16S rRNA sequencing analysis of the oral and fecal microbiota in colorectal cancer positives versus colorectal cancer negatives in Iranian population

BACKGROUND

Colorectal cancer (CRC) poses a significant healthcare challenge, accounting for nearly 6.1% of global cancer cases. Early detection, facilitated by population screening utilizing innovative biomarkers, is pivotal for mitigating CRC incidence. This study aims to scrutinize the fecal and salivary microbiomes of CRC-positive individuals (CPs) in comparison to CRC-negative counterparts (CNs) to enhance early CRC diagnosis through microbial biomarkers.

MATERIAL AND METHODS

A total of 80 oral and stool samples were collected from Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran, encompassing both CPs and CNs undergoing screening. Microbial profiling was conducted using 16S rRNA sequencing assays, employing the Nextera XT Index Kit on an Illumina NovaSeq platform.

RESULTS

Distinct microbial profiles were observed in saliva and stool samples of CPs, diverging significantly from those of CNs at various taxonomic levels, including phylum, family, and species. Saliva samples from CPs exhibited abundance of Calothrix parietina, Granulicatella adiacens, Rothia dentocariosa, and Rothia mucilaginosa, absent in CNs. Additionally, Lachnospiraceae and Prevotellaceae were markedly higher in CPs' feces, while the Fusobacteria phylum was significantly elevated in CPs' saliva. Conversely, the non-pathogenic bacterium Akkermansia muciniphila exhibited a significant decrease in CPs' fecal samples compared to CNs.

CONCLUSION

Through meticulous selection of saliva and stool microbes based on Mean Decrease GINI values and employing logistic regression for saliva and support vector machine models for stool, we successfully developed a microbiota test with heightened sensitivity and specificity for early CRC detection.

Therapeutic effects of probiotics and herbal medications on oxalate nephrolithiasis: a mini systematic review

Background and Objectives

The majority of all kidney stone cases are oxalate urolithiasis with a high risk of recurrence. Beside its widespread occurrence, kidney stones are characterized by severe complications and high treatment costs. Probiotics and herbal medications could be forthcoming therapeutic interventions in the management of oxalate kidney stones.

Materials and Methods

The PubMed/MEDLINE database was searched for keywords "Oxalobacter formigenes" AND "Oxalate" OR "oxalate degradation" AND "Lactobacillus" OR "Bifidobacterium" OR "recombinant Lactobacillus" OR "Bacillus subtilis", and "urolithiasis" AND "herbal extract". The search returned 253 results, 38 of which were included in the review.

Results

Most of the oxalate-degrading probiotics belong to the Oxalobacter formigenes, Lactobacillus, Bifidobacterium, and Bacillus genus with a minimum dosage of 107 CFU in the form of capsules, sachets, and lyophilized powder. Oxalate concentration in media was 5-50mM with an incubation time ranging from 24h to 14 days. The majority of the studies suggested that probiotic supplementation might be useful for reducing urinary excretion of oxalate and urea and alleviation of stone formation. Different herbal extracts were used on murine models of nephrolithiasis (induced by 0.5-3% ethylene glycol) with reduction of renal inflammation and urinary parameters, and calcium oxalate crystals.

Conclusion

Several strains of probiotics and herbal extracts confer protective effects against kidney stone/nephrolithiasis, indicating their promising nature for being considered as elements of preventive / adjuvant therapeutic strategies.

Probiotics: truths and illusions

The Article Abstract is not available.  

Efficacy of light chain 3-fused protein multi epitope in protection of mice challenged with Mycobacterium tuberculosis

The new strategy for vaccine development such as the fused protein multi-epitope capable of preventing the reactivation of latent tuberculosis infection (LTBi) can be an effective strategy for controlling tuberculosis (TB) worldwide. This study was conducted to evaluate the immunity of experimentally infected BALB/c mice with Mycobacterium tuberculosis after injection of DNA construct. Nineteen female BALB/c mice were divided into three groups and injected with 0.50 mL of M. tuberculosis. After 3 weeks, lung and spleen samples from the infected mice were examined. The protective effects of light chain 3-fused protein multi-epitope against TB were evaluated for post-exposure and therapeutic exposure. The lungs and spleens of the mice were aseptically removed after death for histopathology analysis. The bacterial colonies were counted, and the cells were stained after 3 weeks of incubation. No significant differences were observed between the post-exposure and therapeutic exposure groups. The pathological changes in the lung tissue of mice in these groups included an increase in the thickness of interalveolar septa, hyperemia, and intraparenchymal pulmonary hemorrhage centers (positive control), scattered hyperemic areas (negative control), and hyperemia in the interstitial tissue, scattered hyperemic areas in the lung parenchyma and lymphocytic infiltration centers (experimental group). Flow cytometry of the post-exposure and therapeutic exposure models showed insignificant changes in all three groups. It seems necessary to develop a post-exposure and therapeutic exposure vaccine strategy that focuses on LTBi to prevent the progression of the active disease. In this regard, multi-epitope vaccines should be designed to induce both cellular and humoral immunity.

Molecular Characteristics of Staphylococcus aureus Strains Isolated from Nasal Cavity and Wound Infections Among Diabetic Patients

Staphylococcus aureus is the most common pathogen contributing to diabetic foot infections (DFI). Nasal transmission of S. aureus potentially increases the risk of endogenous infection. The aim of this study was to determine the genetic diversity and antibiotic resistance profile of S. aureus isolates in nasal and wound samples from diabetic patients. A cross-sectional study was conducted from July 2018 to September 2019. S. aureus was isolated from the anterior nares and wounds of diabetic patients. All S. aureus isolates were characterized by detection of resistance and virulence genes (mecA, ermA, ermC, hla, hlb, hlg, sea, lukDE, pvl), staphylococcal cassette chromosome mec (SCCmec)-typing and staphylococcal protein A (spa)-typing. A total of 34 S. aureus were isolated from the wounds of 115 diabetic patients with DFI. Twenty-four S. aureus isolates were collected from the anterior nares of patients, and thirteen patients had concurrent S. aureus in nasal and wound specimens. The prevalence of methicillin-resistant S. aureus (MRSA) in nasal specimens was noticeable (41.7%), and the most common spa-type in nasal and wound specimens was t14870. Nearly half of the patients with concurrent S. aureus in wound and nasal specimens had similar isolates from both sites. Our data suggest that detection and screening of S. aureus colonization in the nasal cavity may prevent subsequent endogenous infections, particularly with MRSA strains.

Respiratory Bacterial and Fungal Superinfections During the Third Surge of the COVID-19 Pandemic in Iran

Objective: We characterized bacterial and fungal superinfection and evaluated the antimicrobial resistance profile against the most common superinfection-causing pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, and Staphylococcus aureus). Methods: In a cross-sectional study, 192 respiratory samples were collected from patients with and without SARS-COV-2 admitted to a teaching hospital in Tehran. Superinfection proportions and the antibiotic resistance profile were assessed and compared with demographic, comorbidities, and other clinical factors. Results: Superinfection rate was 60% among COVID-19 patients (p = 0.629). Intensive care unit admission (p = 0.017), mortality rate (p ≤ 0.001), and antiviral and corticosteroid therapy (p ≤ 0.001) were significantly more common among patients with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). The most common superinfections were caused by K. pneumoniae (42.7%, 82/192), A. baumannii (14.6%, 28/192), and S. aureus (13%, 25/192). A. baumannii isolates exhibited greater antibiotic resistance. Forty-four percent (11/25) of S. aureus isolates were cefoxitin resistant and also confirmed as methicillin-resistant S. aureus by PCR. Conclusion: The rise of difficult-to-treat infections with a high burden of antibiotic resistance, coupled with an increase in mortality rate of SARS-COV-2 superinfected individuals, illustrates the impact of the COVID-19 pandemic on antimicrobial resistance. Post-pandemic antimicrobial resistance crisis management requires precise microbiological diagnosis, drug susceptibility testing, and prescription of antimicrobials appropriate for the patient's condition.

Bismuth nanoparticles against microbial infections

The destructive effect of infectious diseases on human life and the emergence of antibiotic-resistant strains highlight the importance of developing new and appropriate treatment strategies, one of which is the use of metals as therapeutic agents. Bismuth nanoparticles are an example of prominent metal-containing drugs. The therapeutic effects of bismuth-based drugs in the treatment of wounds have been proven. Various laboratory studies have confirmed the antimicrobial effects of bismuth nanoparticles, including the clinical treatment of ulcers caused by Helicobacter pylori. Therefore, considering the performance of this nanoparticle and its potent effect on infectious agents and its therapeutic dimensions, the present study fully investigated the properties and performance of this metal-based nanoparticle.

Microbial Profile and Antibiotic Susceptibility Pattern in Diabetic Patients with Mild, Moderate, and Severe Foot Infections in Tehran

It is estimated that 10-25% of diabetic patients will encounter diabetic foot ulcers (DFU) during their lifetime. This study evaluated the microbiology of DFUs and determined the antibiotic resistance pattern of bacterial isolates based on the severity of wounds and infections in different grades of ulcer. The specimens were collected from115 diabetic foot infections (DFI) deep tissue by needle aspiration and biopsy. The aerobic and anaerobic cultures and antimicrobial susceptibility testing were carried out. The presence of resistance genes including metallo-beta-lactamases (MBL), extended-spectrum β-lactamase (ESBL), ermA, ermC, and mecA was also determined. A total of 222 microorganisms were isolated. The prevalence of poly-microbial infections was 69.6%. Bacterial isolates comprised 64.2% Gram-positive bacteria (GPB), 33.5% Gram-negative bacteria (GNB), and five isolates of anaerobic bacteria were also detected. The most prevalent GPB and GNB were Staphylococcus spp. (52.2%) and Escherichia coli (33.3%), respectively. The prevalence of poly-microbial infections and GNB was positively associated with increased grades of Wagner and IDSA classifications. Among Staphylococcus aureus isolates, resistance to clindamycin (73.5%), ciprofloxacin (70.6%), and erythromycin (70.6%) were noticeable. GNB was also highly resistant to cephalosporins and ciprofloxacin. ESBL genes were detected in approximately 40% of isolates of Enterobacteriaceae. The prevalence of ermA, ermC, and mecA genes in S. aureus isolates were 8.8%, 32.3%, and 14.7%, respectively. In conclusion, our data suggest that GPBs are the most common isolates from DFIs. Furthermore, with the development of wounds and infection, the prevalence of GNB in DFIs are increased.

Expression of Toll-Like Receptors 2, 4 and 5 in Relation to Gut Microbiota in Colon Neoplasm Patients with and without Inflammatory Bowel Disease

Background:

Toll-Like Receptors (TLRs) are the critical mediators of inflammatory routs in the gut, which play an essential role in regulating the immune responses towards various ligands derived from pathogenic bacteria. Also, TLR signaling has been implicated in the development of Inflammatory Bowel Disease (IBD), Adenomatous Polyp (AP), and Colorectal Cancer (CRC). Here, we aimed to examine the expression of some TLRs concerning certain fecal bacteria in AP and CRC patients with and without IBD.

Methods:

This case-control study collected fecal and colonic tissue samples from 93 patients versus Normal Controls (NC) via colonoscopy. Fecal samples were used for DNA extraction, and the abundance of selected fecal bacteria was determined by absolute real-time PCR. Also, the gene expression of TLR2, 4, and 5 was analyzed using RT-PCR on the colonic tissues of participants.

Results:

Compared to NC individuals, in AP and CRC patients, the mRNA expressions of TLR4 and TLR2 were significantly increased while TLR5 was decreased. A meaningful association between TLRs mRNA expression levels and the abundance of some selected fecal bacteria was detected. Also, there was a significant relationship between participant’s food regimes, smoking habit and intestinal TLRs expression.

Conclusion:

Our study proposed the important role of TLRs during adenomatous and CRC formation. Alterations in TLRs expression associated with certain gut bacteria may contribute to disease development.

Bacterial community of chronic rhinosinusitis patients and therapeutic ultrasound efficacy: clinical trial study

Background and Objectives

Bacterial involvement in chronic rhinosinusitis (CRS) condition made it difficult to treat using available antibiotic therapy. Therapeutic ultrasound was investigated here to evaluate bacterial diversity and quantity before and after continuous/pulsed ultrasound strategy compared to control patients.

Materials and Methods

Totally, 34 CRS patients were studied in three groups, including continuous ultrasound, pulsed ultrasound and control. Bacterial culture and identification were done before and after treatment. Computed tomography scan (CT scan) and questionnaire scores were recorded two times before and after intervention.

Results

The most prevalent bacterial isolates were non-hemolytic Streptococci (34 patients), coagulase-negative Staphylococcus (33 patients), Gram-negative cocci (26 patients), Staphylococcus aureus (19 patients), Streptococcus pneumoniae (five patients) and Streptococcus pyogenes (five patients). Both continuous and pulsed ultrasound could significantly reduce the quantity of bacterial isolates after treatment. CT scan and questionnaire results support the effectiveness of therapeutic ultrasound.

Conclusion

The quantity of clinically important bacteria was significantly reduced using ultrasound treatment and recovery of patients was supported by CT scan and questionnaire scores. Alternative therapeutic ultrasound could be an effective procedure in CRS patients.

Post-neurosurgical meningitis; gram negative bacilli vs. gram positive cocci

Background

Post-neurosurgical meningitis is a significant cause of mortality and morbidity. In this study we aimed to compare the differences of clinical, laboratory features and outcomes between the post-neurosurgical meningitis caused by gram-negative bacilli (GNB) and gram-positive cocci (GPC).

Methods

Cases of post-neurosurgical meningitis (with positive CSF culture) were included. After classifying patients as GNB and GPC groups, clinical and paraclinical data were compared.

Results

Out of 2667 neurosurgical patients, CSF culture was positive in 45 patients. 25 (54.3%) were GNB, 19 (41.3%) GPC. The most common microorganisms were Klebsiella pneumoniae (n=14, 31.1%), Coagulase negative staphylococcus (n=8, 17.8%), Staphylococcus aureus (n=6, 13.3%), Acinetobacter baumannii (n=4, 8.9%), Pseudomonas aeruginosa (n=2, 4.4%), and Escherichia coli (n=2, 4.4%). There were no correlation between CSF Leakage, Surgical site appearance, presence of drain, Age and GCS between two groups (P=0.11, P=0.28, P=0.06, P=0.86, P=0.11 respectively). The only different laboratory indexes were ESR (86.8 mm/h vs. 59.5 mm/h, P=0.01) and PCT (13.1 ng/ml vs. 0.8 ng/ml, P=0.02) which were higher in GNB cases. 20% (n=5) of patients with GNB meningitis received preoperative corticosteroid, while none of GPC cases received (P=0.03). The median length of hospitalization for GNB and GPC cases was 56 and 44.4 days respectively (P=0.3).

Conclusion

The GNB antibiotic coverage should be designed more carefully in post-neurosurgical meningitis especially in patients with recent corticosteroid therapy and elevated ESR and procalcitonin.

Evaluation of in vitro activity of ceftaroline on methicillin resistant Staphylococcus aureus blood isolates from Iran

Background and Objectives:

Ceftaroline (CPT) is a novel cephalosporin with potent activity against methicillin-resistant Staphylococcus aureus (MRSA). Despite its recent introduction, CPT resistance in MRSA has been described worldwide. We aimed in the current study to evaluate the in vitro activity of CPT against 91 clinical MRSA and 3 MSSA isolates.

Materials and Methods:

Susceptibility of isolates to CPT was tested using E-test and disk diffusion (DD) method. The nucleotide sequence of the mecA gene and molecular types of isolates with reduced susceptibility to CPT were further studied to identify resistance conferring mutations in PBP2a and the genetic relatedness of the isolates respectively.

Results:

Overall, 92.5% of isolates were found to be CPT susceptible (MICs≤1mg/l) and 7 MRSA isolates were characterized with MIC=2mg/l and categorized as susceptible dose dependent. Compared to E-test, DD revealed a categorical agreement rate of 93.6% and the obtained rates for minor, major /very major error were found to be 6.3% and 0% respectively. The MRSA isolates with increased CPT MICs (n=7), belonged to spa types t030 (n=6) and t13927 (n=1) and all carried N146K substitution in PBP2a allosteric domain, except for one isolate which harbored a wild-type PBP2a.

Conclusion:

While resistance to CPT was not detected we found increased CPT MICs in 7.69% of MRSA isolates. Reduced susceptibility to CPT in the absence of mecA mutations is indicative of contribution of secondary chromosomal mutations in resistance development.

Distribution of ciprofloxacin-resistance genes among ST131 and non-ST131 clones of Escherichia coli isolates with ESBL phenotypes isolated from women with urinary tract infection

Background and Objectives:

Escherichia coli (E. coli) sequence type 131 (ST131) is associated with extended-spectrum beta-lactamase (ESBL) production and fluoroquinolone resistance. This study aimed to investigate the prevalence of ST131, ESBL, and plasmid-mediated quinolone resistance (PMQR) genes in the ciprofloxacin-resistant (CIP^R) and ESBL producers from women with UTI.

Materials and Methods:

The CIP-resistant ESBL producing (CIP^R/ESBL⁺) E. coli isolates were screened for ST131-by specific PCR of mdh and gyrB. The ESBL and PMQR genes were screened by single PCR. The ST131 and non-ST131 isolates were selected to determine the mutations of gyrA and parC using PCR and sequencing, and also their genetic background by the Pasteur-MLST scheme.

Results:

Overall, 55% (33/60) CIP^R/ESBL⁺ isolates were identified as ST131 (94% O25b-ST131). Resistance rate to ampicillin-sulbactam (70%), aztreonam (97%) and gentamicin (61%), the prevalence of aac(6′)-Ib-cr (66%), bla _CTX-M-15 (82%), the profile of qnrS+aac(6′)-Ib-cr (30%), and the double mutation in the parC was significantly higher in ST131 than non- ST131 isolates. The coexistence of PMQR and ESBL genes was found in more than 50% of ST131 and non-ST131 isolates. ST131 isolates differentiated into PST43 and PST506.

Conclusion:

Management of women with UTI caused by the CIP^R/ESBL⁺ isolates (ST131) co-harbored PMQR, ESBL, and chromosomal mutations, is important for their effective therapy.

The piriformis abscess: a case-based review

This study reports a 43 years-old man diagnosed with piriformis pyomyositis. A literature review was conducted by searching MEDLINE via Pubmed for English language case reports, published from 8^th December 2019 to 20^th January 2020. Patients' symptoms, laboratory tests, imaging, treatment, and other comorbidities were evaluated. Thirty-two cases diagnosed with piriformis pyomyositis, of which 21 patients developed piriformis abscess (including one new patient added by us) of which 52.4% were female, and the mean age was 26.98 ± 17.5. The most common manifestations were fever, lower back pain, and limited ambulation with increased ESR, CRP, or leukocytosis. Staphylococcus aureus was the most prevalent (57.14%) pathogen isolated. The authors suggested gynecologic manipulations, muscle overuse, and other co-infections as probable risk factors. However, we fail to find any association between these factors and abscess formation (p>0.05). Piriformis abscess should be regarded as a probable diagnosis in patients with gluteal pain, fever, and limited ambulation that have raised inflammatory markers or leukocytosis. MRI and CT scans are beneficial in diagnosing pyomyositis in early-stage. Full recovery is expected with timely antibiotic and surgical treatments.

Genotyping and Drug Susceptibility Patterns of M. Tuberculosis Isolated from HIV Seropositive Patients in Tehran Iran

AIM

This study aims to investigate the prevalence and drug-resistance M. tuberculosis isolated from HIV seropositive individuals in Tehran, Iran.

BACKGROUND

Human immunodeficiency virus (HIV) is one of the most important risk factors for developing active tuberculosis (TB).

OBJECTIVE

The objective is to determine the rate of transmission and drug-resistant M. tuberculosis (MTB) strains isolated from HIV seropositive patients in Tehran province, Iran.

METHODS

This study consecutively enrolled 217 TB/HIV coinfected patients from April 2018 to August 2019 at Emam Khomeini referral hospital and 5 other health centers in Tehran province. The isolates were genotyped using 15 loci Mycobacterial interspersed repetitive unit-variable number tandem repeats (MIRU-VNTR). Minimum inhibitory concentration (MIC) was determined for 6 drugs. In addition, mutations were assessed in rpoB, katG, inhA, and ahpC genes using Reverse Blot Hybridization Assay System.

RESULTS

A 20 (9.2%) patients were culture-positive for M. tuberculosis and typed by MIRU-VNTR, 13 (65%) strains formed 5 clusters, but 6 (30%) isolates had a unique pattern. The total Hunter- Gaston discrimination index (HGDI) for all 15 loci was 0.846, and the cluster size was 2 to 4 patients. The estimated proportion of recent transmission was 45%. The mutation was identified in 1 isolate, lost inhAW1 and mutation in MT1 loci, which was resistant to isoniazid (INH). Moreover, 1 (5%) and 3 (15%) isolates were resistant to INH and ethambutol (EMB), respectively, of which 1 was resistant to INH and EMB.

CONCLUSION

The transmission rate of TB in HIV patients was relatively high; however, the prevalence of drug-resistant strains and TB infection in females was insignificant in this study (p < 0.05); none of the isolates was MDR strains.

The 7H11 Agar Medium Supplemented with Calf Bovine Serum for Susceptibility Testing of Mycobacterium tuberculosis Isolates Against Pyrazinamide

Despite its importance, pyrazinamide (PZA) is a blind spot in drug susceptibility testing in tuberculosis laboratories. The aim of this study was to set up a reliable agar-based proportion method for detection of PZA-resistant phenotypes using Middlebrook 7H11 agar supplemented with calf bovine serum (CBS) compared with albumin/dextrose/catalase (ADC) enrichment and pncA/rpsA sequencing results. The 7H11 agar medium supplemented with 10% ADC or 10% CBS (pH 6.2) and 100 μg/mL PZA was used to detect PZA resistance among 64 Mycobacterium tuberculosis isolates. Sanger sequencing and whole-genome sequencing were performed to track mutations in the pncA, rpsA, and their upstream regions. A total of 43 rifampicin/multidrug-resistant, 20 drug-susceptible, and 1 isoniazid mono-resistant M. tuberculosis isolates were investigated. The 7H11+ADC and 7H11+CBS could detect 22 and 23 PZA-resistant strains, respectively. With the same specificity, the sensitivity and accuracy of 7H11+CBS was found to be a little greater than 7H11+ADC in PZA resistance detection compared with sequencing results. Twenty-four mutant strains were found to have different mutations in pncA-upstream, pncA and rpsA genes, in which Gly97Asp was the most dominant mutation. The results obtained from 7H11+CBS were comparable to the results of 7H11+ADC. Therefore, the 7H11 agar proportion method would be a less-expensive test using CBS and produces reliable results.

Molecular identification and antibiotic resistance pattern of actinomycetes isolates among immunocompromised patients in Iran, emerging of new infections

Recent advancements in DNA-based approaches have led to the identification of uncommon and rare bacterial pathogens. In this study, by utilizing a DNA-based approach, a total of 1043 clinical specimens were processed for the identification of actinobacteria targeting the 16S rRNA and gyrB genes. Drug susceptibility testing was also conducted using micro-broth dilution and PCR. Two isolates of Nocardia flavorosea and Rhodococcus erythropolis were reported for the first time in Iran. Also, Nocardiopsis dassonvillei, Streptomyces olivaceus, and Streptomyces griseus were reported for the first time in Asia. Infections caused by Nocardia caishijiensis and Prauserella muralis have also been reported in this study. The first Asian case of pulmonary infection caused by Nocardia ignorata and the first global case of brain abscess caused by Nocardia ninae and Nocardia neocaledoniensis have been reported in this study. Overall 30 isolates belonging to 6 genera (Nocardia, Streptomyces, Rodoccoccus, Nocardiopsis, Rothia, and Prauserella) were detected in 30 patients. All 30 isolates were susceptible to amikacin and linezolid. Three isolates including Nocardia otitidiscaviarum (n = 2) and Nocardia flavorosea (n = 1) were resistant to trimethoprim-sulfamethoxazole which were the first trimethoprim-sulfamethoxazole resistant clinical actinomycetes in Iran. Isolation of rare species of actinomycetes particularly Nocardia spp. requires urgent action before they spread clinically particularly among immunocompromised patients.

Antibiotic resistance pattern of Bacteroides fragilis isolated from clinical and colorectal specimens

BACKGROUND

Bacteroides fragilis is a part of the normal gastrointestinal flora, but it is also the most common anaerobic bacteria causing the infection. It is highly resistant to antibiotics and contains abundant antibiotic resistance mechanisms.

METHODS

The antibiotic resistance pattern of 78 isolates of B. fragilis (22 strains from clinical samples and 56 strains from the colorectal tissue) was investigated using agar dilution method. The gene encoding Bacteroides fargilis toxin bft, and antibiotic resistance genes were targeted by PCR assay.

RESULTS

The highest rate of resistance was observed for penicillin G (100%) followed by tetracycline (74.4%), clindamycin (41%) and cefoxitin (38.5%). Only a single isolate showed resistance to imipenem which contained cfiA and IS1186 genes. All isolates were susceptible to metronidazole. Accordingly, tetQ (87.2%), cepA (73.1%) and ermF (64.1%) were the most abundant antibiotic-resistant genes identified in this study. MIC values for penicillin, cefoxitin and clindamycin were significantly different among isolates with the cepA, cfxA and ermF in compare with those lacking such genes. In addition, 22.7 and 17.8% of clinical and GIT isolates had the bft gene, respectively.

CONCLUSIONS

The finding of this study shows that metronidazole is highly in vitro active agent against all of B. fragilis isolates and remain the first-line antimicrobial for empirical therapy.

Pulmonary Nocardiosis in Pemphigus Vulgaris Patients from Tehran, Iran

OBJECTIVE

Nocardiosis is an opportunistic infection in individuals who had organ transplants and in patients with immunosuppressive diseases such as pemphigus Vulgaris (PV), diabetes mellitus, and HIV. Nocardiosis rate has not been assessed in Iranian PV patients, and this was the first study to estimate nocardiosis rate in these patients.

METHODS

In this study, 103 patients with PV were examined. BAL samples were obtained and direct smear was prepared and visualized by microscopy after PAS staining. Samples were cultured on antibiotic-containing blood and chocolate agar media. DNA extraction and PCR were performed on positive cultures, and final identification was done by 16S rRNA gene sequencing. Drug susceptibility testing was done by microbroth dilution method.

RESULTS

Four positive cultures (3.88%) were found in the samples (n = 103). According to sequence analysis, 2 isolates were identified as Nocardia cyriacigeorgica and 2 as Nocardia otitidiscaviarum and Nocardia cerradoensis. Nocardia cerradoensis was isolated from an invasive brain infection. Isolated bacteria were susceptible to majority of the tested antibiotics, except for 2 strains of Nocardia cyriacigeorgica and Nocardia cerradoensis. This was the first isolation of Nocardia cerradoensis of human infection in Asia. Patients with PV are susceptible to nocardiosis, similar to other immunocompromised patients.

CONCLUSION

Pemphigus Vulgaris is a severe autoimmune disease which is treated by a high dosage of corticosteroids. Opportunistic infections are one of the greatest challenges of these patients. One of the neglected agents of opportunistic infection in this disorder is Nocardiosis which can cause a high mortality rate in PV patients.

Selective screening and characterization of plant growth promoting bacteria for growth enhancement of tomato, Lycopersicon esculentum

Background and Objectives

Plant Growth-promoting Bacteria (PGPB) can replace the dangerous chemical fertilizers and pesticides. The aim of this study was to isolate the PGPBs for Lycopersicon esculentum plant and to determine the appropriate volume for inoculation.

Materials and Methods

Plants samples were collected from tomato fields. Nitrogen fixing-PGPBs were isolated from rhizoplane and rhizosphere. Five isolates were screened based on their growth abilities and examined for PGPB traits including phosphate solubilization, and IAA, ammonia and HCN production. After high cell density cultivation, the cells were separated by centrifugation and freeze dried after resuspension in cryoprotectant. The powders were inoculated into sterile soil with a dose of 10⁶, 10⁷ and 10⁸ CFUs/g. Tomato (Lycopersicon esculentum) seeds were sown in soil and after 42 days the shoot length was measured.

Results

Most of the potent PGPBs with high growth capacity were isolated from rhizoplane. Maximum phosphate solubilization was 289.7 μg/ml by NFB12 which isolated from rhizoplane. This strain produced the maximum level of IAA. NFB12 produced ammonia without the ability of production of HCN. This strain enhanced shoot length in dosed dependent manner. Surprisingly, inoculation of soil with 10⁸ CFUs/g dramatically decreased the shoot length by 21%. Based on molecular approach NFB12 was identified as Bacillus megaterium.

Conclusion

Isolation of specific PGPBS is recommended for sustainable plant production. Our results showed that NBF12 improves tomato plant growth and its effect on tomato plant growth is does dependent. Maximum growth rate of tomato was observed with 10⁷ CFUs/g soil inoculation of NFB12 while higher inoculation showed negative effect.

Incidence, Clinical Manifestation, Treatment Outcome, and Drug Susceptibility Pattern of Nontuberculous Mycobacteria in HIV Patients in Tehran, Iran

Background

Nontuberculous mycobacterial (NTM) infections have radically increased worldwide due to the increase in HIV infections. The disease activity increases with progressive immunodeficiency.

Methods

A total of 216 HIV seropositive patients suspected of having mycobacterial infection were recruited for this study. Clinical samples were collected from each patient and cultured on Lowenstein-Jensen media. Detection and species identification were simultaneously done using Reverse Blot Hybridization Assay System. Also, the minimum inhibitory concentrations (MIC) for each isolate were determined in 7H9 broth media for 10 antibiotics.

Results

In this study, 4 rapid and 4 slow-growing NTM species were isolated and identified. Mycobacterium fortuitum was the most common NTM species, 3/8 (37.5%), followed by Mycobacterium kansasii, 2/8 (25%). The cases were identified as pulmonary disease, 5/8 (62.5 %), disseminated infection, 2/8 (25%), and skin abscess, 1/8 (12.5%). M. chelonae and Mycobacterium avium were isolated from patients diagnosed with disseminated infection with treatment failure. The skin abscess was caused by infection with M. simiae. The results of the MIC testing were as follows: M. kansasii and M. fortuitum were susceptible to amikacin (AMK); M. avium to clarithromycin (CLA); M. fortuitum 2/3 (67%) to ciprofloxacin (CIP); 1/2 (50%) of M. kansasii isolates to CLA, and M. chelonae to rifampin (RIF), linezolid (LIN), AMK, and CIP at medium and high concentrations.

Conclusion

AMK showed incredible in vitro activity against M. kansasii and M. fortuitum. Also, M. avium was susceptible to CLA, whereas M. simiae and M. chelonae were resistant to the tested drugs in this study.

Distribution of Pathogenicity Island Markers and H-Antigen Types of Escherichia coli O25b/ST131 Isolates from Patients with Urinary Tract Infection in Iran

Escherichia coli serogroup O25b-sequence type 131 (E. coli O25b/ST131) is known as a multidrug-resistant organism with high virulence potential and has received attention internationally. We aim to investigate the prevalence of O25b/ST131 and the distribution of bla_CTX-M-15, pathogenicity island (PAI) markers, phylogenetic groups, and H-antigen typing in the E. coli O25b/ST131 isolated from patients with urinary tract infection (UTI) in Tehran, the capital of Iran. Seventy (26.9%) E. coli isolates were identified as O25b/ST131. There was also a significant difference in the prevalence of virulence genes, including papA, sfa, sat, cnf1, iutA, kpMII, traT, and usp, in the O25b/ST131 isolates rather than non-O25b/ST131 ones (p ≤ 0.05). Furthermore, 78% of the O25b/ST131 isolates carried four to seven PAIs, while 71% of non-O25b/ST131 isolates carried two to four PAI markers (p ≤ 0.05). Our study showed that in addition to H4, other H-antigens may play a role in the O25b/ST131 virulence potential. Besides, a significant association was found between the history of previous UTIs and infection among the O25b/ST131 clone isolates. Pulsed-field gel electrophoresis revealed circulating of O25b:H4-ST131/PST43 clone in both hospital and community. Approximately one in every three uropathogenic E. coli isolates was the O25b/ST131 clone, representing a significant public health threat. Practical investigation on O25b/ST131 can be helpful in better understanding of ST131 evolution and controlling UTI in hospitals.

Ventilator-associated Pneumonia: Multidrug Resistant Acinetobacter vs. Extended Spectrum Beta Lactamase-producing Klebsiella

INTRODUCTION

Ventilator-associated pneumonia (VAP) has been considered as a healthcare-associated infection with high mortality. Acinetobacter baumannii and Klebsiella pneumoniae are the common causes of VAPs around the world.

METHODOLOGY

This research was a retrospective observational study in the intensive care unit (ICU) in a tertiary referral collegiate hospital in Tehran between March 2016 and May 2018. Patients who fulfilled VAP due to documented Multidrug Resistant Acinetobacter baumannii (MDR-AB) or Extended Spectrum Beta Lactamase-producing Klebsiella pneumoniae (ESBL-KP) criteria were enrolled. General demographic features, duration of hospital stay, antimicrobial treatment regimens, duration of ICU admission, the period of mechanical ventilation (MV) and 30-day mortality were documented and compared.

RESULTS

210 patients were found with clinical, microbiological and radiological evidence of VAP. In total, 76 patients with MDR-AB and 76 patients with ESBL-KP infections were matched in the final analysis. Duration of hospitalization in the patients with MDR-AB was significantly more than that of patients infected with ESBL-KP (p-value: 0.045). Patients diagnosed with MDR-AB VAP had a 65.8% mortality rate compared to 42.1% in the ESBL-KP infection group (p = 0.003).

CONCLUSIONS

Results of the present study demonstrated that VAPs caused by MDR-AB may be more hazardous than ESBL-KP VAPs because they could be accompanied by a longer hospitalization course and even a higher mortality.

Molecular characterization, antibiotic resistance pattern and capsular types of invasive Streptococcus pneumoniae isolated from clinical samples in Tehran, Iran

Background

Streptococcus pneumoniae causes serious infections worldwide. The aim of this study was to determine the molecular characteristic, antibiotic resistance pattern and capsular types of invasive S. pneumoniae in Tehran, Iran.

Results

Of the 44 pneumococcal invasive isolates, 39 (89%) were isolated from children and 5 (11%) from adults. The results show that all pneumococcal isolates were susceptible to linezolid but had varying resistance to trimethoprim-sulfamethoxazole (86%), erythromycin (73%), tetracycline (66%), clindamycin (43%), penicillin (16%), chloramphenicol (14%) and levofloxacin (2%). The range of erythromycin, tetracycline and penicillin MICs were 2 - ≥ 256 μg/mL, 4 - ≥ 48 μg/mL, and 0.047 - ≥ 256 respectively. All of the penicillin resistant isolates were multidrug resistant (MDR) and in addition to penicillin were resistant to tetracycline, erythromycin and trimethoprim-sulfamethoxazole. The most common capsular types detected in 64% of the pneumococcal isolates was 6A/B, 19A, 15A, 23F. The multilocus sequence typing (MLST) of 10 pneumococcal isolates revealed 9 different sequence types (STs), including ST 15139 (capsular type 19A) and ST 15140 (capsular type 23F), which have not previously been reported.

Conclusions

The study revealed that the S. pneumoniae isolates belonged to diverse capsular types and clones with high rate of resistance to erythromycin, tetracycline, and penicillin.

The critical role of Faecalibacterium prausnitzii in human health: An overview

Faecalibacterium prausnitzii (F. prausnitzii) is one of the most abundant bacterial species in the colon of healthy human adults and representing more than 5% of the total bacterial population. Recently, it has been known as a major actor in human intestinal health and a biosensor. Changes in this species population richness and quantity have been observed in many illnesses and several investigations have reported that abundance of F. prausnitzii is reduced in different intestinal disorders. In the current review, we aim to consider literature from various library databases and electronic searches (Science Direct, PubMed, and Google Scholar) which were randomly collected and serve as an overview of different features of F. prausnitzii including metabolites, anti-inflammatory action, and correlation of dysbiosis of this bacterium with various complications in human.

Toxigenic and non-toxigenic patterns I, II and III and biofilm-forming ability in Bacteroides fragilis strains isolated from patients diagnosed with colorectal cancer

Background

Enterotoxigenic Bacteroides fragilis (ETBF) associated with the initiation and progression of colorectal cancer (CRC) has been alarmingly reported all over the world. In this study, simultaneous investigation of toxigenic and non-toxigenic patterns I, II and III and biofilm formation ability of Bacteroides fragilis isolated from patients with colorectal cancer was performed.

Methods

Thirty-one patients diagnosed with CRC and thirty-one control subjects were recruited in this study. Specimens were cultured on BBE and BBA culture media. Classical phenotypic identification tests and PCR was performed to verify Bacteroides fragilis presence. Also, biofilm-forming ability and expression of bft gene were assessed under biofilm and planktonic forms.

Results

A total of 68 B.fragilis was isolated from all colorectal tissue, of which 13 isolates (19.1%) (11 isolates from CRC and 2 from normal tissue) were positive for bft gene. The abundance patterns of I, II and III were as follow in descending order; pattern I > pattern III > pattern II in CRC subjects and pattern II > pattern III > pattern I in normal tissues. Also, pattern I showed higher biofilm formation ability compared to other patterns. Toxin expression was significantly reduced in biofilm form comparing with planktonic form.

Conclusions

Based on our findings, there was a difference between the abundance of patterns I, II, and III and biofilm formation in isolates obtained from CRC and normal tissues. Biofilm formation ability and toxin encoding gene (bft) are two main virulence factors in B. fragilis pathogenicity which require more investigation to treat B. fragilis infections effectively.

Detection of Nocardia, Streptomyces and Rhodococcus from bronchoalveolar lavage specimens of patients with HIV by Multiplex PCR Assay

Background

Nocardia, Streptomyces and Rhodococcus are life threatening opportunistic pathogens under immunodeficiency conditions, particularly among patients infected with HIV. Rapid and accurate detection of these infections can improve immune health quality, patient management and appropriate treatment. The aim of this study was to design a novel multiplex-PCR assay for rapid diagnosis of these three organisms directly from bronchoalveolar lavage (BAL) specimens of patients infected with HIV.

Methods

The genus specific primers were designed for direct-detection of Nocardia, Streptomyces and Rhodococcus in a single tube multiplex PCR. This PCR specifically amplified the target genes from pure cultures. It subsequently was applied on BAL specimens of 29 HIV positive patients that had previously been culture negative for actinomycete bacteria, of which Nocardia, Streptomyces and Rhodococcus are members.

Results

Of 29 respiratory clinical specimens, there were positive for Nocardia spp. and one was positive for Streptomyces spp using the multiplex PCR assay. The sequencing of the PCR products identified the species as Nocardia cyriacigeorgica (n=2), Nocardia farcinica and Streptomyces albus.

Conclusion

This novel multiplex PCR assay yielded reliable results for accurate identification of Nocardia, Streptomyces and Rhodococcus from BAL while the results of bacterial culture were negative.

Whole Genome Sequencing Results Associated with Minimum Inhibitory Concentrations of 14 Anti-Tuberculosis Drugs among Rifampicin-Resistant Isolates of Mycobacterium Tuberculosis from Iran

Accurate and timely detection of drug resistance can minimize the risk of further resistance development and lead to effective treatment. The aim of this study was to determine the resistance to first/second-line anti-tuberculosis drugs in rifampicin/multidrug-resistant Mycobacterium tuberculosis (RR/MDR-MTB) isolates. Molecular epidemiology of strains was determined using whole genome sequencing (WGS)-based genotyping. A total of 35 RR/MDR-MTB isolates were subjected to drug susceptibility testing against first/second-line drugs using 7H9 Middlebrook in broth microdilution method. Illumina technology was used for paired-end WGS applying a Maxwell 16 Cell DNA Purification kit and the NextSeq platform. Data analysis and single nucleotide polymorphism calling were performed using MTBseq pipeline. The genome-based resistance to each drug among the resistant phenotypes was as follows: rifampicin (97.1%), isoniazid (96.6%), ethambutol (100%), levofloxacin (83.3%), moxifloxacin (83.3%), amikacin (100%), kanamycin (100%), capreomycin (100%), prothionamide (100%), D-cycloserine (11.1%), clofazimine (20%), bedaquiline (0.0%), and delamanid (44.4%). There was no linezolid-resistant phenotype, and a bedaquiline-resistant strain was wild type for related genes. The Beijing, Euro-American, and Delhi-CAS were the most populated lineage/sublineages. Drug resistance-associated mutations were mostly linked to minimum inhibitory concentration results. However, the role of well-known drug-resistant genes for D-cycloserine, clofazimine, bedaquiline, and delamanid was found to be more controversial.

Molecular identification of mutations conferring resistance to rifampin, isoniazid and pyrazinamide among Mycobacterium tuberculosis isolates from Iran

Here, we aimed to determine the susceptibility of 70 Mycobacterium tuberculosis isolates obtained from different regions of the country to 8 anti-tuberculosis (anti-TB) drugs and possible underlying mechanisms causing resistance to rifampin, isoniazid, and pyrazinamide. The susceptibility of 70 isolates of M. tuberculosis to anti-TB drugs was tested using proportion method. Strains showing resistance to the first line anti-TB drugs were subjected to PCR amplification and sequencing of the rpoB, katG, ahpC, pncA genes, inhA promoter and oxyR-ahpC intergenic regions to detect resistance conferring mutations. Overall, 77.1% and 77.1% of isolates were resistant to at least one of the tested first- and second-line drugs, respectively. Within the rpoB gene the highest rate of mutation was found in codons 531(450) (56.3%), and 533(452) (12.5%). Also, codons 315 (42.4%) of katG, positions -48, -72 and -77 of oxyR-ahpC (total= 3, 9.1%) and -15 of inhA promoter region (33.3%) were the most altered positions in isoniazid resistant isolates. Only a single mutation was detected for pncA among resistant isolates. High prevalence of resistance to essential anti-TB drugs among M. tuberculosis strains isolated from retreated tuberculosis cases is alarming issue necessitating immediate action to prevent the spread of drug resistant isolates in the country.

Simultaneous use of oxalate-degrading bacteria and herbal extract to reduce the urinary oxalate in a rat model: A new strategy

Objective:

Urinary stones with oxalate composition can cause kidney failure. Recent findings evidenced that probiotics are effective in reducing oxalate absorption in these subjects based on their high colonic absorption levels at baseline. The purpose of this study was to evaluate the effect of the simultaneous use of oxalate-degrading bacteria, Urtica dioica and T. terrestris extract in reducing urinary oxalate.

Materials and Methods:

Anti-urolithiatic activity of Urtica dioica and T. terrestris extract and probiotic by using ethylene glycol induced rat model. In this study, 4 strains of Lactobacillus and 2 strains of Bifidobacterium and also 2 strains of L. paracasei (that showed high power in oxalate degrading in culture media) were used. Male Wistar rats were divided into four groups (n=6). The rats of group-I received normal diet (positive control group) and groups-II (negative control group), III, IV rats received diet containing ethylene glycol (3%) for 30 days. Groups III rats received Urtica dioica and T. terrestris extract. Groups IV rats received extracts + probiotic for 30 days.

Findings:

The results show that the use of herbal extracts (Urtica dioica and T. terrestris) reduced the level of urinary oxalate and other parameters of urine and serum. Also, the accumulation of calcium oxalate crystals in the kidney tissue was significantly reduced.

Conclusion:

Considering that the formation of calcium oxalate crystals can cause inflammation and tissue damage in the kidney, the use of herbal extracts with oxalate degrading bacteria can be a new therapeutic approach to preventing the formation of kidney stones.

Enterotoxigenic Bacteroides fragilis: A Possible Etiological Candidate for Bacterially-Induced Colorectal Precancerous and Cancerous Lesions

Enterotoxigenic Bacteroides fragilis (ETBF) produces Bacteroides fragilis toxin (BFT), which is associated with acute diarrheal, inflammatory bowel disease, and colorectal cancer (CRC). In experimental models, ETBF has been shown to contribute to colon carcinogenesis. The present study was conducted to investigate mucosal colonization of ETBF in the colon to find a possible association between the presence of ETBF and precancerous and cancerous lesions. The mucosal biopsies of involved sites were obtained from 68 patients with precancerous and cancerous lesions and 52 healthy controls (HC). The samples were cultured on Bacteroides Bile Esculin agar. Then, specific primers were designed to detect B. fragilis and bft gene using quantitative real-time PCR, and the possible links of ETBF with clinicopathological characteristics was evaluated. Also real-time PCR was performed to detect the bft gene subtypes. Bacteroides fragilis was detected in 51% of the patients and 48% of HCs cultures. The 16SrRNA gene was found to be present in 63 and 81% of the patients and HCs' samples, respectively. Moreover, the bft gene was detected in 47 and 3.8% of the patients and HCs, respectively. Also, B. fragilis was significantly more abundant in the patients' samples compared to those of HCs. In the patient group, higher odds ratio (OR) of ETBF was significantly associated with serrated lesions and adenoma with low-grade dysplasia. The bft1 gene was the most prevalent subtype of bft gene, followed by the bft2 gene. This was the first study in Iran to demonstrate increased positivity of ETBF in patients with precancerous and cancerous lesions. In this study, the bft gene was found to be associated with CRC, especially in the patients with precancerous lesions and initial carcinogenic lesions. Moreover, the results suggest that mucosal BFT exposure is common and could be a risk factor and a screening marker for developing CRC.

Identification of Non-Tuberculosis Mycobacteria by Line Probe Assay and Determination of Drug Resistance Patterns of Isolates in Iranian Patients

The potentially pathogenic Non-Tuberculosis Mycobacteria (NTM) are emerging nowadays which result in pulmonary and non-pulmonary infections in human. This group of bacteria consists of at least 200 different species. While the pulmonary disease is the most common form of NTM infections, NTM can cause diffused infections as well as extrapulmonary infections in every organ, such as bone marrow, skin, eye, and brain. The NTM cause tuberculosis-like infections, therefore, correct identification of these Mycobacteria is necessary to avoid faulty treatment. Different species of NTM isolates were identified from clinical specimens using phenotypic methods and Line Probe Assay. Minimum Inhibitory Concentration for selected antibiotics was obtained by the broth micro-dilution method. Totally, 42 NTM isolates were identified in this study. Moreover, the frequency of NTM between all positive mycobacterium cultures was estimated at 12%. The most common Rapidly Growing Mycobacteria included Mycolicibacterium fortuitum (30.9%), Mycobacterium abscessus (7.1%), and Mycobacterium chelonae (2.3%), whereas Mycobacterium simiae (40.4%), Mycobacterium kansasii (16.6%), and Mycobacterium avium complex (2.3%) were the most recurring among the Slowly Growing Mycobacteria. Amikacin, clarithromycin, and ciprofloxacin were the most effective antibiotics against isolated NTM. The NTM isolates are frequently being separated from Iranian patients, and are mostly resistant to the wide spectrum of antibiotics. Correct identification and determination of antibiotic susceptibility can be helpful in the healing process of the patients who suffer from non-tuberculosis mycobacterial infections.

The Inhibitory Effects of Lactobacillus Supernatants and Their Metabolites on the Growth and Biofilm Formation of Klebsiella pneumoniae

BACKGROUND

Klebsiella pneumoniae is a common cause of hospital-acquired infections, including urinary tract infection (UTI). Biofilm formation makes the K. pneumoniae infection more complicated and carrying extended-spectrum beta-lactamases (ESBLs) genes, it limits antibiotic choices for treatment. Lactobacillus strains are known as natural protective barriers against UTIs.

OBJECTIVES

This is a small in-vitro study aimed to determine the effect of probiotic Lactobacillus strains and some types of their metabolites on the growth and biofilm of UTI isolates and reference strain of Klebsiella pneumoniae.

METHODS

The efficacy of Lactobacillus supernatants and antibiotics in the prevention and elimination of K. pneumoniae biofilms was determined using a quantitative adherence assay. A rapid colorimetric microplate bioassay was applied for the detection of survived bacterial cells after treatment with antibacterial agents. Biofilm phenotypes were studied by scanning electron microscopy (SEM).

RESULTS

The results showed that seven out of eight ESBL producing uropathogenic K. pneumoniae isolates in this study were able to produce biofilm. Lactobacillus supernatants at 1:1 to 1:16 dilutions, had more than 95% biofilm-inhibitory and biofilm-killing properties on a strong biofilm producer isolate. Supra-MIC levels of antibiotics had a much lower anti-biofilm effect than Lactobacillus supernatant and left considerable alive biofilm cells.

CONCLUSIONS

Although antibiotic resistance increases in biofilm forms of Klebsiella pneumoniae, Lactobacillus supernatants have strong antibiofilm efficacy even in lower concentrations of MIC. Biofilm formation decreases considerably in the presence of Lactobacillus supernatants. Hydrogen peroxide is an effective product against growth and biofilm formation of Klebsiella pneumoniae.

Reducing urinary oxalate by simultaneous using Sankol herbal drop with oxalate-degrading bacteria

BACKGROUND AND OBJECTIVES

Oxalate degrading bacteria and herbal extracts are new strategy for reducing hyperoxaluria. In Iranian traditional medicine, Sankol oral drop is widely used as an antispasmodic drug to reduce stones from urinary tract. This study aimed to evaluate the synergistic effect of oxalate-degrading bacteria and Sankol oral drop in reducing urinary oxalate in rat model.

MATERIALS AND METHODS

Several bacterial strains, including Lactobacillus (4), Bifidobacterium (2) and L. paracasei (2) (very strong in degrading oxalate in vitro) were used in this study. Male Wistar rats were divided into 6 groups (n = 6). The rats of Group I received normal diet and drinking water + 60% ethanol (positive group). Groups II (negative group), III, IV, V, and VI rats received diet containing ethylene glycol (3%) for 30 days. Groups III rats received Sankol with minimum concentration (7.5 ml/kg/b.w), Group IV rats received Sankol with maximum concentration (9 ml/kg/b.w), Group V rats received Sankol with minimum concentration + probiotic, and Group VI rats received Sankol with maximum concentration + probiotic for 30 days.

RESULTS

Treatment with Sankol (maximum concentration) and oxalate-degrading probiotic bacteria significantly reduced urinary oxalate (P = .0001). At the end of treatment period, rats in groups II (negative control) showed a high score of CaOx crystal, while rats in VI groups did not show any CaOx crystal.

CONCLUSION

This is the first study on the simultaneous use of Sankol herbal drop and oxalate-degrading probiotic bacteria that showed a significant reduction in urinary oxalate.

Efficacy Of Line Probe Assay In Detection Of Drug-Resistant Pulmonary Tuberculosis In Comparison With GeneXpert And Phenotypic Methods In Iran And Genetic Analysis Of Isolates By MIRU-VNTR

Background

Successful treatment of tuberculosis depends on early diagnosis and use of appropriate drug susceptibility testing in a timely manner. In the present study, LPA efficacy was assayed in detection and drug susceptibility testing of pulmonary tuberculosis in comparison to available methods in Iran and phylogenetic analyses of isolated cases carried out by MIRU-VNTR.

Methods

This study was conducted at the Tehran Regional Reference Laboratory for Tuberculosis. All sputum specimens were subjected to smear, culture, and drug susceptibility testing (DST), GeneXpert, and LPA. Finally, 15-locus-based MIRU-VNTR was used for molecular genotyping.

Results

From a total of 920 sputum specimens, 6.08% (n=56) were identified as MTBC by culture, 6.8% (n=63) by GeneXpert, and 6.5% (n=60) by LPA. Phenotype DST and LPA methods confirmed the resistance of 4 and 14 specimens to rifampin (RIF) and isoniazid (INH); two cases were considered as multidrug-resistant (MDR). Using GeneXpert, four cases were identified as RIF-resistant. Based on LPA results, inhA and katG mutations were detected in 100% and 21.4% of INH-resistant cases, respectively. All 56 culture positive Mycobacterium tuberculosis isolates were placed in 29 different clusters using MIRU-VNTR genotyping. Two MDR-TB, 2 RIF mono-resistant, and 12 INH mono-resistant cases were placed in different clusters.

Conclusion

LPA is an appropriate method for early detection and accurate diagnosis of TB and drug-resistant cases that makes it possible to distinguish INH mono-resistant cases from MDR cases in Iran.

Endocarditis with Aeromonas salmonicida

Aeromonas salmonicida (A. salmonicida) is a facultative Gram-negative bacillus, inhabiting in water. It is a common source of furunculosis and septicemia in fish. Report on the human infection with this organism is rare. A male farmer referred with weakness and intermittent fever. He had cardiac valves’ regurgitation due to fever with rheumatic heart disease. He had a history of swimming in well water. Transthoracic echocardiography (TTE) revealed a mobile mass of 1.3 × 0.9 cm attached to the mitral valve chordae, suggestive of a vegetation. Aeromonas salmonicida was isolated from the blood. After cardiac surgery and taking ceftriaxone for 4 weeks, he was discharged in good general condition. Five previous case reports of human infection with this organism were found. The patient was the sixth human case, and the first endocarditis, reported with this organism. A. salmonicida is a rare agent for human infection. Contact with water is a risk factor for this type of infection. It seems that the use of modern diagnostic methods has been effective in identifying the microorganism.

Molecular detection of Campylobacter jejuni in patients with Crohn's disease in Iran

Background: Crohn's disease is one of the most significant intestinal disorders and is known as inflammatory bowel disease; Campylobacter spp. are one of the leading causes of bacterial gastroenteritis in humans.

Methods: In this study, 60 tissue samples, including 30 cases with Crohn’s disease and 30 cases with no inflammatory bowel disease, were collected. Patients were referred to Taleghani hospital and Behboud clinic between March 2015 and May 2016. Biopsies were used for DNA extraction and assessment of Campylobacter jejuni in patients with Crohn's disease and controls using polymerase chain reaction and quantitative real-time polymerase chain reaction. All positive amplified fragments were sequenced. The gene encoding 16S rRNA, specific to Campylobacter genus, was amplified.

Results: The results were positive for Campylobacter genus in patients with Crohn's disease compared to healthy individuals. The quantitative real-time PCR showed a significantly higher prevalence of Campylobacter jejuni, particularly in hippurate hydrolase in tissue specimens of patients with Crohn's disease compared to control group. The correlation between Campylobacter jejuni and diarrhea symptoms in patients with Crohn's disease and controls was investigated. One positive case of Campylobacter jejuni found in patients without diarrhea was compared with 13 patients with diarrhea.

Conclusion: The present study demonstrated the alarmingly high rate of Campylobacter jejuni prevalence in Crohn's disease patients with diarrhea symptoms. However, further investigation is needed to determine the possible causing factors of this disease.

Prevalence and Mechanisms of Carbapenem Resistance in Acinetobacter baumannii: A Comprehensive Systematic Review of Cross-Sectional Studies from Iran

Introduction: Carbapenem-resistant Acinetobacter baumannii (CRAB) is recognized to be among the most difficult antimicrobial-resistant gram-negative bacilli to control and treat. An understanding of the epidemiology of CRAB and the mechanisms of resistance to carbapenems is necessary to develop strategies to curtail their spread. Methods: Electronic databases were searched from January 1995 to December 2017 for all studies, which: (1) provide data on the frequency and antibiotic resistance profile of the isolated A. baumannii and (2) describe the mechanisms of carbapenem resistance in detail. Results: Sixty-eight studies were found referring to mechanisms of carbapenem resistance in clinical isolates of A. baumannii, and 56 studies were found referring to the frequency of CRAB. The pooled frequency of carbapenem resistance was 85.1% (95% confidence interval [CI]: 82.2-88.1) in 8,067 clinical isolates of A. baumannii. Resistances due to bla_OXA23 (55.3%), bla_OXA24 (41.4%), and bla_OXA58 (5.2%) genes were the most prevalent reported mechanisms of resistance to carbapenem, respectively. Conclusions: Our data warn that CRAB will rise if the current situation remains uncontrolled. Better control infection strategies and antibiotic managements, particularly in the health care systems, are needed to limit the spread of this pathogen.

Molecular characterization of multidrug and extensive drug-resistant Mycobacterium tuberculosis isolates from Iran

Tuberculosis (TB) is one of the main causes of death among curable infectious diseases and one of the top 10 causes of death worldwide. Hence, molecular typing of MTB strains is necessary for epidemiological studies and helps to identify risk factors for TB transmission. Therefore, the present study was conducted to determine molecular typing of drug-resistant M. tuberculosis strains isolated from Iran using the RFLP-PGRS method. Thirty-two MDR strains and one XDR strain were isolated from TB patients in four major cities of Iran. MTB isolates were subjected to drug susceptibility testing. Whole genomic DNA from mycobacterial colonies were extracted and hybridized with PGRS probe in RFLP analysis. All fingerprinted MDR and XDR isolates were grouped into 13 clusters. The largest cluster (cluster 3) contained 48.4% (n = 16) of all isolates. Clusters 1, 4, and 6 included 2, 4, and 2 isolates, respectively. Two isolates were in cluster 7, one was H37Rv standard strain, which was used as a control strain in this study, and eight isolates were placed in single clusters. This study provides information about molecular epidemiology of MDR-TB in Iran. The alarming increase in the incidence of MDR isolates, especially Beijing strains, raises concerns for TB control programs in Iran.

Expression analysis of 10 efflux pump genes in multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis clinical isolates

OBJECTIVES

Active extrusion of antituberculosis drugs via efflux pumps (EPs) has been suggested as contributing to drug resistance in Mycobacterium tuberculosis. This study was conducted to determine the role of 10 drug efflux transporters in the development of drug resistance in a series of clinical M. tuberculosis isolates.

METHODS

A total of 31 clinical M. tuberculosis isolates without drug exposure [21 multi/extensively drug-resistant (M/XDR-TB) and 10 drug-susceptible isolates] were studied. The expression profile of 10 EP genes, including efpA, mmr, stp, drrA, drrB, mmpL7, Rv1250, Rv1634, Rv2994 and Rv1258c, was investigated against the H37Rv standard strain by quantitative reverse transcription PCR (RT-qPCR).

RESULTS

Among the 21M/XDR-TB isolates, 10 showed significantly increased levels of gene expression (>4-fold) for at least one of the studied EPs. Moreover, of the isolates with overexpressed genes, three and seven lacked genetic alterations in the surveyed regions of the rpoB+katG+inhA and katG+inhA genes, respectively. Whilst no elevation was observed in the expression of mmr, Rv1250, Rv1634 and Rv1258c genes in any of the isolates, drrA, stp and drrB were found to be the most commonly overexpressed, being overexpressed in seven, five and three isolates, respectively. Decreased minimum inhibitory concentrations (MICs) of rifampicin, but not isoniazid, were observed in the presence of the efflux pump inhibitor carbonyl cyanide 3-chlorophenylhydrazone (CCCP).

CONCLUSION

Overexpression of EP genes can contribute to the emergence of a MDR phenotype in M. tuberculosis. Inhibition of EPs may provide a promising strategy for improving tuberculosis treatment outcomes in patients infected with M/XDR-TB isolates.

The activity of Levisticum officinale W.D.J. Koch essential oil against multidrug-resistant Mycobacterium tuberclosis

BACKGROUND AND OBJECTIVES

Essential oils are used for controlling and preventing human diseases and the application of those can often be quite safe and effective with no side effect. The essential oils have been found to have antiparasitic, antifungal, antiviral, antioxidant and especially antibacterial activity including antibacterial activity against tuberculosis. In this study the chemical composition and anti-TB activity of essential oil extracted from Levisticum officinale has been evaluated.

MATERIALS AND METHODS

The essential oil of L. officinale was obtained by the hydro distillation method and the oil was analyzed by GC-FID and GC-MS techniques. The antibacterial activity of essential oil was evaluated through Minimum Inhibitory Concentration (MIC) assay using micro broth dilution method against multidrug-resistant Maycobacterium tuberculosis. The molecular modeling of major compounds was evaluated through molecular docking using Auto Dock Vina against-2-trans-enoyl-ACP reductase (InhA) as key enzyme in M. tuberclosis cell wall biosynthesis.

RESULTS

The hydrodistillation on aerial parts of L. officinale yielded 2.5% v/w of essential oil. The major compounds of essential oil were identified as α-terpinenyl acetate (52.85%), β- phellandrene (10.26%) and neocnidilide (10.12%). The essential oil showed relatively good anti-MDR M. tuberculosis with MIC = 252 μg/ml. The results of Molecular Docking showed that affinity of major compounds was comparable to isoniazid.

CONCLUSION

The essential oil of aerial parts extracted from L. officinale was relatively active against MDR M. tuberculosis, and molecular docking showed the major compounds had high affinity to inhibit 2-trans-enoyl-acyl carrier protein reductase (InhA) as an important enzyme in M. tuberculosis cell wall biosynthesis.

Applying simple linear combination, multiple logistic and factor analysis methods for candidate fecal bacteria as novel biomarkers for early detection of adenomatous polyps and colon cancer

BACKGROUND

Colorectal cancer (CRC) is the third leading cause of cancer, and presents a considerable disease burden, worldwide. Recently, the gut microbiota has been proposed as a potential risk factor for CRC, and even adenomatous polyps (AP). Here, the aim of this study was to investigate the role of selected gut bacteria as fecal bacterial biomarkers, in early detection of CRC and AP.

MATERIAL AND METHODS

Fecal samples (n = 93) were collected from Taleghani Hospital, Tehran, Iran, between 2015 and 2017, from normal controls (NC), AP cases and CRC stage I patients, who were undergoing screening for colonoscopy. Absolute quantitative real time PCR (qPCR) assays were established for the quantification of bacterial marker candidates, in all cases and control groups. In order to evaluate the diagnostic value of bacterial candidates in distinguishing CRC from a polyp, receiver operating characteristic curve (ROC) was performed. Multiple logistic regressions were used to find the best combinations of the bacterial candidates, then, combinations were analyzed based on three methods, including linear combination, multiple logistic and factor analysis models.

RESULTS

According to the logistic model, combination of Fusobacterium nucleatum, Enterococcus feacalis, Streptococcus bovis, Enterotoxigenic Bacteroides fragilis (ETBF) and Porphyromonas spp. showed improved diagnostic performance, compared to each bacterium alone, as area under the receiver operating characteristic (AUROC) increases to 0.97, with 95% confidence interval. It was found that a simple linear combination was an appropriate model for discriminating AP and CRC cases, compared to the NC, with a sensitivity of 91.4% and specificity of 93.5%.

CONCLUSION

Our results indicated that based on fecal bacterial candidates, statistical simple linear combination model and ROC curve analysis, early detection of AP and CRC might be possible.

Molecular Epidemiology and Drug Resistance Pattern of Carbapenem-Resistant Klebsiella pneumoniae Isolates from Iran

The emergence and dissemination of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates and their involvement in several nosocomial outbreaks are of high concern. This study was conducted to investigate the genetic relatedness and molecular determinants of carbapenem resistance in 100 CRKP isolates. Susceptibility to carbapenems as well as other antibiotics was determined by using disk diffusion method. The Modified Hodge test was performed for detection of carbapenemase production. The minimum inhibitory concentrations of selected antibiotics were determined by broth microdilution method. The presence of bla_OXA-48, bla_KPC, bla_NDM, and bla_VIM carbapenemase genes was examined by PCR, and clonal relatedness of CRKP isolates was investigated by pulsed-field gel electrophoresis (PFGE) analysis. bla_OXA-48 was the most frequent carbapenemase gene (72%), followed by bla_NDM (31%). None of the isolates harbored bla_KPC and bla_VIM genes. PFGE separated the majority of isolates into 10 clusters, including the major clusters A and B, carrying bla_OXA-48, and clusters C and D, carrying bla_NDM, and 4 isolates had a unique PFGE pattern. An increased rate of colistin resistance (50%) was detected among the isolates. Tigecycline was found to be the most active agent against CRKP isolates. Our results revealed that high prevalence of bla_OXA-48 and bla_NDM carbapenamses and resistance to colistin are alarming threats, necessitating an immediate action to prevent the spread of carbapenem-colistin-resistant K. pneumoniae isolates in Iran.

Specific immune responses induced by multi-epitope DNA derived from Mycobacterium tuberculosis DosR antigens

One third of the world population are latently infected with Mycobacterium tuberculosis and are at the risk of reactivation of tuberculosis (TB). The most effective strategy for control of TB worldwide is the development of a vaccine that inhibits progression of latent TB to active infection. In this study, two optimized constructs consisting of multi-epitopes DNA derived from three latency antigens Rv2029c, Rv2031c, and Rv2627c fused with or without light chain 3 (LC3) are synthetized. The immunogenicity effectiveness of two DNA constructs was evaluated in the mouse model. LC3-fused multi-epitope DNA construct induced strong specific Th1 immune responses with high increase in IFN-γ⁺ CD4⁺ and IL-2⁺ CD4⁺ T cell populations (both with p < 0.0001) and IFN-γ⁺ IL-2⁺ CD4⁺ T cell population (p < 0.0001) compared with empty vector, BCG, and multi-epitope DNA construct groups. The LC3-fused construct induced IFN-γ⁺ CD8⁺ T cell population (p < 0.0001) compared with empty vector and BCG groups but could not induce the T cell population compared with construct without LC3. Importantly, LC3-fused DNA construct did not induce epitope-specific IL-4 and IL-10 from CD4⁺ and CD8⁺ T cell populations. The results indicated that LC3-fused multi-epitope DNA construct has a potential to be investigated for future development of a new TB vaccine.

High genetic diversity among Mycobacterium tuberculosis strains in Tehran, Iran

INTRODUCTION

Tuberculosis (TB) still remains an important public health problem in Iran. The genotyping of Mycobacterium tuberculosis isolates is expected to lead to a better understanding of M. tuberculosis transmission in Tehran, the most populated city of Iran.

MATERIALS AND METHODS

A total of 2300 clinical specimens were obtained from TB suspected patients who were referred to a TB center in Tehran from Jan 2014 to Dec 2016. Identification was performed using both conventional and molecular methods. The presence of resistance to rifampicin was examined by the GeneXpert MTB/RIF. The standard 15-locus mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing method was applied to genotype of clinical isolates.

RESULTS

Of 2300 specimens, 80 isolates were identified as M. tuberculosis by using biochemical and molecular tests. Of 80 M. tuberculosis isolates, 76 (95%) had unique genotypic profiles and 4 (5%) shared a profile with one or more other strains. Based on single loci variation (SLV) 4 clonal complexes were observed. NEW-1 was found to be the most predominant lineage (22.5%) followed by West African (1.25%), Central Asian (CAS)/Delhi (1.25%), Bovis (1.25%), H37Rv (1.25%) and multiple matches (1.25%). Loci MIRU10, MIRU26, MTUB21 and QUB26 were found as highly discriminative. No mutation was detected in the hotspot region of rifampicin by using GeneXpert MTB/RIF.

CONCLUSIONS

Our study findings show that there was considerable genotypic diversity among M. tuberculosis isolates in Tehran. The 15-locus MIRU-VNTR showed high HGDI and could be used as a first-line genotyping method for epidemiological studies.

Molecular Mechanisms of Colistin Resistance Among Pandrug-Resistant Isolates of Acinetobacter baumannii with High Case-Fatality Rate in Intensive Care Unit Patients

Colistin is considered a last-hope antibiotic against extensively drug-resistant isolates of Acinetobacter baumannii. Resistance to colistin has been rarely reported for A. baumannii. Genetic alterations in the PmrA-PmrB two-component system and lipid A biosynthesis genes may be associated with colistin resistance. We investigated molecular mechanisms of colistin resistance in three clinical colistin-resistant (ColR) and two colistin-susceptible (ColS) A. baumannii isolates. A ColR mutant was generated in vitro by repetitive drug exposure. The pmrA, pmrB, lpxA, lpxC, and lpxD genes were amplified and sequenced. To evaluate association between colistin resistance and upregulation of pmrCAB operon, transcriptional level of the pmrC gene encoding for lipid A phosphoethanolamine (PEtN) transferase was quantified by reverse transcription quantitative PCR (RT-qPCR) analysis. All clinical and in vitro-selected ColR isolates harbored at least one point mutation in the pmrB gene, including A142V, P233S, T235I, and A227V substitutions as well as duplication of H325. No alteration was found in the pmrA and other amino acid substitutions identified in the pmrB as well as lpx genes did not seem to be involved in colistin resistance as they were found in both ColS and ColR isolates. RT-qPCR analysis revealed a correlation between colistin resistance and pmrC overexpression. Specific alterations in the PmrB, linked to overproduction of PEtN transferase, triggered colistin resistance in the studied A. baumannii isolates.