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SARS-CoV-2 genome surveillance projects provide a good measure of transmission and monitor the circulating SARS-CoV-2 variants at regional and global scales. Iran is one of the most affected countries still involved with the virus circulating in at least five significant disease waves, as of September 2021. Complete genome sequencing of 50 viral isolates in an early phase of outbreak in Iran, shed light on the origins and circulating lineages at that time. As part of a genomic surveillance program, we provided an additional 319 complete genomes from October 2020 onwards. The current study is the report of complete SARS-CoV-2 genome sequences of Iran in the March 2020-May 2021 time interval. We aimed to characterize the genetic diversity of SARS-CoV-2 in Iran over one year. Overall, 35 different lineages and 8 clades were detected. Temporal dynamics of the prominent SARS-CoV-2 clades/lineages circulating in Iran is comparable to the global perspective and introduces the 19A clade (B.4) dominating the first disease wave, followed by 20A (B.1.36), 20B (B.1.1.413), 20I (B.1.1.7) clades, dominating second, third and fourth disease waves, respectively. We observed a mixture of circulating 20A (B.1.36), 20B (B.1.1.413), 20I (B.1.1.7) clades in winter 2021, paralleled in a diminishing manner for 20A/20B and a growing rise for 20I, eventually prompting the 4th outbreak peak. Furthermore, our study provides evidence on the entry of the Delta variant in April 2021, leading to the 5th disease wave in summer 2021. Three lineages are highlighted as hallmarks of SARS-CoV-2 outbreak in Iran; B4, dominating early periods of the epidemic, B.1.1.413 (specific B.1.1 lineage carrying a combination of [D138Y-S477N-D614G] spike mutations) in October 2020-February 2021, and the co-occurrence of [I100T-L699I] spike mutations in half of B.1.1.7 sequences mediating the fourth peak. Continuous monthly monitoring of SARS-CoV-2 genome mutations led to the detection of 1577 distinct nucleotide mutations, in which the top recurrent mutations were D614G, P323L, R203K/G204R, 3037C>T, and 241C>T; the renowned combination of mutations in G and GH clades. The most frequent spike mutation is D614G followed by 13 other frequent mutations based on the prominent circulating lineages; B.1.1.7 (H69_V70del, Y144del, N501Y, A570D, P681H, T716I, S982A, D1118H, I100T, and L699I), B.1.1.413 (D138Y, S477N) and B.1.36 (I210del). In brief, mutation surveillance in this study provided a real-time comprehensive picture of the SARS-CoV-2 mutation profile in Iran, which is beneficial for evaluating the magnitude of the epidemic and assessment of vaccine and therapeutic efficiency in this population.

It has been about a century since the discovery of the first antibiotic, and during this period, several antibiotics were produced and marketed. The production of high-potency antibiotics against infections led to victories, but these victories were temporary. Overuse and misuse of antibiotics have continued to the point that humanity today is almost helpless in the fight against infection. Researchers have predicted that by the middle of the new century, there will be a dark period after the production of antibiotics that doctors will encounter antibiotic-resistant infections for which there is no cure. Accordingly, researchers are looking for new materials with antimicrobial properties that will strengthen their ammunition to fight antibiotic-resistant infections. One of the most important alternatives to antibiotics introduced in the last three decades is antimicrobial peptides (AMPs), which affect a wide range of microbes. Due to their different antimicrobial properties from antibiotics, AMPs can fight and kill MDR, XDR, and colistin-resistant bacteria through a variety of mechanisms. Therefore, in this study, we intend to use the latest studies to give a complete description of AMPs, the importance of colistin-resistant bacteria, and their resistance mechanisms, and represent impact of AMPs on colistin-resistant bacteria. KEY POINTS: • AMPs as limited options to kill colistin-resistant bacteria. • Challenge of antibiotics resistance, colistin resistance, and mechanisms. • What is AMPs in the war with colistin-resistant bacteria?

Abstract: Alzheimer's disease (AD), a neurological disorder, despite significant advances in medical science, has not yet been definitively cured, and the exact causes of the disease remain unclear. Due to the importance of AD in the clinic, large expenses are spent annually to deal with this neurological disorder, and neurologists warn of an alarm to increase this disease in the elderly people in the near future. It has been believed that microbiota dysbiosis lead to Alzheimer’s as a multi-step disease. In this regard, the presence of footprints of perturbations in the oral microbiome and the predominance of pathogenic bacteria and their effect on the nervous system especially AD is a very interesting topic that has been considered by researchers in the last decade. Some studies have looked at the mechanisms by which oral microbiota cause AD. However, many aspects of this interaction are still unclear as to how oral microbiota composition can contribute to this disease. Understanding this interaction requires extensive collaboration by interdisciplinary researchers to explore all aspects of the issue. So, in this review has attempted to give the mechanisms of shift of oral microbiota in AD in order to reveals the link between microbiota composition and this disease with the help of researchers from different fields.

This study was aimed to evaluate occurrence of antibiotic resistance and the presence of resistance determinants among clinical isolates of Acinetobacter baumannii. This cross-sectional study from January to September 2018 was performed on 59 A. baumannii strains isolated from clinical samples in the north of Iran. Isolates were identified by standard microbiologic tests and molecular method. Antimicrobial susceptibility testing was carried out by disk diffusion and broth microdilution methods. The presence of carbapenem resistance genes was detected by PCR method. All isolates were resistant to cefepime, meropenem, imipenem and ceftazidime. The lowest resistance rate was observed against doxycycline with 33.9%. Minimum inhibitory concentration (MIC) results showed that all carbapenem-resistant A. baumannii (CRAB) isolates were susceptible to colistin with MIC50 and MIC90 values of 1/2 µg/mL. Among 59 CRAB, blaOXA-23-like was the most prevalent gene (86.4%) followed by blaOXA-24-like (69.5%). Meanwhile, none of the clinical isolates harbored blaOXA-58-like gene. We found a high prevalence of CRAB strains harboring OXA-type carbapenemases in the north of Iran. Our results suggests that the presence of OXA-type genes was not directly correlated with the increase of imipenem MIC level, but can be clinically important as they contribute to the selection of CRAB strains.

This case-control study was designed to compare the composition of the predominant oral bacterial microbiome in Alzheimer's disease (AD) and control group.A total of 30 adult participants (15 AD and 15 healthy individuals) were entered in this study. The composition of oral bacterial microbiome was examined by quantitative real-time polymerase chain reaction (qPCR) using bacterial 16S rDNA gene. The levels of systemic inflammatory cytokines in both groups were assessed using enzyme-linked immunosorbent assays (ELISA).The loads of Porphyromonas gingivalis, Fusobacterium nucleatum, and Prevotella intermedia were significantly more abundant in the AD compared to the control group (p 0.05). Although Aggregatibacter actinomycetemcomitans and Streptococcus mutans were relatively frequent in the AD group, no significance difference was observed in their copy number between two groups. Although the concentrations of IL-1, IL-6, and TNF-α were higher in the AD group, there was a significant difference in their levels between the two groups (p 0.05). Finally, there was a significant relationship between increased number of pathogenic bacteria in oral microbiome and higher concentration of cytokines in patient's blood.Our knowledge of oral microbiome and its exact association with AD is rather limited; our study showed a significant association between changes in oral microbiome bacteria, increased inflammatory cytokines, and AD.

Beta-lactam resistance in Gram-negative bacteria, especially Escherichia coli, is a main clinical problem. It is often caused by the production of β-lactamases, particularly extended-spectrum β-lactamases (ESBLs) or AmpC enzymes. This study was undertaken to characterize ESBL and AmpC producers among Escherichia coli isolates from urine samples. During six months, 263 E. coli isolates were detected by standard biochemical tests. The isolates were screened for ESBL production by the double-disk synergy test using Ceftazidime (30 μg) and Cefotaxime (30 μg) disks and confirmed by combined disk diffusion test using Clavulanic acid. AmpC production was confirmed by an AmpC disk test based on filter paper disks impregnated with EDTA. The presence of genes encoding TEM, SHV, CTX-M, CIT, FOX, MOX, ACC, and EBC were detected by PCR. 263 E. coli isolates were selected for the combined disk (Ceftazidime, Cefotaxime, and Clavulanic acid) assay in the disk agar diffusion test. In the combined disk assay, among 263 isolates, 121 (46%) isolates were detected as ESBLs, and none of the isolates were AmpC producers. PCR performed on all ESBL producers and blaSHV, blaTEM, and blaCTX-M were detected in 42 (34.7%), 44 (36.4%), and 47 (38.8%) cases, respectively. Also, from 48 Isolates with zone diameters of less than or equal to 18 mm to Cefoxitin, 7 (14.6%), 4 (8.3%), and 9 (18.8%) cases contained MOX, EBC, and CIT genes, respectively. DHA, FOX, and ACC genes were not detected in any sample. Since pathogens evolve in the hospital setting, updating local data, such as this research, offers scientific evidence to improve the outcome of nosocomial infections.

Male infertility account for nearly 50% of infertility cases. Cadmium is regarded as a well-known toxic metal for industrial applications; high amounts of cadmium in the human body can result in chronic toxicity. Melatonin as a free radical scavenger has anti-inflammatory, and even anti-cancer and antiapoptotic functions.In this work, we evaluated the protective effect of melatonin on human sperm parameters treated by cadmium.This was an experimental study carried out from May to December 2019.A total of 41 fresh semen samples were collected from fertile men and were divided into 4 groups: (1) control, (2) sperm +25 Nm cd, (3) sperm +25 nM cd +0.1 mM melatonin,(4) sperm +0.1 mM melatonin treated for 60 min. In all groups, semen analysis was performed for motility, viability and DNA fragmentation index (DFI).The groups were compared using the ANOVA test.The group treated with cadmium showed a significant decrease in rapid and slow motility, and survival rate compared with the control group (The use of melatonin reduces the amount of cadmium damage in human sperm

Background Escherichia coli and Klebsiella pneumoniae as an important part of Enterobacterales family are important causes of both community- and hospital-acquired infections. The present study aimed to investigate the prevalence of antibiotics resistance and molecular characteristics of uropathogenic isolates of E. coli and K. pneumoniae in Iranian patients. Methods This cross-sectional study performed on 223 Escherichia coli and 68 Klebsiella pneumoniae isolates obtained from hospitalized patients in the north of Iran. The isolates were identified by standard microbiologic tests and confirmed by API 20E strip. Disk diffusion method was applied to determine antibiotic susceptibility pattern. The presence of β-lactamases encoding genes was evaluated by PCR method. Analysis of the mutations and homology among sequences was done by the CLC sequence viewer (Qiagen, Denmark), and phylogenetic trees were constructed by the neighbor-joining method (Bootstrap: 1000 times). Results The overall rates of extended-spectrum β-lactamases (ESBLs)-producing E. coli and K. pneumoniae isolates were 37.7% and 32.4%, respectively. The overall presence of blaSHV, blaNDM-1, and blaOXA-1 genes was detected in 16 (5.5%), 12 (4.1%), and 48 (16.4%) of isolates, respectively. The neighbor-joining analysis for E. coli KU985246.1 strain showed that the most related blaNDM-1 sequences were from China, Singapore, UK, Thailand, and Bangladesh. While K. pneumoniae KU985245.1 strains were mostly related to blaNDM-1 sequences form Myanmar, and China. Conclusion In summary, the remarkable rate of ESBL-producing uropathogenic Enterobacterales along with the first prevalence of NDM-1 β-lactamases can be a serious concern in our region.

Antibiotic resistance is an increasing phenomenon and has become a serious public health concern. Nowadays, limited therapeutic options exist for the treatment of invasive infections caused by drug...

Background Urinary tract infections (UTIs) are one of the most frequent human infectious diseases causing considerable amount of morbidity and mortality. The present study aimed to investigate the occurrence of antibiotics resistance and virulence genes among Escherichia coli strains isolated from UTIs in the north of Iran. Methods This cross-sectional study was performed at 5 teaching hospitals in Rasht in the north of Iran. Totally, 129 E. coli isolates were identified by standard microbiologic tests. Antimicrobial susceptibility pattern was determined using disk diffusion method. The presence of virulence genes was detected by PCR method. Results The results of antibiotic susceptibility showed that the highest resistance rates were to ampicillin (78.3%) followed by nalidixic acid (74.4%) and trimethoprim/sulfamethoxazole (69.8%). On the other hand, the highest susceptibility was toward nitrofurantoin (96.1%) and imipenem (92.2%). Further analysis revealed that the rate of ESBL-producing and multiple-drug resistant isolates was 51.2% and 84.5%, respectively. Molecular analysis revealed that traaT (87.6%) gene was the most prevalent virulence factors followed by fyuA (86%) and kpsmt (76%) genes. Also, fimH gene was the most frequently detected adhesion-associated gene with 74.4%. Conclusion In summary, our results showed a remarkable rate of drug resistance and heterogeneity for virulence factors among E. coli strains isolated from UTIs in the north of Iran. The emergence of such strains can be a predictive marker for their persistence in the hospital and consequently a significant threat for hospitalized patients.

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the global outbreak of coronavirus disease 2019 (Covid-19), which has been considered as a pandemic by WHO. SARS-CoV-2 encodes four major structural proteins, among which spike protein has always been a main target for new vaccine studies. This in silico study aimed to investigate some physicochemical, functional, immunological, and structural features of spike protein using several bioinformatics tools. Method We retrieved all SARS-CoV-2 spike protein sequences from different countries registered in NCBI GenBank. CLC Sequence Viewer was employed to translate and align the sequences, and several programs were utilized to predict B-cell epitopes. Modification sites such as phosphorylation, glycosylation, and disulfide bonds were defined. Secondary and tertiary structures of all sequences were further computed. Results Some mutations were determined, where only one (D614G) had a high prevalence. The mutations did not impact the B-cell and physicochemical properties of the spike protein. Seven disulfide bonds were specified and also predicted in several N-link glycosylation and phosphorylation sites. The results also indicated that spike protein is a non-allergen. Conclusion In summary, our findings provided a deep understanding of spike protein, which can be valuable for future studies on SARS-CoV-2 infections and design of new vaccines.

We aimed to describe SARS-CoV-2 strains in Iranians from nine distributed cities infected during two months expanding late 2020 and early 2021 by genotyping known informative single nucleotide in five PCR amplicons. Two variants associated with haplotype H1 (clade G) and nine additional variants associated with other haplotypes were genotyped, respectively, in RNA isolates of 244 and 85 individuals. The variants associated with the H1a (GR) and H1b (GH) haplotypes were most prevalent, indicating a significant change in infection pattern with passage of time. The most important findings were that recombinant genomes and co-infection, respectively, were surmised in 44.7% and 12.9% of the samples extensively genotyped. Partners of many of the recombinations were relatively common strains. Co-existing viruses were among those currently circulating in Iran. In addition to random mutations, co-infection with different existing strains and recombination between their genomes may significantly contribute to the emergence of new SARS-CoV-2 strains.

Antibiotic resistance causes around 700,000 deaths a year worldwide. Without immediate action, we are fast approaching a post-antibiotic era in which common infections can result in death. Pseudomonas aeruginosa is the leading cause of nosocomial infection and is also one of the three bacterial pathogens in the WHO list of priority bacteria for developing new antibiotics against. A viable alternative to antibiotics is to use phages, which are bacterial viruses. Yet, the isolation of phages that efficiently kill their target bacteria has proven difficult. Using a combination of phages and antibiotics might increase treatment efficacy and prevent the development of resistance against phages and/or antibiotics, as evidenced by previous studies. Here, in vitro populations of a Pseudomonas aeruginosa strain isolated from a burn patient were treated with a single phage, a mixture of two phages (used simultaneously and sequentially), and the combination of phages and antibiotics (at sub-minimum inhibitory concentration (MIC) and MIC levels). In addition, we tested the stability of these phages at different temperatures, pH values, and in two burn ointments. Our results show that the two-phages-one-antibiotic combination had the highest killing efficiency against the P. aeruginosa strain. The phages tested showed low stability at high temperatures, acidic pH values, and in the two ointments. This work provides additional support for the potential of using combinations of phage–antibiotic cocktails at sub-MIC levels for the treatment of multidrug-resistantP. aeruginosainfections.

Staphylococcus aureus as a major causes of nosocomial infections is responsible for a variety of infections from a mild superficial skin and soft tissue infections to toxic shock syndrome. S. aureus strains produces a range of virulence factors that facilitate their pathogenicity such as toxic shock syndrome toxin-1 (TSST-1). The aim of this study was to investigate vancomycin susceptibility and TSST-1 encoding gene in S. aureus strains isolated from patients and ICU staff in the north of Iran. In this cross-sectional study, during 6 months from December 2017 to June 2018, a total of 95 S. aureus strains isolated from patients, staff and hospital environment. Minimum inhibitory concentration (MIC) of vancomycin was determined by the E-test strip. All isolates were susceptible to vancomycin with MIC50 and MIC90 of 1 and 1.5 μg/mL, respectively. Among 95 S. aureus, 23 isolates (24.2%) were harboring tst gene. The tst gene was found in 31% and 21.2% of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible Staphylococcus aureus (MSSA), respectively. Moreover, vanA gene was not found in any of the tested isolates. Our findings highlight the risk of the presence of tst carrying S. aureus in hospital environments and the importance of routine surveillance to prevent the spread and controlling of nosocomial infections, especially in ICU. Although, all S. aureus in our region were susceptible to vancomycin, suggest that the empiric use of this antibiotic for staphylococcal infections should be prescribed in a logical manner in order to prevent the treatment failure.

Objectives Tonsillotomy with radiofrequency (RF) is one of the newest treatments for chronic tonsillitis, but the mechanism of RF effects and complications are still pending. The aim of this study was to evaluate the effects of RF on the histological and bacteriological characteristics of the tonsils (Case-control study). Materials and methods In fifty-two patients with chronic tonsillitis in 2017–2018, immediately after tonsillectomy, the tonsils were divided into 2sections; one sample treated with RF, and the other one considered as control, without intervention. All tonsil samples sent for histological and bacteriological study: morphometric assays made by Digitizer software, and type of bacterial colonies identified by microbiological and biochemical tests. Willcoxon and McNemar tests were used for statistical analysis and level of significance was p ≤ .05. Results Tonsil mucosal thickness (2202.98 ± 323.09 vs. 2463.94 ± 357.61 μm) and size of the tonsil nodule (28,000.42 ± 9608.75 vs. 36,692.81 ± 7040.74 μm2) were significantly lower in the RF+ group than other group (p = .001 and p = .01, respectively). There was no significant differences in thickness of the tonsil epithelium (p = .075), number of lymphoid nodules (p = .860), and the number of reticular tonsil epithelium (p = .813) between the two groups. Bacterial growth in RF- and RF+ groups had no statistically significant difference (p = .06), however, the average colony count of S. aureus in RF+ tonsils were significantly lower, and total number of bacterial colonies were significantly lower in RF+ group(1405 ± 156 vs. 2471 ± 156), (p = .001). Conclusion RF surgery has significant effects on size of the nodules, thickness of the mucous layer and bacteriological characteristics of tonsil tissue. Especially S. aureus seems to be more sensitive to RF effects.

Klebsiella is an opportunistic human pathogen and responsible for many of nosocomial infections. Gram-negative bacteria can acquire antibiotic resistance genes through several mechanisms including integrons. This study aimed to determine the prevalence of antibiotic resistance pattern, and class 1–3 integrons in clinical isolates of Klebsiella among Iranian patients. From March to September 2016, plasmid DNA of 169 Klebsiella isolates was extracted after determining their resistance pattern and ESBL production by disk diffusion method. The presence of class 1–3 integrons was detected by targeting integrase genes with polymerase chain reaction (PCR) method. Out of 169 Klebsiella, 41.1% of Klebsiella pneumoniae and 18.2% of Klebsiella oxytoca isolates were ESBL-positive. The most resistance rate in both species was against ampicillin. Class 1 and 2 integrons were detected in 15.8% and 5.9% of ESBL-producing K. pneumoniae, respectively. In case of K. oxytoca, class 1 and 2 integrons were positive equally in 18.2% of isolates. The results of our study showed a significant association between the presence of integrons and antibiotic resistance in clinical isolates of Klebsiella. Drug-resistant Klebsiella strains complicate the management and treatment of nosocomial infections, hence prudent use of antibiotics therapy and effective control measures of infection are mandatory.

Helicobacter pylori is a causative agent of gastric disorders and associated with gastric adenocarcinoma. Different kind of gene products such as induced by contact with epithelium (iceA), vacuolating cytotoxin (vacA), and cytotoxin-associated gene A (cagA) confers the ability to this bacterium to destroy gastric cells and can lead to gastric cancer. The aim of the present study was to evaluate the frequency and association of iceA and vacA allelic genes variations of H. pylori strains and gastric disorders. This cross-sectional study included 90 nonduplicated H. pylori isolates from gastric biopsy of 300 patients in the north of Iran. DNA was extracted from all isolated strains and polymerase chain reaction (PCR) was used to determine the prevalence of iceA and vacA genes allelic variants. In overall, from 90 samples of H. pylori iceA, vacA s1/s2, vacA m1 and vacA m2 genes were detected in 68.9%, 33.3%, 53.3%, and 37.8% of patients, respectively. Regard to the distribution of the virulence genes, the co-occurrence of iceA/vacA m1 (20%) was the most prevalent genotype followed by iceA (14.4%) and iceA/vacA m2 (10%). In summary, as a first reports from Guilan province in the north of Iran we showed the association of iceA and vacA allelic variations in different types of gastric disorders. In this regard, we found a significant association between the presence of iceA/vacA m1 genotype and gastric diseases.

Antimicrobial resistance of Escherichia coli is an increasing problem that makes treatment complicated. Integrons may help bacteria to acquire novel combinations of resistance genes which can play an important role in antibiotic resistance. This study aimed to determine the prevalence of class I-III integrons in clinical isolates of E. coli and their probable relation to multi-drug resistant (MDR) and extended-spectrum beta-lactamases (ESBLs). During the eight months from November 2014 to July 2015, plasmid DNA of 193 E. coli isolates was extracted after determining their resistance pattern and ESBL production by disk diffusion method. To detect the presence of class I–III integrons polymerase chain reaction (PCR) was performed for all isolates. Among 193 isolates, 37.3% of isolates were ESBL-producing. Also, 79.3% and 13% were positive for intl I and intl II genes, respectively; while intl III gene was not detected. Overall, 65.9% and 81.8% of isolates were MDR which isolated from urinary and non-urinary samples respectively. Our results indicated a negative association between the presence of class I and II integrons and resistance to some of the studied antibiotics. The contrary results may be due to empty or nonfunctional integrons or presence of gene cassettes on prophages or transposons instead of integrons.

Background: Organic manures are the source of many pathogenic bacteria which could be dangerous for human health. Bacterial transmission and retention in soil is important for processes ranging from contaminant degradation during in situ bioremediation to transport of pathogenic bacteria into groundwater. Methods: The aim of this study was to evaluate the transport of Escherichia coli and chloride (Cl) in the soil saturation conditions, considering the importance of preferential flow using synthetic macrospores (different diameters of macrospores including 0, 1 and 2 cm) and HYDRUS-2D model. Also, the effect of different salinity levels of water (including electrical conductivity of 1, 2 and 4 dSm-1) on the transmission of E. coli was investigated. The preferential flow system was prepared and designed using two sand sizes including fine sand and coarse sands in the columns. Results: The results showed that the retention of E. coli increased with the ionic strength of the solution, while the effect of E. coli in the fine sand was greater than that of the coarse sand. This bacterial transfer behavior was well described by numerical simulations. The importance of preferential flow in bacterial transfer showed that it increases at higher ionic strength, even if overall transmission is reduced. Although the bacterial transmission is facilitated in salinity, the results of this study showed that with increase of ionic strength of the soil solution, the amount of bacterial purification was increased that could be effective in controlling groundwater contamination with saline water management. Conclusion: According to the results, with increase of ionic strength of the soil solution, the amount of bacterial purification was increased that could be effective in controlling groundwater contamination with saline water management, so that the least transition has taken place and the conditions for the use of unconventional water sources were also created, without the environmental problem of the risk of groundwater pollution. Keywords: Escherichia coli

The emergence of extended-spectrum beta-lactamases (ESBL) producing strains become a great concern, because few antimicrobial agents remain active against them. Due to the lack of data on the genotyping characteristics and antibiotics resistance of clinical isolates of Klebsiella pneumoniae in the north of Iran, this study aimed to determine the occurrence of ESBL-producing isolates and their molecular characteristics in order to analyses their epidemiological relationships. This cross-sectional study performed on 60 K. pneumoniae isolates which were recovered from different clinical specimens within May and November 2016. Isolates were identified by standard microbiologic tests and confirmed by API 20E strip. Antimicrobial susceptibility testing was carried out by disk diffusion method. The genetic relatedness among the isolates was assessed by RAPD-PCR. Totally, the lowest level of susceptibility was toward amoxicillin/clavulanat, and nalidixic acid. On the other hand, the highest level of susceptibility was toward imipenem (86.7%). The rate of ESBL-producing isolates was 45% (27/60). There was a significant association between production of ESBLs and higher antibiotic resistance in tested isolates. The RAPD-PCR dendrogram revealed 5 major clusters with a similarity of 80% which indicates the high relatedness of the studied isolates. Twenty-one isolates out of the 27 ESBL-producing isolates were clustered in cluster A. In summary, results showed the high prevalence of multiple-drug resistant and ESBL-producing K. pneumoniae isolates in our ICUs. Also, results revealed a significant similarity between ESBL-producing isolates that necessitate restricted infection control policies and rational prescription and use of antibiotics.

Klebsiella pneumoniae is a Gram-negative bacterium which causes several human infections. Treatment of infections related to K. pneumoniae has become problematic, because of increasing trend of extended spectrum β-lactamases producing (ESBLs) strains. The present study was aimed to detect the prevalence of ESBL-producing Klebsiella spp. and KPC-2, CMY-2 and OXA-48 β-lactamase encoding genes in clinical isolates of Klebsiella spp. isolated from hospitalized patients. In this cross-sectional study carried out from February to August 2014, 144 isolates of Klebsiella spp. were collected from different clinical specimens in hospitals in the North of Iran. Klebsiella isolates were identified using standard microbiological procedure. Antimicrobial susceptibility patterns were determined using disk diffusion method in accordance with CLSI recommendation. The presence of antibiotic resistance genes were investigated by PCR method. Among 144 Klebsiella spp., 118 isolates were identified as K. pneumoniae and 26 isolates as Klebsiella oxytoca. Antibiotic susceptibility test showed the most resistance rates were against amoxicillin (96.5%) and ampicillin (95.8%). On the other hand, the most effective antibiotic was revealed to be imipenem with resistance rate of 4.9% (Table 2). Among 144 isolated Klebsiella strains, 57 cases (39.6%) were ESBL producers. The OXA-48 and KPC-2 genes were not detected among Klebsiella spp. during the present study, but 21.1% of isolates contained CMY-2 gene. This is the first report of CMY-2 gene detection in Klebsiella spp. in Iran. The homology between CMY-2 genes identified in isolates from Northern Iran and in other countries showed the wide dispersion of this gene around the world.

Introduction: Helicobacter pylori (H. pylori) infection has remained as a global health problem. Animal studies demonstrated the role of H. pylori oipA gene in the development of gastric cancer. The aim of this study was the cloning and expression of Helicobacter pylori oipA gene in a bicistronic vector harboring mice IL-18 gene. Materials and methods: The target gene encoding oipA was amplified from a codon-optimized clone by PCR, and then double-digested by restriction enzymes. The pIRES-Igk/mIL18/Fc plasmid was simultaneously digested by BstXI/NotI enzymes to elicit the eGFP segment. PCR product of oipA was inserted into pIRES-Igk/mIL18/Fc plasmid using T4 ligase. Transformation into DH5α strain was done. Cloning was confirmed by PCR, enzymatic digestion and sequencing. Expression of the oipA and IL-18 mRNA was assessed by means of TaqMan Real-time PCR. Results: Electrophoresis of PCR product, enzymatic digestion and sequencing showed that the H. pylori oipA gene was successfully cloned into pIRES-Igk/mIL18/Fc to generate mIL-18-pIRES2-oipA plasmid. The results of Real-time PCR confirmed the successful expression of both oipA and IL-18 in mouse macrophage cell line. Conclusion: Considering the role of oipA in pathogenesis of H. pylori and potent activity of IL-18 as a molecular adjuvant, the results of the present study showed that the expression of codon-optimized oipA gene in bicistronic vector including mouse IL-18 is successful. So, it could be considered as an appropriate genetic vaccine candidate for H. pylori in future investigations.

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a significant threat to human health. It is a multidrug-resistant (MDR) pathogen capable of causing a variety of diseases. Also, MRSA is one of the most important nosocomial pathogens in burn infection. As a treatment strategy against MRSA infections, phage therapy has the potential of becoming an alternative remedy. Objectives: The present study aimed to isolate and characterize a lytic bacteriophage from hospital sewage to be effective against burn wound-infecting MRSA isolates. Methods: Staphylococcus aureus strains were isolated from hospitalized burn patients. The strains were confirmed as MRSA by the Kirby-Bauer disk diffusion method using penicillin, methicillin, and oxacillin, as well as the PCR assay for the mecA gene. The phage was isolated from the hospital sewage and tittered by the double layer agar (DLA) method. The spot test was used for host range determination. The latent period and burst size were estimated from a one-step growth curve. The phage morphology was observed by electron microscopy. The nature of the nucleic acid of the isolated bacteriophages was confirmed by Rnase A, Dnase I, and six restriction enzymes. Results: The titer, latent period, and burst size of the isolated phage were determined to be 1 A� 109 PFU/mL, 20 min, and 190 PFU per infected cell, respectively. It displayed a broad host range for MRSA bacteria by the spot test (27 out of 30 isolates). Electron microscopy observation demonstrated that the phage belonged to the Myoviridea family. Digestion profiles of Rnase A, Dnase I, and six restriction enzymes in 1 agarose gel electrophoresis showed that the genome of the isolated phage was a double-stranded DNA with a size of < ~ 23 kbp. Conclusions: The isolated phage (MH-1) was active against a wide range of MRSA strains recovered from burn patients. Its specificity and remarkable lytic effects on MRSA strains emphasized that it could be a suitable candidate for use in prophylaxis and treatment of these clinical infections. © 2020, Archives of Clinical Infectious Diseases.

Objective: To evaluate in vitro the antimicrobial effect of Listerine-green tea mouthwash on Streptococcus mutans (SM) in comparison with 0.12% Chlorhexidine (CHX) and Listerine-Zero. Material and Methods: The sensitivity and growth inhibition of SM bacterial species were evaluated and compared between Listerine-green tea, 0.12% CHX and Listerine-Zero mouthwashes. Sixty plates containing SM colonies were prepared in three groups (n=20), and growth inhibition zones were measured using the disk diffusion agar test in mm. Data were analyzed with SPSS 21. One-way ANOVA was used to compare the efficacy of the three mouthwashes tested. Post hoc Tukey tests were used for two-by-two comparisons. Statistical significance was defined at P

Background Escherichia coli and Klebsiella pneumoniae as an important part of Enterobacterales family are important causes of both community- and hospital-acquired infections. The present study aimed to investigate the prevalence of antibiotics resistance and molecular characteristics of uropathogenic isolates of E. coli and K. pneumoniae in Iranian patients. Methods This cross-sectional study performed on 223 Escherichia coli and 68 Klebsiella pneumoniae isolates obtained from hospitalized patients in the north of Iran. The isolates were identified by standard microbiologic tests and confirmed by API 20E strip. Disk diffusion method was applied to determine antibiotic susceptibility pattern. The presence of β-lactamases encoding genes was evaluated by PCR method. Analysis of the mutations and homology among sequences was done by the CLC sequence viewer (Qiagen, Denmark), and phylogenetic trees were constructed by the neighbor-joining method (Bootstrap: 1000 times). Results The overall rates of extended-spectrum β-lactamases (ESBLs)-producing E. coli and K. pneumoniae isolates were 37.7% and 32.4%, respectively. The overall presence of blaSHV, blaNDM-1, and blaOXA-1 genes was detected in 16 (5.5%), 12 (4.1%), and 48 (16.4%) of isolates, respectively. The neighbor-joining analysis for E. coli KU985246.1 strain showed that the most related blaNDM-1 sequences were from China, Singapore, UK, Thailand, and Bangladesh. While K. pneumoniae KU985245.1 strains were mostly related to blaNDM-1 sequences form Myanmar, and China. Conclusion In summary, the remarkable rate of ESBL-producing uropathogenic Enterobacterales along with the first prevalence of NDM-1 β-lactamases can be a serious concern in our region.

Antibiotic resistance is an increasing phenomenon and has become a serious public health concern. Nowadays, limited therapeutic options exist for the treatment of invasive infections caused by drug-resistant strains, particularly methicillin-resistant

Escherichia coli is an important cause of hospital-acquired infections worldwide. Antimicrobial resistance leads to treatment failure of hospital infections caused by E. coli. Production of extended-spectrum β-lactamases (ESBLs) is one of the major causes of antibiotic resistance in these bacteria. This study aimed to investigate the frequency of blaTEM and blaCTX-M genes in ESBL-producing E. coli strains isolated from clinical specimens of patients admitted to six hospitals in the north of Iran. A total of 160 E. coli strains were isolated from various clinical samples of hospitalised patients. Antibiotic resistance patterns were determined by the Kirby-Bauer disk diffusion method. The double-disk phenotypic confirmatory test was carried out amongst β-lactam-resistant isolates to detect ESBL-producing strains. Plasmid DNA of ESBL-producing strains was extracted and subjected to PCR for detection of the blaTEM and blaCTX-M genes, and isolates were extensively verified by sequencing. The highest resistance rate was to amoxicillin; all E. coli isolates (100%) were susceptible to imipenem. Amongst the 160 clinical E. coli isolates, 83 (51.9%) were ESBL-positive, of which 27 (32.5%) and 72 (86.7%) were positive for blaTEM and blaCTX-M, respectively. This study is the first report of an ESBL phenotype disseminated in hospitals in the north of Iran. These findings showed that there was a direct relationship between the development of resistance to β-lactam antibiotics and production of TEM and CTX-M enzymes.

Aims and objectives: Tuberculosis (TB) is estimated to have caused the deaths of 1 billion people in the last 200 years. Methods: In the first step, the microplate alamar blue assay (MABA) was used for the detection of seventy-eight clinical isolates from Golestan Regional Tuberculosis Reference Laboratory (GRTRL) and the results were compared with the proportion method. In second step, the MABA was used for the susceptibility testing of 35 clinical isolates and the results were compared with the proportion method. Results: For the MABA, the sensitivity was 100 (90.97-100), specificity was 74.36 (57.87-86.96), positive predictive value (PPV) was 79.59 (65.66-89.76), negative predictive value (NPV) was 100 (88.06-100). The concentrations of isoniazid (INH) and rifampicin (RMP) ranged from 1.0-0.01 μg.mL and 2.0-0.03 μg.mL, respectively. For the proportion method, the INH concentration was between 1.0-0.03 μg.mL and the RMP concentration was between 2.0-0.06 μg.mL. For the MABA to RMP, the sensitivity was 100 (89.11-100), specificity was 100 (29.24-100), PPV was 100 (89.11-100), NPV was 100 (29.24-100), and for the MABA to INH, the sensitivity was 84.38 (67.21-94.72), specificity was 66.67 (9.43-99.16), PPV was 96.43 (81.65-99.91), NPV was 28.57 (3.67-70.96). Conclusion: We found the high accuracy between the MABA-RMP and the proportion method. In fact, the rapid and low-cost MABA assay is inexpensive and alternative assays for the detection of RMP resistant tuberculosis in low-income countries.