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BACKGROUND: Type 2 diabetes as the most prevalent metabolic disorder, is one of the major causes of morbidity and mortality worldwide. Recent studies suggest that body microbiota may play a role in developing metabolic disorders including type 2 diabetes. The objective of the present study was to investigate the blood microbiota composition in Iranian pre-diabetic and type 2 diabetic patients compared to healthy individuals. METHODS: Blood samples were taken after 12-h fasting from 90 participants, 30 healthy individuals, 30 type 2 diabetes patients and 30 pre-diabetic participants. The buffy coat layer separated by centrifugation at 800 and DNA was extracted using a column-based method. Composition and load of blood microbiota was evaluated by real-time PCR method using genus specific 16S rRNA primers. RESULTS: The load of Akkermansia, and Faecalibacterium was higher in normal volunteers compared to pre-diabetic and type 2 diabetes group (p< 0.05). The load of Bifidobacterium was higher in normal volunteers compared to type 2 diabetes patients (p= 0.02). In contrast, the load of Lactobacillus and Escherichia coli was higher in pre-diabetics and type 2 diabetes patients compared to normal volunteers (p< 0.05). The load of Bacteroides fragilis was not statistically different between studied groups but it was higher in males compared to female group (p= 0.04). the load of other bacteria was not significantly different between male and female participants. CONCLUSION: There is difference between microbiota composition in white blood cells of pre-diabetic and type 2 diabetes patients compared to healthy people. Determination of blood microbiota pattern may have a role in diagnosis and preventive of type 2 diabetes in a certain population. For more clarification about correlation between blood microbiota and type 2 diabetes, larger studies with more participants in different ethnical populations is suggested.

Coronaviruses are a large family of viruses that cause illnesses ranging from the common cold to more severe diseases such as Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), and the 2019 novel coronavirus infection (COVID-19). Currently, there is no analyzed data to examine the outbreak of COVID-19 by continent and no determination of prevalence trends; this article reviews COVID-19 epidemiology and immunology. Original research, reviews, governmental databases, and treatment guidelines are analyzed to present the epidemiology and immunology of COVID-19. Reports from patients who were COVID-19 infected showed typical symptoms of neutrophilia, lymphopenia, and increased systemic inflammatory proteins of IL-6 and C reactive protein (CRP). These observations agree with the results of severe conditions of MERS or lethal cases of SARS, in which there is an increased presence of neutrophils and macrophages in the airways. Additionally, analyzed data showed that Europe (49.37%), the Americas (27.4%), and Eastern Mediterranean (10.07%) had the most cumulative total per 100,000 population confirmed cases, and Africa (6.9%), Western Pacific (3.46%), and South-East Asia (2.72%) had the lowest cumulative total per 100,000 population confirmed cases. In general, the trend lines showed that the number of confirmed cases (cumulative total) and deaths (cumulative total) would decrease eventually.

BackgroundA growing body of evidence has shown the association between tuberculosis (TB) infection and lung cancer. However, the possible effect of strain‐specific behavior ofMycobacterium tuberculosis(M.tb) population, the etiological agent of TB infection in this association has been neglected. In this context, this study was conducted to investigate this association with consideration of the genetic background of strains in theM.tbpopulation.ResultsWe employed the elastic net penalized logistic regression model, as a statistical-learning algorithm for gene selection, to evaluate this association in 129 genes involved in TLRs and NF-κB signaling pathways in response to two differentM.tbsub-lineage strains (L3-CAS1and L 4.5). Of the 129 genes, 21 were found to be associated with the two studiedM.tbsub-lineages. In addition,MAPK8IP3gene was identified as a novel gene, which has not been reported in previous lung cancer studies and may have the potential to be recognized as a novel biomarker in lung cancer investigation.ConclusionsThis preliminary study provides new insights into the mechanistic association between TB infection and lung cancer. Further mechanistic investigations of this association with a large number ofM.tbstrains, encompassing the other mainM.tblineages and using the whole transcriptome of the host cell are inevitable.

OBJECTIVES: Osteoporosis is characterized by slow deterioration in bone mass and disruption of its structure, leading to an increased risk of bone fractures. Gut microbiota plays an important role in the transport and absorption of nutrients needed for bone health. Akkermansia muciniphila is one of the gut microbiota members that its beneficial role in prevention of metabolic disorder was suggested. The aim of the current pilot study was the assessment of fecal A. muciniphila in patients with osteoporosis and osteopenia. METHODS: A total of 36 subjects including eight with osteoporosis (three men and five women), eight with osteopenia (two men and six women), and 20 normal controls (six men and 14 women) were selected. Microbial genome was extracted from fresh stool samples. The bacterial load was determined by quantitative real-time PCR using 16S rRNA specific primers. RESULTS: The participants’ mean age in the osteoporosis, osteopenia and control groups were 61.71, 45 and 45.05 years, respectively. The majority of osteoporosis patients were post-menopause women, while in osteopenia group was pre-menopause. There were significant differences in terms of age, T-score, Z-score, and menopause among groups (P value

Hepatic stellate cell (HSC) activation is a key phenomenon in development of liver fibrosis. Recently, Akkermansia muciniphila has been introduced as a next-generation microbe residing in the mucosal layer of the human gut. Due to the probable risks associated with the use of live probiotics, the tendency to use heat-killed bacteria has been raised. Herein, we investigated the potential anti-fibrotic effects of heat-killed A. muciniphila MucT on activation of HSCs. The human LX-2 cells were stimulated by various concentrations of LPS to evaluate the optimal concentration for HSC activation. Cell viability of LX-2 cells treated with LPS and heat-killed A. muciniphila MucT was measured by MTT assay. Scanning electron microscopy was used to analyze the morphology of heat-killed bacteria. Quiescent and LPS-stimulated LX-2 cells were coinfected with heat-killed A. muciniphila MucT. The gene expression of α-SMA, TIMP, Col1, TGF-β, TLR4, and PPARγ was analyzed using quantitative real-time PCR. Our results showed that LPS treatment led to a significant increase in fibrosis markers in a concentration-independent manner (P

BACKGROUND: Type 2 diabetes, as the most prevalent metabolic disorder, is one of the leading causes of death worldwide. Recent studies showed a significant association between intestinal microbiota and type 2 diabetes. These studies have shared evidences that alteration in the composition of intestinal microbiota can disrupt the balance of the host homeostasis and lead to metabolic disorders such as type 2 diabetes. In the present study, we compared the intestinal microbiota composition in three groups of type 2 diabetes patients, pre-diabetic patients and healthy individuals of Iranian population. METHODS: After obtaining informed consent, stool samples were collected from 90 individuals of three studied groups. The DNA was extracted using column-based method. Intestinal microbiota composition was evaluated by quantitative real-time PCR using specific bacterial 16S rRNA primers. The difference of bacterial load was compared between three groups. RESULTS: The prevalence of Akkermansia muciniphila and Bifidobacteria species in healthy group was higher than type 2 diabetes group (P Value 0.006 and 0.001, respectively). In contrast, the load of Lactobacillus (P Value 0.044), Escherichia coli (P Value 0.005), and Bacteroides fragilis (P Value 0.017) in type 2 diabetes group, and the frequency of E. coli (P Value 0.001) and Bacteroides fragilis (P Value 0.004) in pre-diabetic group was significantly higher than healthy group. Moreover, the frequency of Faecalibacterium prausnitzii in healthy group was significantly higher compared to two other groups (P Value 0.005). CONCLUSION: There is a correlation between intestinal microbiota composition and type 2 diabetes. Determination and restoration of this microbiota composition pattern may have a possible role in prevention and control of type 2 diabetes in a certain population.

Several investigations have been conducted during the past years to examine the correlation between dysbiosis and both intestinal and extra-intestinal diseases such as inflammatory bowel disease (IBD) and ulcerative colitis (UC).E. coli Nissle 1917 (EcN) is a nonpathogenic gram-negative strain utilized in numerous gastrointestinal issues, consisting of diarrhea, uncomplicated diverticular malady, IBD and specifically UC. Many investigations have been done to examine the capability of assertive bacteria, inclusive of commensal and probiotic strains to enhance IBD in clinical testing. Bacterial secreted factors have been investigated to detect the EcN agents that facilitate the regulation of tight junction. These agents candiffuse smoothly through the mucin layer before reaching intestinal epithelial cells. Outer membrane vesicles (OMVs) are known as intercellular communicasomes as they facilitate the distal transfer of active compounds between cells. A few investigations have detailed immune-modulatory attributes for EcN through various systems that could be liable for its clinical viability in IBD. Today, the function of gut microbiota extracellular vesicles in health and disease has become a focus of attention as they serve as vehicles for the transmission of microorganisms to distal tissues of many bacterial effectors.

Background OObesity is a complex disorder influenced by various genetic and environmental factors. It has been shown that gut microbiota, which colonizes gastrointestinal tract, has a substantial role as an environmental factor in the pathophysiology of obesity. Since the composition of gut microbiota alters with regard to different criteria, such as ethnicity, geographical location, diet, lifestyle, age, and gender, we aimed to determine firmicutes/bacteroidetes (F/B) ratio and the abundance of important gut microbiota members, Akkermansia muciniphila, Faecalibacterium prausnitzii, Roseburia, Bifidobacterium, and Prevotella in Iranian obese and normal weight individuals, for the first time. Methods In this study, 50 normal and 50 obese subjects were recruited and classified based on their BMI into normal weight and obese groups. Stool samples were collected. Following DNA extraction from the samples, quantitative PCR was conducted based on 16s rDNA universal primers. Finally, the correlation between the bacterial abundance and obesity was analyzed by statistical analyses. Results We observed a significant increase of F/B ratio in the obese group, compared to the normal weight group (p = 0.002). Although A. muciniphila (p = 0.039) and Bifidobacterium (p = 0.049) abundance significantly decreased, the abundance of F. prausnitzii (p = 0.046) significantly elevated with BMI increase in the studied groups. Conclusion Owing to the importance of the gut microbiota composition in obesity development, determination and targeted restoration of gut microbiota pattern could be valuable in the control and treatment of obesity in certain populations.

BACKGROUND: Regarding the role of gut microbial dysbiosis in hyperglycemia, we aimed to compare the main gut bacterial composition among type 1 and type 2 diabetic patients and healthy non-diabetic adults. METHODS: A total of 110 adult subjects (49 patients diagnosed with type 2 diabetes, 21 patients diagnosed with type 1 diabetes and 40 healthy persons) were included in this case-control study. The intestinal microbiota composition was investigated by quantitative real-time polymerase chain reaction (qPCR) method targeting bacterial 16S rRNA gene. Comparison between three groups was done using one-way analysis of variance. RESULTS: The participants’ mean age in the type 1 diabetes, type 2 diabetes and control groups was 35.4, 57.2 and 38.0 years, respectively. Higher level of Escherichia, Prevotella and Lactobacillus was observed in both type 1 and type 2 diabetic patients compared with the healthy group (P ˂0.001). In contrast, bacterial load of Bifidobacterium, Roseburia and Bacteroides was higher in healthy control group (P

Laparoscopic sleeve gastrectomy (LSG) is an effective treatment option in patients with morbid obesity, with rare long-term sideeffects. In this report, we present a 42-year-old woman who reported positional vertigo and unilateral gradual hearing loss plus continuous tinnitus after LSG. The patient had no signs or symptoms of mental health disorders and the results of the haematological and serum biochemical tests were normal. However, audiometric test revealed mild sensorineural hearing loss with magnitude in high-frequency tones. Also, acoustic reflex threshold showed neural pathway damage, particularly at high frequencies, with no reflex. Pure tone audiometry showed signs of nerve damage in the inner ear. One possible justification for these complications might be eustachian tube dysfunction due to muscle relaxation. Muscle relaxation itself may occur as a result of adipose tissue loss around the ear muscles. Further evidence, however, would be required to better determine whether these complications are attributable to LSG, and to illuminate exact underlying reasons for such complications.

Mixed (polyclonal) infections are one of the main problems in tuberculosis (TB) management. The best available method for detecting polyclonal infections in TB is mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). According to multiple studies, MIRU-VNTR method can be applied to detect TB-related polyclonal infections in sputum samples or cultures. Setup of MIRU-VNTR on smear slides can be an efficient approach, regardless of the limitations of cultures and sputum samples in many laboratories. The present study aimed at investigating the diagnostic potential of MIRU-VNTR on smear slides in detecting mixed infections. Ziehl-Neelsen-stained microscopic slides were prepared from 14 clinical specimens. For amplifying 24 MIRU-VNTR loci, PCR assay was performed on the smear slides, clinical specimens, and cultures. Based on the 24-locus MIRU-VNTR analysis, polyclonal infections were reported in 42.85% of smear slides, while the corresponding rate was estimated at 57.1% (8/14) in the clinical samples. In the corresponding cultures, the rate of mixed infection was 7.14% (1/14). Use of smear slides can be a safe option for transferring clinical specimens between environmental and reference laboratories. Considering their significant impact on TB treatment, it is essential to diagnose mixed infections in low-resource countries with a high prevalence of mixed infections. The present findings show that direct MIRU-VNTR on smear slides can be conveniently used for the detection of mixed infections.

BACKGROUND: Modifying gut dysbiosis has achieved great success in managing type 2 diabetes mellitus (T2DM) and also T2DM affected the gut microbial composition. OBJECTIVES: To determine the research trend of scientific publications on the relationship between gut microbiota and T2DM through a bibliometric and descriptive approach. METHOD: We included originals and reviews related to both topics of gut microbiota and T2DM through searching in Scopus up to 31 December 2019 and then characterized their bibliometric profiles including the number of publications, citations, institutions, journals, countries, and the collaboration network of authors, countries, terms and keywords. Moreover, we performed a descriptive evaluation of the clinical trials based on their intervention type and its influence on gut dysbiosis. RESULTS: We achieved 877 articles (436 originals and 441 reviews) according to our inclusion criteria. The annual publications were constantly increased over time and reached 220 publications in 2019. Out of 436 original articles, 231 animal studies and 174 human studies were found. The majority of human studies were clinical trials (n = 77) investigating the influence of drugs (n = 21), regimens (n = 21), pre/pro/symbiotic (n = 19), surgeries (n = 15), or both drug and regimen (n = 1) on gut dysbiosis. Roux-en-Y gastric bypass and metformin were assessed the most in these trials. Obesity side by side T2DM has been assessed in this area of literature based on term and keyword analyses showing their possible similar pathways mediated by gut microbiota. CONCLUSION: The exponentially growing documents on gut microbiota and T2DM had been published during the last decade and revealed gut microbiota alteration mediated antidiabetic effect of many interventions. Thus, we suggest other researchers to consider this pathway in efficacy assessment of therapeutic modalities and to find the optimal composition of gut microbiota that guarantees healthy insulin sensitivity. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40200-021-00920-1.

Merkel cell polyomavirus (MCPyV) infects most people asymptomatically, but recent reports indicate that the virus may be related to carcinogenesis. This study aimed to evaluate the impact of MCPyV on the development of papillary thyroid cancer (PTC). Totally, 1057 samples, including 412 fresh biopsy samples (FBS) and 645 paraffin-embedded PTC biopsy samples (PEBS), and 1057 adjacent non-cancerous samples were assessed for the presence of MCPyV DNA and RNA. MCPyV DNA was positive in 215 (20.3%) of samples, including 126 (30.6%) in FBS and 89 (13.8%) in PEBS. In MCPyV-positive samples, the mean MCPyV copy number was higher in the patients with FBS (2.3 × 10–1 ± 0.5 × 10–1 copies/cell) compared to PEBS (0.7 × 10–4 ± 0.1 × 10–4 copies/cell) and adjacent non-PTC normal samples (0.3 × 10–5 ± 0.02 × 10–5 copies/cell), indicating a statistically significant difference (P LT-Ag RNA expression was higher in FBS compared to PEBS, while VP1 gene transcript was not detected in any samples. Although our findings showed the presence of MCPyV in a subset of PTC Iranian patients, further research is required to confirm these findings.

Akkermansia muciniphila, as a member of the gut microbiota, has been proposed as a next-generation probiotic. Liver fibrosis is the main determinant of liver dysfunction and mortality in patients with chronic liver disease. In this study, we aimed to determine the beneficial effects of live and pasteurized A. muciniphila and its extracellular vesicles (EVs) on the prevention of liver fibrosis. The response of hepatic stellate cells (HSCs) to live and pasteurized A. muciniphila and its EVs was examined in quiescent, lipopolysaccharide (LPS)-activated LX-2 cells. Liver fibrosis was induced in 8-week-old C57BL/6 mice, using a high-fat diet (HFD) and carbon tetrachloride (CCl4) administration for 4 weeks. The mice were concomitantly treated via oral gavage with three forms of bacteria. The relative expression of different fibrosis and inflammatory markers was assessed in the tissues. Histological markers, serum biochemical parameters, and cytokine production were also analyzed, and their correlations with the relative abundance of targeted fecal bacteria were examined. All A. muciniphila preparations exhibited protective effects against HSC activation; however, EVs showed the greatest activity in HSC regression. Oral gavage with A. muciniphila ameliorated the serum biochemical and inflammatory cytokines and improved liver and colon histopathological damages. The relative expression of fibrosis and inflammatory biomarkers was substantially attenuated in the tissues of all treated mice. The composition of targeted stool bacteria in the live A. muciniphila group was clearly different from that in the fibrosis group. This study indicated that A. muciniphila and its derivatives could successfully protect against HFD/CCl4-induced liver injury. However, further studies are needed to prove the beneficial effects of A. muciniphila on the liver. IMPORTANCE Akkermansia muciniphila, as a member of the gut microbiota, has been proposed as a next-generation probiotic. Liver fibrosis is the main determinant of liver dysfunction and mortality in patients with chronic liver disease. In this study, we aimed to determine the beneficial effects of live and pasteurized A. muciniphila and its extracellular vesicles (EVs) on the prevention of liver fibrosis. The results of the present study indicated that oral administration of live and pasteurized A. muciniphila and its EVs could normalize the fecal targeted bacteria composition, improve the intestinal permeability, modulate inflammatory responses, and subsequently prevent liver injury in HFD/CCl4-administered mice. Following the improvement of intestinal and liver histopathology, HFD/CCl4-induced kidney damage and adipose tissue inflammation were also ameliorated by different A. muciniphila treatments.

There are limited studies on the coinfection of coronavirus disease 2019 (COVID-19) with nontuberculous mycobacteria. Here, we briefly describe the reactivation of Mycobacterium simiae infection in a patient who had recovered from COVID-19 in October 2020, Iran. During the pandemic of COVID-19, other infectious agents should not be ignored.

Background: Obesity is a multifactorial disorder, and gut microbiota has a fundamental role in its pathophysiology. Bacteroides spp. has significant roles in gut microbiota- host interactions that determine health and disease development. Since the gut microbiota pattern changes based on different criteria in each population, we studied the abundance of two important Bacteroides strains, Bacteroides fragilis, and Bacteroides thetaiotaomicron, in Iranian obese and normal-weight subjects for the first time. Methods: In this study, 100 participants were recruited and classified based on their body mass index (BMI). The subjects were divided into normal (average BMI, 22.37 kg/m2) and obese (average BMI, 29.10 kg/m2) groups. Bacterial DNA was extracted from the samples, and quantitative polymerase chain reaction (qPCR) was conducted based on 16s rDNA universal primers. Finally, the correlation between bacterial abundance and obesity was investigated. Results: The results of qPCR showed that the relative abundance means of B. fragilis in normal weight and obese subjects was 8.68 × 1012 and 9.27 × 1012 cfu/mL, respectively. Also, the relative abundance mean of B. thetaiotaomicron in normal weight and obese subjects was 2.32 × 1012 and 5.39 × 1012 cfu/mL, respectively. Although obese subjects had more B. fragilis and B. thetaiotaomicron abundance compared to subjects with normal weight, no significant difference was identified between relative abundance of B. fragilis (P = 0.79) and B. thetaiotaomicron (P = 0.18) in the two groups. Conclusions: Although obese subjects had more B. fragilis and B. thetaiotaomicron abundance compared to normal-weight subjects, no significant difference was identified between the two groups. Since Bacteroides spp. have significant role in gut microbiota-host interaction, determination of their abundance in obesity development and targeting restoration of gut microbiota pattern could be valuable in controlling obesity. In this regard, dietary intervention could be based on determination of gut microbiota pattern in certain populations.

As the ongoing COVID-19 pandemic posed a huge challenge to global public health, emphasis on personal hygiene caused extraordinary daily use of detergents and household cleaning products. Since antibacterial cleaning products have the capacity to change the environmental microbiome, increased exposure to household disinfectants could be associated with alterations in human microbiota composition and function. Moreover, the emerging links between household cleaning products and occurrence of non-communicable diseases and antibiotic resistance may involve the gut microbiome. The mediating effects of disturbed gut microbiota on associations between home use of cleaning products and life-long health consequences have been documented in some observational studies. Regarding the evidence associated reduction in exposure to non-pathogenic commensal bacteria and gut dysbiosis, further study is required to assess the effect of massive use of cleaning products during COVID-19 pandemic on long-term host health mediated by the altered microbiota. In this context, recommendations to consume probiotics and fermented foods might reverse the consequences by alleviating dysbiosis.

MicroRNAs are non-coding RNAs, playing an important role in regulating many biological pathways, such as innate immune response against various infections. Different studies confirm that many miRNAs act as important regulators in developing a strategy for the survival of Mycobacterium tuberculosis in the host cell. On the other hand, an innate immune response is one of the important aspects of host defense against Mycobacterium. Considering the importance of miRNAs during tuberculosis infection, we focused on studies that performed on the role of various miRNAs related to pathogenic bacteria, M. tuberculosis in the host. Also, we have introduced important miRNAs that can be used as a biomarker for the detection of Mycobacterium.

Purpose Nontuberculous mycobacteria (NTM) infection is an increasing problem worldwide whose clinical significance is still largely unknown. The aim of this study was to investigate the epidemiology of NTM infection from respiratory samples and to determine their clinical significance. Patients and methods This cross-sectional study was performed on 7,825 clinical samples from December 2015 to December 2017. Detection was conducted using phenotypic and genotypic (hsp65 PCR-RFLP, rpoB, and 16S rRNA genes sequencing) methods. All clinical information including symptoms and radiological findings was extracted from patients' records. Results A total of 478 were confirmed to have respiratory samples which were culture positive for mycobacteria, with the prevalence of NTM infection obtained as 53 (11.1%). Overall, Mycobacterium (M.) fortuitum was the most frequent NTM isolate, followed by M. simiae, M. kansasii, M. gordonae, and M. conceptionense. There was a relationship between NTM isolates and gender (P=0.039), symptoms (P=0.048), and radiographic findings (P=0.013). Bronchiectasis, infiltration, and cavitary lesion were the most frequent radiological findings in M. fortuitum, M. simiae, and M. kansasii, respectively, with cough being the most frequent symptom. Conclusion We reported five different NTM isolates in respiratory samples with a high frequency of M. fortuitum. NTM infections may play an important role in causing pulmonary disease and in tuberculosis management in endemic settings. Nevertheless, more studies are required to further examine the clinical significance of NTM isolates.

Aim The presence of occult hepatitis C virus (HCV) infection (OCI) is still controversial, however, this infection cannot be ignored. Therefore, the current study aimed at assessing the OCI frequency in patients on chronic hemodialysis (CHD) and also evaluating the association between OCI incidence with clinical parameters and interferon lambda 3/4 (IFNL3/4) gene polymorphisms. Methods A total of 515 patients on CHD and HCV negative markers were selected. Plus- and minus-stranded HCV-RNA was tested in peripheral blood mononuclear cell samples by reverse transcription-polymerase chain reaction and then genotyped using the restriction fragment length polymorphism method. Results The frequency of OCI was 11.3% in patients on CHD. Among 58 patients with OCI, 25.8%, 62.1%, and 12.1% were infected with HCV-1a, HCV-1b, and HCV-3a, respectively. The mean alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase levels were 31.9 ± 24.8, 32.3 ± 19.1, and 171.6 ± 88.9, respectively. None of the patients with OCI had a history of liver disease. Multivariate logistic regression analysis indicated that cholesterol, triglyceride, low-density lipoprotein, 25-hydroxyvitamin D, platelets, duration of hemodialysis, HCV subtypes, IFNL3 rs12979860 TT, IFNL3 rs8099917 GG, IFNL3 rs12980275 GG, and IFNL4 ss469415590 ΔG/ΔG genotypes were associated with OCI. Conclusion There was a moderate prevalence of OCI in Iranian patients on CHD. The current study findings indicated that this infection was associated with clinical parameters and unfavorable genotypes of IFNL3 single nucleotide polymorphisms and IFNL4 ss469415590. Further studies are required to determine the correlation between OCI incidence with clinical parameters and host genetic factors.

The prevalence of nontuberculous mycobacteria (NTM) has increased in tuberculosis (TB)-suspected clinical samples. These bacteria are now recognized as important emerging pathogens, which affect both immunocompetent and immunocompromised individuals. The aim of this study was to evaluate the frequency of NTM in clinical samples and to efficacy of genomic loci as targets for detection of NTM species. This cross-sectional study was performed on 8166 clinical samples to determine the presence of NTM species from April 2013 to December 2015. The phenotypic methods were applied for preliminary NTM identification. The PCR-RFLP assay of heat shock protein-65 (hsp-65) gene and multilocus sequence analysis based on 16S-23S internal transcribes spacer (ITS), rpoB, and 16S rRNA genes were applied for species identification. In a total of 520 isolates from TB-suspected cases, 61 samples (11.7%) were identified as NTM. Overall, Mycobacterium (M.) fortuitum (63.9%) was the most frequently encountered species, followed by M. kansasii (9.8%), M. simiae (9.8%), M. abscessus (6.7%), M. gordonae (4.9%), M. flavescens (3.3%), and M. setense (1.6%). Moreover, sequencing of 16S rRNA and rpoB genes could identify all NTM species. In conclusion, we showed that the samples were infected by six NTM species, and M. fortuitum was the most frequent NTM strain. Based on the findings, 16S rRNA and rpoB genes were superior to ITS gene in identification of NTM species.

Objectives The gut dysbiosis has been implicated as a mediator to obesity and its manipulation could be an appropriate approach to sustainable weight loss. In this systematic review, our primary objective was to assess the potential manipulation of gut microbiota by herbal products in obesity. Materials and methods We did a comprehensive search in PubMed, Web of Science, Scopus and Cochrane databases for all clinical trials and animal studies exploring the effects of various herbal products on gut microbiota composition in obesity documented up to May 2017. Results Our initial search yielded 2766 articles. After screening abstracts and full texts, 68 articles were included (55 animal studies and 13 clinical trials). The studies differed in their methodologies, type of interventions and intervention lengths. The weight loss was only reported in 23% of trials and in 64% of animal studies. An increasing tendency in Bifidobacterium species and butyrate-producing bacteria such as Faecalibacterium prausnitzii were observed after consuming non-digestible carbohydrates, although these changes did not always correlate with weight loss. Supplementation with high concentration of polyphenols reduced body weight gain in animal studies and inhibited growth of detrimental species such as Clostridia and Enterobacteria while the growth of Lactic acid bacteria and Akkermansia muciniphila is enriched. Conclusions Alteration of gut microbiota after interventions has been affected by the baseline composition of gut microbiota. This systematic review shows that consumption of herbal products might have beneficial effects on restoring healthy gut microbiome besides body fat reduction.

Tuberculosis (TB) is a sizable public health threat in the world. This study was conducted to determine the differential protein composition between susceptible and MDRTB strains. Tuberculosis proteins were extracted by Triton™ X-114 and ammonium sulfate. Two-dimensional gel electrophoresis protein spots were selected for identification by mass spectrometry and mRNA expression levels were measured by real- time PCR. 2DE-Western blot and T cell epitope prediction for identified proteins were made by the IEDB server. The result shows at least six protein spots (Rv0147, Rv3597c, Rv0379, Rv3699, Rv1392 and Rv0443) were differentially expressed in MDRTB isolates. However, difference in mRNA gene expression was not found in the six mRNA genes. 2DE-Western blot procedures indicated strong reaction against MDRTB proteins corresponds to 13, 16 and 55 kDa areas that might be used as new diagnostic tools. In conclusion, these MDRTB proteins identified in this study could be reliable TB diagnostic candidates or therapeutic targets.

This study investigates the short-term effects of the coronavirus disease 2019 (COVID-19) pandemic lockdown on tracing and detection of tuberculosis (TB) patients in Tehran, Iran. Results of this study have demonstrated that due to the significant decrease in the identification of patients with suspected TB during the COVID-19 outbreak in Tehran, it is imperative that patients with suspected TB be tracked and diagnosed more quickly to make up for some of the decline in TB diagnosis in recent months and to recover lost cases.

Background: Variations of serum biomarkers and bacterial diversity of the gastrointestinal tract in obese patients with diabetes or hypothyroid are poorly understood. The aim of this study was to p...

Primary ciliary dyskinesia is a rare autosomal recessive disorder that causes oto-sino-pulmonary disease. We report a case of pulmonary infection related to mimivirus in a 10-year-old boy with primary ciliary dyskinesia that was identified using molecular techniques. Our findings indicate that the lineage C of mimivirus may cause pneumonia in humans.

Background Variations of serum biomarkers and bacterial diversity of the gastrointestinal tract in obese patients with diabetes or hypothyroid are poorly understood. This study broadened our understanding of recent findings in this regard. Methods A total of 120 obese patients (18 with diabetes, 23 with hypothyroid, and 79 patients without either diabetes or hypothyroid (control)) were recruited in this study. Serum biomarkers such as biochemical, hormonal (insulin and glucagon), and cytokine levels (IL-6, IL-1β, TNF-α, IL-10, and TGF–β 1) were measured under fasting conditions. Bacterial diversity of gut microbiota was also quantitated by real-time PCR using 16S rRNA gene-based specific primers. Results Average value of blood sugar (P: 0.0184), insulin, HOMA-IR, TGF-β 1, IL-6, IL-1β, IFNγ, IL-10 (Pfor each < 0.001), phylum Actinobacteria (OR: 1.5, P: 0.032), Firmicutes (OR: 0.6 P: 0.058), and Akkermansia muciniphilai (OR: 0.4, P: 0.053) was significantly different in diabetic vs. non-diabetic obese patients but was not significantly different in hypothyroid vs. non-hypothyroid obese patients. Average value of Bifidobacterium, Bacteroidetes, Prevotella spp., Bacteroides fragilis group, Clostridium cluster IV, Roseburia spp., and Firmicutes to Bacteroidetes ratio (F/B) was not significantly different between these groups either in crude or adjusted models. Conclusion While there are some associations between serum biomarkers or bacterial diversity with diabetes prediction in obese patients, this prognostication is less likely in obese patients with hypothyroid. Further investigation is warranted in the application of identified preclinical biomarkers in the diagnosis of diabetes or hypothyroid in obese patients.

PURPOSE: Microbiota-derived metabolites could alter the brain tissue toward the neurodegeneration disease. This study aims to select the genes associated with Propionic acid (PPA) and compromise Alzheimer’s disease (AD) to find the possible roles of PPA in AD pathogenesis. METHODS: Microbiota-derived metabolites could alter the brain tissue toward the neurodegeneration disease. This study aims to select the genes associated with Propionic acid (PPA) and compromise Alzheimer’s disease (AD) to find the possible roles of PPA in AD pathogenesis. RESULTS: Amongst all genes associated with PPA and AD, 284 genes to be shared by searching databases and were subjected to further analysis. AD-PPA genes mainly involved in cancer, bacterial and virus infection, and neurological and non-neurological diseases. Gene Ontology and pathway analysis covered the most AD hallmark, such as amyloid formation, apoptosis, proliferation, inflammation, and immune system. Network analysis revealed hub and bottleneck genes. MCODE analysis also indicated the seed genes represented in the significant subnetworks. ICAM1 and CCND1 were the hub, bottleneck, and seed genes. CONCLUSIONS: PPA interacted genes implicated in AD act through pathways initiate neuronal cell death. In sum up, AD-PPA shared genes exhibited evidence that supports the idea PPA secreted from bacteria could alter brain physiology toward the emerging AD signs. This idea needs to confirm by more future investigation in animal models. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40200-020-00564-7) contains supplementary material, which is available to authorized users.

Brucellosis is the most common zoonotic disease worldwide and still there is no vaccine for human use. The commercial animal vaccines also have major problems that limit their use. Therefore, there is a need for an effective Brucella vaccine which is multivalent and produces a good protective immunity with minimal disadvantages. Due to their heterogeneous composition and diverse functions, OMVs are promising acellular vaccine candidates against brucellosis. In the present study, the potential of Poly(I:C) or CpG ODN 1826+ Montanide ISA 70 VG adjuvant formulations were evaluated to enhance the immunity and protection levels conferred by OMVs against Brucella challenge in mice. The results indicated that both vaccine regimens were able to induce strong Th1-biased responses and confer protective levels significantly higher than REV.1 live vaccine. With regard to the results, it is concluded that OMVs in either adjuvant can be introduced as a new vaccine candidate against B. melitensis infection.

Background No conclusive treatment is available for irritable bowel disease (IBD). Adherence to a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) might alleviate clinical symptoms of IBD. However, no study has investigated the effect of low FODMAPs diet on the intestinal microbiota and inflammatory biomarkers in patients with IBD. The aim of current study is to examine the effect a low FODMAP diet on IBD symptoms, inflammation, and the intestinal microbiota in patients with ulcerative colitis. Methods and analysis This study is a randomized clinical trial. Thirty patients with mild to moderate ulcerative colitis will be randomly allocated to receive a low FODMAP diet (n = 15) or to continue their usual diet as control (n = 15), for 4 weeks. The quantity of intestinal microbiota including Clostridium cluster IV, Faecalibacterium prausnitzii, Rosburia spp., Lactobacillus spp., Bifidobacteria spp., Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., and the Firmicutes to Bacteroidetes ratio and calprotectin and lactoferrin levels will be explored in fecal samples from patients. In addition, anthropometric measures and biochemical assessments including serum concentrations of highly sensitive-C reactive protein (hs-CRP), tumour necrosis factor-α (TNF-α) and IL-1β will be taken from patients at baseline and end of the study. The study has been registered in IRCT (IRCT20181126041763N1; registration date: 2019-01-18). Discussion Consumption of a low-FODMAP diet might decrease systemic and intestinal inflammation, change the bacterial population in the gut, and modulate clinical symptoms in patients with ulcerative colitis. Further studies investigating the effect of such a diet on other variables, including other bacterial species and inflammatory cytokines, are required to confirm future findings of this trial.

International audience; BACKGROUND: Patients with mixed-strain Mycobacterium tuberculosis infections may be at a high risk of poor treatment outcomes. However, the mechanisms through which mixed infections affect the clinical manifestations are not well recognized. Evidence suggests that failure to detect the pathogen diversity within the host can influence the clinical results. We aimed to investigate the effects of different genotypes in mixed infections and determine their relationship with heteroresistance in the treatment of Iranian tuberculosis patients. METHODS: One of the genotypes was identified in the culture and another genotype pattern in the mixed infection was predicted by comparing the pattern of MIRU-VNTR between the clinical specimens and their respective cultures in each patient. For all patients, the drug susceptibility testing was carried out on three single colonies from each clinical sample. The follow-up of patients was carried out during six months of treatment. RESULTS: Based on MIRU-VNTR profiles of clinical samples, we showed that 55.6% (25/45) of the Iranian patients included in the study had mixed infections. Patients with mixed infections had a higher rate of treatment failure, compared to others (P = 0.03). By comparing clinical sample profiles to profiles obtained after culture, we were able to distinguish between major and hidden genotypes. Among hidden genotypes, Haarlem (L4.1.2) and Beijing (L2) were associated to treatment failure (6/8 patients). CONCLUSIONS: To conclude, we propose a procedure using the MIRU-VNTR method to identify the different genotypes in mixed infections. The present findings suggest that genotypes with potentially higher pathogenicity may not be detected when performing experimental culture in patients with mixed infections.

Epigenetics regulate gene function without any alteration in the DNA sequence. The epigenetics represent one of the most important regulators in different cellular processes and have initially been developed in microorganisms as a protective strategy. The evaluation of the epigenetic mechanisms is also important in achieving an efficient control strategy in tuberculosis (TB). TB is one of the most significant epidemiological concerns in human history. Despite several in vivo and in vitro studies that have evaluated different epigenetic modifications in TB, many aspects of the association between epigenetics and TB are not fully understood. The current paper is aimed at reviewing our knowledge on histone modifications and DNA methylation modifications, as well as miRNAs regulation in TB.

Purpose. Although Mycobacterium fortuitum (M. fortuitum) is not an organism rarely isolated from respiratory samples, its clinical importance is still not fully understood, which therefore prompted our current study. Methodology. We evaluated respiratory samples from 6800 patients with suspected tuberculosis from May 2014 to May 2016, for the detection of M. fortuitum using phenotypic and genotyping methods. Results/Key findings. Of the 40 patients with M. fortuitum lung disease, 35 had two or more positive culture results. The mean age of these 35 patients was 50.7±18.4 years, and 20 (57.1 %) were men. Sputum (68.6 %), haemoptysis (51.4 %), cough (45.7 %) and gastroesophageal disease (22.9 %) were the major presenting symptoms. Cystic fibrosis, other bacterial lung diseases and lung cancer were the main underlying pulmonary diseases. Five patients (12.5 %) were human immunodeficiency virus (HIV) positive. The most common chest X-ray findings were reticulonodular opacities (53.3 %). Multivariate logistic regression analysis revealed that cigarette smoking history (OR 0.334, 95 % CI 0.125–0.843, P=0.048) and underlying lung disease (OR 0.393, 95 % CI 0.216–0.588, P=0.023) were significant predictors for positive M. fortuitum infection. Conclusion. These results demonstrated the high frequency of M. fortuitum in respiratory samples and that this bacterium causes transient infection or colonization in patients with underlying pulmonary conditions, such as cystic fibrosis and cigarette smoking-induced. Additionally, it appears that infection with M. fortuitum is particularly common and may be important in patients with HIV.

Helicobacter pylori (H. pylori) is a model organism for understanding host-pathogen interactions and infection-mediated carcinogenesis. Gastric cancer and H. pylori colonization indicates the strong correlation. The progression and exacerbation of H. pylori infection are influenced by some factors of pathogen and host. Several virulence factors involved in the proper adherence and attenuation of immune defense to contribute the risk of emerging gastric cancer, therefore analysis of them is very important. H. pylori also modulates inflammatory and autophagy process to intensify its pathogenicity. From the host regard, different genetic factors particularly affect the development of gastric cancer. Indeed, epigenetic modifications, MicroRNA and long non-coding RNA received more attention. Generally, various factors related to pathogen and host that modulate gastric cancer development in response to H. pylori need more attention due to develop an efficacious therapeutic intervention. Therefore, this paper will present a brief overview of host-pathogen interaction especially emphases on bacterial virulence factors, interruption of host cellular signaling, the role of epigenetic modifications and non-coding RNAs.

Background Bariatric surgeries have turned to be a popular therapeutic option for morbid obesity nowadays. Gut microbiota is supposed to be responsible as a part of the bariatric surgeries success. In this systematic review, we detailed the human studies which investigated the effect of different bariatric surgeries on the composition of gut microbiota. Methods We did a comprehensive search in PubMed, Web of Science, and Scopus for all clinical trials and longitudinal observational studies documented up to December 2015. Results Our initial search yielded 1423 articles. After screening abstracts and full texts, 7 articles were included. In 6 studies, the type of surgical intervention was Roux-en-Y gastric bypass (RYGB) where one study assessed vertical banded gastroplasty (VBG), too. Only in one study the effect of laparoscopic sleeve gastrectomy (LSG) had been investigated. RYGB caused an increase in Proteobacteria and a decrease in Firmicutes. LSG led to less severe intestinal microbiota alteration compared to RYGB. Fecalibacterium prausnitzii species with anti-inflammatory properties increased after LSG. However, inconsistent alterations have been shown in abundance of Fecalibacterium species after RYGB. Conclusion Weight loss after bariatric surgeries are associated with microbiota modifications caused by surgical procedures.

Mycobacterium tuberculosis, acid fast bacilli from the family of Mycobacteriaceae, is the causative agent of most cases of tuberculosis. Tuberculosis, as a communicable disease, remains a serious public health threat, killing more than one million people globally every year. Primary diagnosis of tuberculosis bacilli (TB) relies mainly on microscopic detection of acid fast bacilli (AFB), but the method suffers from low sensitivity and the results largely depend on the technician’s skill. New diagnostic tools are necessary to be introduced for rapid and accurate detection of the bacilli in sputum samples. We, in collaboration with Anda Biologicals, have developed a new platform, named as “Patho-tb”, for rapid detection of AFB with high sensitivity and with low dependence on human skills. Evaluation of Patho-tb test performance was done in two settings: (1) primary field study conducted using 38 sputa from high TB prevalence area of Iran (Zabol city near to the Afghanistan border), and (2) main study conducted using 476 sputa from Tehran, capital of Iran. Patho-tb was applied for processed sputum samples in parallel with routine diagnostic methods (including AFB microscopy, culture and PCR). All test results were compared to final clinical diagnostic state of an individual and diagnostic sensitivity (DSe), specificity, positive predictive value, negative predictive value and accuracy of each test results were calculated using standard formulations. Analytical sensitivity and specificity of the Patho-tb test were also determined. Calculated values for five above mentioned parameters are as follows: for field study: AFB (DSe: 29.6, DSp: 81.8, PPV: 80, NPV: 23.1, AC: 44.7), Patho-tb (DSe: 63, DSp: 72.7, PPV: 85, NPV: 44.4, AC: 65.8), and for main study: AFB (DSe: 86.1, DSp: 99.4, PPV: 98.5, NPV: 93.9, AC: 95.2), Patho-tb (DSe: 97.4, DSp: 92.9, PPV: 86.5, NPV: 98.7, AC: 94.3). Reproducibility of Patho-tb test results were near to 100% (Cohen’s kappa value between 0.85 and 1). The detection limit of Patho-tb test with 100% positivity rate was 3 × 103 cells/ml of sputum. In the field study, Patho-tb test was 33.4% more sensitive than AFB microscopy, while the improvement was only 11.3% during the main study. Patho-tb results are easy to interpret and the test can be merged with other screening tests, like AFB. Totally, Patho-tb test alone or in conjunction with AFB microscopy is a useful screening tool for TB detection especially in poor geographical lab conditions. Keywords: Mycobacterium tuberculosis, Diagnostic tests, Communicable diseases, Diagnostic techniques, Sensitivity and specificity, Sputum, Pulmonary tuberculosis

Mycobacterium canariasense had only been isolated in humans from blood and contaminated catheters. We report a case of pulmonary disease associated with M. canariasense infection that was identified by multilocus sequence analysis; the illness was initially ascribed to M. tuberculosis. M. canariasense should be considered a cause of respiratory infection.

Background Mycobacterium tuberculosis possesses five resuscitation-promoting factors, Rpf A to E, which are required for the resuscitation of dormancy in mycobacteria. This study explores the transcriptional profile of all five rpfs of M. tuberculosis, in response to sub-MIC concentration of rifampin, in multidrug and mono-rifampin resistant clinical isolates. Methods Thirteen multidrug and two rifampin mono resistant clinical isolates were analyzed. Drug susceptibility testing and determination of MIC were performed. The relative expression of rpfs was measured, by real-time quantitative PCR. Results A significant upregulation of relative expression (p

The methicillin-resistant Staphylococcus aureus infection is a hot topic area in microbiology research. Here a novel vaccine candidate consisting of recombinant PBP2a and autolysin proteins were used. The proteins over expressed in E.coli BL21 (DE3) cells, and purified by the Ni-NTA affinity column and conjugated using EDAC and ADH as a linker and spacer, respectively. To investigate the immunogenicity and protective effects of recombinant proteins, 5 and 20μg of proteins in various formulations were subcutaneously injected in different groups. Two booster vaccinations were carried out in three-week intervals and blood samples were collected three weeks after each injection. To evaluate the immune response, total IgG, IgG1, IgG2a, and IgG2b were analyzed. Immunization of mice with r-autolysin and r-autolysin-PBP2a mixture raised total IgGantibody. Additionally, both IgG1 and IgG2a responses induced. Opsonophagocytosis assay showed that anti r-PBP2a and r-autolysin IgG not only promoted phagocytosis of S.aureus, but also decreased the number of viable bacterial cells. Furthermore, survival rate of experimental mice increased in the bacteremia infection. Our results demonstrated that active vaccination with a mixture of r-PBP2a/r-autolysin and conjugate form vaccine reduced the mortality rate and protected mice against lethal MRSA challenge as well as single proteins.

Cigarette smoking is the leading cause of lung cancer worldwide. In this study, we evaluated the serum autoantibody (AAb) repertoires of non-small cell lung cancer (NSCLC) patients and smokers (SM), leading to the identification of overactivated pathways and hubs involved in the pathogenesis of NSCLC. Surface- and solution-phase biopanning were performed on immunoglobulin G purified from the sera of NSCLC and SM groups. In total, 20 NSCLC- and 12 SM-specific peptides were detected, which were used to generate NSCLC and SM protein datasets. NSCLC- and SM-related proteins were visualized using STRING and Gephi, and their modules were analyzed using Enrichr. By integrating the overrepresented pathways such as pathways in cancer, epithelial growth factor receptor, c-Met, interleukin-4 (IL-4) and IL-6 signaling pathways, along with a set of proteins (e.g. phospholipase D (PLD), IL-4 receptor, IL-17 receptor, laminins, collagens, and mucins) into the PLD pathway and inflammatory cytokines network as the most critical events in both groups, two super networks were made to elucidate new aspects of NSCLC pathogenesis and to determine the influence of cigarette smoking on tumour formation. Taken together, assessment of the AAb repertoires using a systems biology approach can delineate the hidden events involved in various disorders.

Nonencapsulated, nontypeable Hemophilus influenzae (NTHi) remains an important cause of acute otitis and respiratory diseases in children and adults. NTHi bacteria are one of the major causes of respiratory tract infections, including acute otitis media, cystic fibrosis, and community-acquired pneumonia among children, especially in developing countries. The bacteria can also cause chronic diseases such as chronic bronchitis and chronic obstructive pulmonary disease in the lower respiratory tract of adults. Such bacteria express several outer membrane proteins, some of which have been studied as candidates for vaccine development. Due to the lack of effective vaccines as well as the spread and prevalence of NTHi worldwide, there is an urgent need to design and develop effective vaccine candidates against these strains.

Objective Prompt genotyping of Mycobacterium tuberculosis (M. tuberculosis) is crucial for improving molecular epidemiological investigation of tuberculosis (TB). Methods We performed a retrospective study to evaluate the use of 24 loci MIRU-VNTR (mycobacterial interspersed repetitive unit-variable number of tandem-repeat) directly on 135 clinical samples from 84 TB patients. Results There was a direct correlation between genotyping on clinical samples by MIRU-VNTR and bacterial load (P = 0.001). VNTR loci were amplified successfully for 41.5% of the clinical samples (19–24 loci), 32.6% (13–18 loci), 23.7% (7–12 loci) and 2.2% (1–6 loci). Loci of 2401, 577, 2996 and 154 had the highest power to show the mixed strains infection in clinical samples. Conclusions Direct MIRU-VNTR is partially successful in complete genotyping of M. tuberculosis strains. On the other hand, detection of polyclonal infection is undoubtedly reliable based on the direct MIRU-VNTR.

Recent evidence suggests that gut microbiota-derived metabolites affect many biological processes of the host, including appetite control and weight management. Dysbiosis of the gut microbiome in obesity influences the metabolism and excretion of gut microbiota byproducts and consequently affects the physiology of the host. Since identification of the gut microbiota-host co-metabolites is essential for clarifying the interactions between the intestinal flora and the host, we conducted this systematic review to summarize all human studies that characterized the gut microbiota-related metabolites in overweight and obese individuals. A comprehensive search of the PubMed, Web of Science, and Scopus databases yielded 2,137 articles documented up to July 2018. After screening abstracts and full texts, 12 articles that used different biosamples and methodologies of metabolic profiling and fecal microbiota analysis were included. Amino acids and byproducts of amino acids, lipids and lipid-like metabolites, bile acids derivatives, and other metabolites derived from degradation of carnitine, choline, polyphenols, and purines are among the gut microbiota-derived metabolites which showed alterations in obesity. These metabolites play an important role in metabolic complications of obesity, including insulin resistance, hyperglycemia, and dyslipidemia. The results of this study could be useful in development of therapeutic strategies with the aim of modulating gut microbiota and consequently the metabolic profile in obesity.

Background: Twenty-four loci mycobacterial interspersed repetitive unit-variable number tandem repeat analysis (MIRU-VNTR) is extensively used for genotyping and detection of polyclonal infections in tuberculosis. The aim of the present study was to compare the direct and indirect MIRU-VNTR genotyping and detection of polyclonal infections between old and fresh clinical samples. Method: Two series of TB samples were collected for comparison. After genomic DNA extraction from clinical samples and their respective cultures, 24 loci MIRU-VNTR was performed. Results: In the 14 old samples, no mixed infections were observed, in clinical samples and their respective cultures. In nine fresh samples, 44.4% of mixed infection was observed in the clinical samples, but no mixed infections were observed in their respective cultures. Surprisingly, in the old samples, 92.86% of samples (13/14) had an allelic change between clinical samples and their respective cultures. On the other hand, in fresh samples, only one sample (1/9) had an allelic change between clinical samples and their respective cultures. Conclusions: We concluded that 24 loci MIRU-VNTR undoubtedly is successful in direct genotyping of clinical samples, especially for the fresh samples. However, selecting starting material, such as clinical sample or respective culture can be controversial for the old samples. Regarding polyclonal infections, the fresh samples gives us a better view to detect these infections, especially in the clinical sample.

DNA methylation has been introduced as a promising biomarker for different diseases. Alterations in macrophage DNA methylation status have been documented during Mycobacterium tuberculosis (Mtb) infection. We conducted this study using a human methylation PCR array kit, which comprised a panel of 22 genes in TLR2 signaling pathway, in order to gain insights into epigenetic interactions between drug-susceptible and -resistant Mtb strains and THP-1-derived macrophages (one of the main host immunity cells during TB infection). We also evaluated the expression of Rv1988 gene in the studied isolates. It was found that the methylation level of all of the studied inflammatory genes, except Irak-2 and Tbk-1, increased in THP-1 macrophages, which were infected by extensively drug-resistant (XDR) Mtb strains, compared with the mock cells (P

Background and Objectives: Cholera disease remains an important global health problem affecting 3-5 million subjects worldwide. Outer membrane vesicles (OMVs) have been found in a variety of Gram-negative bacteria and act as protective transport vesicles. The aim of this study was to evaluate Immune responses against Vibrio cholerae O1 El Tor clinical strain OMV and compare it with killed whole cell (KWC), complex of (KWC-OMV) as well as the internationally licensed oral cholera vaccine, Dukoral, in serum and intestinal secretions of mice. Materials and Methods: OMVs were prepared by using modified detergent-centrifugation procedure from V. cholerae O1 El Tor clinical strain from 2005 outbreak. The ultrastructure and content of OMVs were investigated via the Scanning Elec- tron Microscopy (SEM) and SDS-PAGE analysis. Three doses of oral immunization were adjusted and total IgG and IgA in serum and intestinal secretion were measured by enzyme-linked immunosorbent assay (ELISA). Results: Extracted OMVs from the V. cholerae were spherical vesicles with a size ranging from 10 to 300 nm. OMV-im- munized mice showed an increased level of total IgG and IgA both in serum and intestinal secretion when compared to the negative controls. Also, there existed a higher level of secretory IgA than the total IgG, suggesting the most of protection against V. cholerae colonization provided by sIgA. Conclusion: Our findings revealed that oral immunization with V. cholerae OMVs might induce a long-term immunity, es- pecially when administered in combination with KWC. This study tested the adjuvant activity of OMVs and may be useful in future nano vaccine research.

Background In order to shorten the course of treatment and its effectiveness, it is essential to gain an in-depth insight into the drug resistance mechanisms of Mycobacterium tuberculosis (M. tuberculosis). Methods In this study, we evaluated the contribution of 26 drug efflux pumps plus target gene mutations to the drug resistance levels in multi-drug resistant (MDR)/pre-extensively drug-resistant (pre-XDR)/extensively drug-resistant (XDR) and mono-drug resistant clinical isolates of M. tuberculosis. The panels of 25 M. tuberculosis clinical strains were characterized for drug resistance-associated mutations with whole-genome sequencing and antibiotic profiles in the presence and absence of efflux inhibitor verapamil (VP). Results Different MICs were observed for the same target gene mutations. Out of the 16 MDR/pre-XDR/XDR isolates, 6 (37.5%) and 3 (18.8%) isolates demonstrated a significant decrease in rifampicin (RIF) MIC and isoniazid (INH) MIC due to the VP exposure (64 μg/mL), respectively. Susceptibility to RIF was fully restored in two isolates after VP exposure. Moreover, the efflux pump genes of Rv2938, Rv2936, Rv1145, Rv1146, Rv933, Rv1250, Rv876, Rv2333, Rv2459, Rv849, and Rv1819 were overexpressed in the presence of anti-TB drugs, showing the contribution of these efflux pumps to the overall resistance phenotype. Conclusions Our results clearly showed that efflux systems, besides spontaneous mutations, play a role in the development of INH/RIF resistance. In addition, although VP was effective in reducing the expression of some efflux pumps, it was not very successful at the phenotypic level.

Background:The thyroid gland influences the metabolic processes in our body by producing thyroid hormones, and thyroid disorders can range from a harmless goiter to life-threatening cancer. A growing number of evidence support the link between gut microbiota composition and thyroid homeostasis. Gut dysbiosis can disrupt the normal gut barrier function, leading to immunologic and metabolic disorders.Objective:The aim of this review was to discuss the main features of gut dysbiosis associated with different thyroid disorders.Results:Gut microbiota contributes to thyroid hormone synthesis and hydrolysis of thyroid hormones conjugates. It has been shown that microbial metabolites may play a role in autoimmune thyroid diseases via modulating the immune system. Intestinal microbiota can contribute to the thyroid malignancies via controlling DNA damage and apoptosis and influencing inflammatory reactions by the microbiota- derived metabolites. However, the pathogenic role of altered gut microbiota in different thyroid disorders has not yet fully elucidated.Conclusion:Further research is needed to assess the role of alterations of the gut microbiota in disease onset and development in order to achieve novel strategies for the prevention and treatment of these diseases.