff variants although they differed in their aggressiveness. Yellow and orange variants of the pathogen were more aggressive on cowpea and common bean, respectively while the red variant showed the same level of aggressiveness on both hosts. Orange- and red-pigmented strains were separated from yellow-pigmented strains in the phylogeny of gyrB sequences. All orange- or red-pigmented strains were clustered in a separate branch from yellow-pigmented strains, except strain CffK31, in phylogeny based on rpoB sequences. In BOX-PCR analysis, Cff strains used in this study were clustered in two distinct genetic groups, with yellow variants of the pathogen separated from the orange and red variants. Overall, our results provide evidence of a remarkable diversity of Cff in Iran, which needs further in-depth investigation.

Characterization, geographic distribution and host range of Curtobacterium flaccumfaciens: An emerging bacterial pathogen in Iran

Bacterial wilt of dry beans, caused by Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff), is one of the most severe diseases affecting dry bean production worldwide. In Iran, the disease outbreak was first reported in 2012, which was limited only to some restricted areas of the country. Subsequently, Cff has rapidly spread and established itself across the major dry bean growing areas of Iran, and currently it represents a severe constraint for growers in terms of crop yield and quality. To better understand the spread of the disease and genetic and phenotypic diversity of the pathogen, including host range, we conducted a comprehensive survey across twelve Iranian provinces, where legume crops are widely grown. In addition, we performed isolations and characterizations of the causal agent. Our results showed that, besides previously reported disease outbreaks from East Azerbaijan and Markazi provinces, legumes cultivated across West Azerbaijan, Zanjan, Ghazvin, Alborz, Fars and Lorestan provinces were widely affected by the pathogen. Cff strains with two different colony variants (yellow and orange) were isolated from the infected tissues which were different in terms of pathogenicity and host range. Ten out of eleven different legume species tested were infected by the pathogen and only yellow sweet clover did not show any symptoms. The yellow variant of the pathogen was more aggressive than the orange one on a number of hosts including cowpea, lima bean, broad bean and pea. Unlike the orange variant, the yellow variant of the pathogen caused disease on wild hairy vetch, a major weed in dry bean growing areas of Iran, thereby suggesting the role of weeds as a potential reservoir of the pathogen. It is concluded that, given the seed-borne nature of the pathogen, frequent phenotypic diversity observed, and a wide host range of the strains, an effective management of the disease requires the development and adoption of a number of tools, still poorly available. In particular, there is an immediate need to develop more sensitive and reliable detection methods (e.g. molecular seed screening techniques) that allow detection of the pathogen from seeds, and help reduce the risk of pathogen introduction into a given area.

Genotyping of Vancomycin Resistant Enterococci in Arak Hospitals

Background: Enterococcal species have emerged as important pathogens in Iran as well as throughout the world. With the increased use of vancomycin, Vancomycin-Resistant Enterococci (VRE) has become an important nosocomial pathogen. Objectives: The aim of the present study was to determine the incidence and antimicrobial susceptibility pattern of VRE and also to determine the most important genes that cause resistance to vancomycin in clinical samples in Arak, Iran. Materials and Methods: In total, 200 enterococci samples were collected from clinical specimens of Arak hospitals. Enterococcal species were identified using standard biochemical tests. Antibiotic susceptibility was tested by the Clinical and Laboratory Standards Institute (CLSI) disk diffusion. Minimum Inhibitory Concentration (MICs) was determined by broth micro dilution. All of the VRE isolates were examined by PCR to detect the presence of VRE genes. Results: Disk diffusion agar showed that 96 strains (48%) were resistant to gentamicin, 89 (44.5%) to ciprofloxacin, 127 (63.5%) to erythromycin, 142 (71%) to tetracycline, 11 (5.5%) to teicoplanin, 32 (16%) to vancomycin, none to linezolid and 96 (48%) to co-trimoxazole. The MICs of the resistant isolates were as follows; 88 strains had MIC ≥ 32 μg/mL to vancomycin and 59 strains had MIC ≥ 32 μg/mL to teicoplanin. Molecular studies revealed that 59.09% of VRE contained VanA genes and 7.95% of VRE contained the VanB genes. None of the strains had vanC1 and vanC2/3 gene. Conclusions: According to the results of this study, rates of vancomycin-resistance in enterococci, in Iran like other parts of the world, is increasing. Therefore accurate methods are required for identifying strains that possess resistance genes because many cases of hospital infections are caused by these strains.

Genotyping of vancomycin resistant enterococci in arak hospitals.

Background:Enterococcal species have emerged as important pathogens in Iran as well as throughout the world. With the increased use of vancomycin, Vancomycin-Resistant Enterococci (VRE) has become an important nosocomial pathogen.Objectives:The aim of the present study was to determine the incidence and antimicrobial susceptibility pattern of VRE and also to determine the most important genes that cause resistance to vancomycin in clinical samples in Arak, Iran.Materials and Methods:In total, 200 enterococci samples were collected from clinical specimens of Arak hospitals. Enterococcal species were identified using standard biochemical tests. Antibiotic susceptibility was tested by the Clinical and Laboratory Standards Institute (CLSI) disk diffusion. Minimum Inhibitory Concentration (MICs) was determined by broth micro dilution. All of the VRE isolates were examined by PCR to detect the presence of VRE genes.Results:Disk diffusion agar showed that 96 strains (48%) were resistant to gentamicin, 89 (44.5%) to ciprofloxacin, 127 (63.5%) to erythromycin, 142 (71%) to tetracycline, 11 (5.5%) to teicoplanin, 32 (16%) to vancomycin, none to linezolid and 96 (48%) to co-trimoxazole. The MICs of the resistant isolates were as follows; 88 strains had MIC ≥ 32 μg/mL to vancomycin and 59 strains had MIC ≥ 32 μg/mL to teicoplanin. Molecular studies revealed that 59.09% of VRE contained VanA genes and 7.95% of VRE contained the VanB genes. None of the strains had vanC1 and vanC2/3 gene.Conclusions:According to the results of this study, rates of vancomycin-resistance in enterococci, in Iran like other parts of the world, is increasing. Therefore accurate methods are required for identifying strains that possess resistance genes because many cases of hospital infections are caused by these strains.