Modified gold nanoparticle colorimetric probe-based biosensor for direct and rapid detection of Mycobacterium tuberculosis in sputum specimens.

The incidence of Mycobacterium tuberculosis (MTB) is increasing due to lack of appropriate diagnostic and therapeutic methods. Therefore, early and accurate detection of this bacteria plays a significant role in controlling tuberculosis. This study aimed to design, develop, and implement a direct and rapid detection method of MTB using modified gold nanoparticle (AuNP) colorimetric probe-based biosensor in sputum specimens. Spherical AuNPs were synthesized by the citrate reduction method and were functionalized using thiol-modified oligonucleotides (AuNP-biosensor). AuNP-biosensor and IS6110 PCR were compared to the gold standard in terms of analytical and clinical sensitivity and specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic odds ratio (DOR), and accuracy in 52 clinical specimens. Gold standard was defined as a positive result in concentrated sputum smear microscopy (SSM), culture, or Xpert MTB/RIF.The AuNP-biosensor had 100% sensitivity and specificity for detection of total sputum DNA in less than 15 min with ready-to-use AuNP-biosensor. PPV, NPV, DOR and accuracy of this method were 100%, 100%, 2325 and 100%, respectively. Considering the promising results of the diagnostic value indices of the AuNP-biosensor, the designed method is an affordable, rapid, reliable, and cost-beneficial way for direct detection of MTB in sputum specimens.

Potential MR Enterography Features to Differentiate Primary Small Intestinal Lymphoma From Crohn Disease.

OBJECTIVE. The purpose of this study was to assess the MR enterographic features of primary small intestinal lymphoma (PSIL) and compare them with active Crohn disease (CD) presenting with severe (≥ 10 mm) mural thickening of the small bowel. MATERIALS AND METHODS. This retrospective study included 15 patients with pathologically proven PSIL and 15 patients with active inflammatory CD with severe mural thickening. Various morphologic, enhancement, and diffusion parameters were compared between the two groups at MR enterography. The ratios of the upstream to involved luminal diameter and mural thickness to luminal diameter in the involved segment were calculated. An attempt was made to define a predictive model (morphologic score) for discriminating PSIL from CD with severe mural thickening. RESULTS. Patients with PSIL were more likely than those with CD to have unifocal disease (66.7% vs 20.0%, p = 0.025), circumferential involvement (86.7% vs 26.7%, p < 0.001), luminal dilatation (60.0% vs 7.0%, p = 0.005), and an attenuated fold pattern (53.3% vs none, p < 0.001). They were less likely to have serosal surface involvement (40.0% vs 100%, p = 0.001) and mesenteric fat infiltration (33.3% vs 100%, p < 0.001). Median upstream to involved luminal diameter ratio (1.5 vs 9.6, p < 0.001) and mural thickness to involved luminal diameter ratio (1.1 vs 4.3, p = 0.044) were significantly lower in patients with PSIL than in those with CD with severe mural thickening. No significant difference was observed in enhancement and diffusion measures. Morphologic score was based on the presence of luminal dilatation, unifocal involvement, mesenteric fat infiltration, and luminal stricture, yielding accuracy of 98% for differentiation between PSIL and CD with severe mural thickening. CONCLUSION. Morphologic features seen at MR enterography rather than enhancement or diffusion parameters may be valuable for differentiation of PSIL from active CD with severe mural thickening with significantly lower ratios of upstream to involved luminal diameter and mural thickness to involved luminal diameter in PSIL.

Mesenteric lymph nodes in MR enterography: are they reliable followers of bowel in active Crohn's disease?

OBJECTIVES: To demonstrate magnetic resonance enterography (MRE) features of mesenteric lymph nodes (LN) in patients with Crohn's disease (CD) and investigate whether they follow enhancement or apparent diffusion coefficient (ADC) parameters of bowel. METHODS: This study was approved by the institutional review board. A total of 788 MREs from patients with CD were retrospectively reviewed. Eighty-eight patients, aged 16-66 years, including 59 active cases, were enrolled based on inclusion criteria. In each MRE, two segments (normal and abnormal) and two LNs (regional and non-regional) were independently suggested, consensually chosen, and analyzed by two radiologists. Signal-to-noise (SNR) and contrast-to-noise (CNR) ratios were calculated to assess signal intensities (SI) at 30, 60 and 180 s after contrast administration, as well as slope of enhancement (SOE). Enhancement parameters and ADC values were compared. RESULTS: Regional LNs showed significantly higher SI30, SI60 and SI180 (CNR&SNR) and lower ADC values in active vs. inactive groups (all p<0.05) without significant difference in number or size. Strong correlations were demonstrated between abnormal segments and regional LNs in active group in terms of SI30, SI60, SI180, SOE0-30 and ADC values (r = 0.679 to 0.774, all p<0.001). SI180, SOE60-180 and ADC values were moderately correlated between abnormal segments and regional LNs in inactive group (r = 0.448 to 0.595, all p<0.05). In logistic regression analyses, SOE0-30 and ADC value of regional LNs independently predicted active CD. CONCLUSION: Mesenteric LNs follow quantitative enhancement and diffusion parameters of bowel in active CD. SOE0-30 and ADC value of LN could predict disease activity. KEY POINTS: • Mesenteric LNs may strongly follow enhancement pattern of bowel in active CD. • DWI parameters of LNs and bowel were strongly correlated in active CD. • SI180 was moderately correlated between bowel and LNs in inactive CD. • DWI parameters were moderately correlated between LNs and bowel in inactive CD. • SOE0-30 and ADC value of mesenteric LN could predict disease activity.

A reappraisal of adult thoracic and abdominal surface anatomy in Iranians in vivo using computed tomography.

Surface anatomy is a core component of human anatomy in clinical practice. It allows clinicians to assess patients accurately and quickly; however, recent studies have revealed variability among individuals and ethnicities. The aim of this study is to investigate possible variations in adult thoracic and abdominal surface anatomy landmarks in an Iranian population. This study used 100 thoracoabdominal CT scans (mean age: 47 ± 17 years, age range: 20-77 years, 47% females), noted the most common locations of clinically relevant surface markings, and analyzed correlations between these variables and age or gender. While many common surface markings in Iranians were consistent with the evidence-based literature, there were some differences. In relation to the corresponding segments of the vertebral column, the superior vena cava formation and the lower border of the pleura adjacent to the vertebral column and right kidney tended to be at higher levels in adult Iranians than a Caucasian population. There were also discrepancies between the Iranian population and commonly-referenced medical textbooks and recent evidence-based literature concerning the vertebral levels of the diaphragmatic openings of the esophagus, aorta, and inferior vena cava. This study emphasizes the need to consider evidence-based reappraisals of surface anatomy to guide clinical practice. Much of our current knowledge of surface anatomy is based on older studies of cadavers rather than living people, and does not take ethnic and individual variations into consideration.

COVID-19 early detection for imbalanced or low number of data using a regularized cost-sensitive CapsNet.

With the presence of novel coronavirus disease at the end of 2019, several approaches were proposed to help physicians detect the disease, such as using deep learning to recognize lung involvement based on the pattern of pneumonia. These approaches rely on analyzing the CT images and exploring the COVID-19 pathologies in the lung. Most of the successful methods are based on the deep learning technique, which is state-of-the-art. Nevertheless, the big drawback of the deep approaches is their need for many samples, which is not always possible. This work proposes a combined deep architecture that benefits both employed architectures of DenseNet and CapsNet. To more generalize the deep model, we propose a regularization term with much fewer parameters. The network convergence significantly improved, especially when the number of training data is small. We also propose a novel Cost-sensitive loss function for imbalanced data that makes our model feasible for the condition with a limited number of positive data. Our novelties make our approach more intelligent and potent in real-world situations with imbalanced data, popular in hospitals. We analyzed our approach on two publicly available datasets, HUST and COVID-CT, with different protocols. In the first protocol of HUST, we followed the original paper setup and outperformed it. With the second protocol of HUST, we show our approach superiority concerning imbalanced data. Finally, with three different validations of the COVID-CT, we provide evaluations in the presence of a low number of data along with a comparison with state-of-the-art.

Nodular lymphoid hyperplasia of terminal ileum: how to avoid overdiagnosis of Crohn's terminal ileitis in MR enterography?

PURPOSE: To investigate the magnetic resonance enterography (MRE) characteristics of nodular lymphoid hyperplasia (NLH) and Crohn's terminal ileitis (CTI). METHODS: Of 1552 MREs from November 2011 to July 2018, 61 individuals with biopsy-proven NLH (n = 24) and CTI (n = 37, 27 with active CTI) were selected based on the inclusion criteria. NLH cases were also followed up for median (range) of 40 (21-61) months. Two board-certified radiologists, blind to clinical data and diagnosis, reviewed MRE in consensus. Conventional, morphological, enhancement, and diffusion parameters were assessed. Mann-Whitney, χ2, and logistic regression analyses were conducted. RESULTS: No NLH patient developed inflammatory bowel disease or lymphoproliferative disorders during the follow-up. Serosal surface irregularity (65% vs. 8%), pseudo-diverticula (27% vs. 0), and mesenteric fat involvement (38% vs. 4%) were more frequent in CTI than NLH (p < 0.01), while mucosal nodularity was more prevalent in NLH (71%) than CTI (19%) (p < 0.001). The upstream luminal diameter (15.0 vs. 12.5 mm, p = 0.015) and mural thickness (6.0 vs. 4.0 mm, p < 0.001) of the terminal ileum showed higher values in CTI than NLH. CONCLUSIONS: Unlike enhancement and diffusion parameters, morphological features (mucosal nodularity, serosal surface irregularity, and mesenteric fat involvement) could distinguish NLH from CTI regardless of CTI activity.

Predictive value of initial CT scan for various adverse outcomes in patients with COVID-19 pneumonia.

BACKGROUND: Chest computed tomography (CT) scan is frequently used in the diagnosis of COVID-19 pneumonia. OBJECTIVES: This study investigates the predictive value of CT severity score (CSS) for length-of-stay (LOS) in hospital, initial disease severity, ICU admission, intubation, and mortality. METHODS: In this retrospective study, initial CT scans of consecutively admitted patients with COVID-19 pneumonia were reviewed in a tertiary hospital. The association of CSS with the severity of disease upon admission and the final adverse outcomes was assessed using Pearson's correlation test and logistic regression, respectively. RESULTS: Total of 121 patients (60±16 years), including 54 women and 67 men, with positive RT-PCR tests were enrolled. We found a significant but weak correlation between CSS and qSOFA, as a measure of disease severity (r: 0.261, p = 0.003). No significant association was demonstrated between CSS and LOS. Patients with CSS>8 had at least three-fold higher risk of ICU admission, intubation, and mortality. CONCLUSIONS: CSS in baseline CT scan of patients with COVID-19 pneumonia can predict adverse outcomes and is weakly correlated with initial disease severity.

Extra-adrenal, non-functional adrenocortical carcinoma presenting with acute abdomen: a case report.

BACKGROUND: Adrenocortical carcinoma is a rare malignancy, with 43% being non-functional. These may arise from adrenal rest anywhere in the embryonic pathway of the adrenal glands. In the context of extra-adrenal and retroperitoneal tumors, the exact pathologic diagnosis is challenging. The case reported here, to the best of our knowledge, is the seventh reported case of extra-adrenal non-functional adrenocortical carcinoma. CASE PRESENTATION: We report a case of extra-adrenal non-functional adrenocortical carcinoma in a 15-year-old Persian boy who presented with an acute abdomen. He underwent surgical resection. Pathologic findings based on immunohistochemistry and cellular morphology confirmed adrenocortical carcinoma. He was treated with mitotane for 24 months. During a follow-up period of 30 months, no recurrence or metastases were found. CONCLUSION: Despite the rarity of extra-adrenal adrenocortical carcinoma, presentation with an acute abdomen may occur, and the tumor may be found anywhere in the adrenal embryonic pathway. On the other hand, tumor behavior and prognosis in children may be different from what we expect in adults.

Molecular identification and distribution of non-tuberculous mycobacteria isolated from clinical specimens by PCR-sequencing method in West of Iran.

BACKGROUND AND AIMS: Infections by non-tuberculous mycobacteria (NTM) has rapidly increased in recent years, due to high infection rates related to the populations at risk like immunocompromised individuals, patients predisposed by prior pulmonary. The aim of this study was to investigate the presence of NTM in clinical samples and genetic diversity using 16S rRNA and rpoB sequence analysis. METHODS: A cross-sectional study was conducted on 45 diverse isolates collected from sputum in 2 years 2014-2015 using standard decontamination procedure. All mycobacterial isolates were grown on LJ medium and also conventional tests for preliminary identification of mycobacteria rely on traits and then DNA extraction. PCR was performed, and sequencing of 16S rRNA and rpoB genes was applied for NTM strains identification. RESULTS: A total of 45 isolates collected, 37 samples (83%) were evaluated as NTM. All NTM strains using molecular methods by sequencing 16S rRNA and rpoB gene were identified, by this way 12 different species have been identified which sequencing of rpoB was able to identify all species. The major species obtained were Mycobacterium simiae (22%), M. fortuitum (19%), and M. abscessus (13%). CONCLUSIONS: The results of our study showed that the patients were infected by a wide range of atypical mycobacteria. It was concluded that 16S rRNA gene sequencing coupled with rpoB marker is a high discriminatory power in identification of NTM. The presence of various species in clinical samples in Iran emphasizes the use of molecular method like sequence analysis of genes is necessary for reliable identification.

Verification of Frequency in Species of Nontuberculous Mycobacteria in Kermanshah Drinking Water Supplies Using the PCR-Sequencing Method.

BACKGROUND: Nontuberculous mycobacteria are habitants of environment, especially in aquatic systems. Some of them cause problems in immunodeficient patients. Over the last decade, 16S rRNA gene sequencing was established in 45 novel species of nontuberculous mycobacteria. Experiences revealed that this method underestimates the diversity, but does not distinguish between some of mycobacterium subsp. To recognize emerging rapidly growing mycobacteria and identify their subsp, rpoB gene sequencing has been developed. OBJECTIVES: To better understand the transmission of nontuberculous mycobacterial species from drinking water and preventing the spread of illness with these bacteria, the aim of this study was to detect the presence of bacteria by PCR-sequencing techniques. MATERIALS AND METHODS: Drinking water samples were collected from different areas of Kermanshah city in west of IRAN. After decontamination with cetylpyridinium chloride, samples were filtered with 0.45-micron filters, the filter transferred directly on growth medium waiting to appear in colonies, then DNA extraction and PCR were performed, and products were sent to sequencing. RESULTS: We found 35/110 (32%) nontuberculous mycobacterial species in drinking water samples, isolates included Mycobacterium goodii, Mycobacterium aurum, and Mycobacterium gastri with the most abundance (11.5%), followed by Mycobacterium smegmatis, Mycobacterium porcinum, Mycobacterium peregrinum, Mycobacterium mucogenicum, and Mycobacterium chelonae (8%). CONCLUSIONS: In this study, we recognized the evidence of contamination by nontuberculous mycobacteria in corroded water pipes. As a result of the high prevalence of these bacteria in drinking water in Kermanshah, this is important evidence of transmission through drinking water. This finding can also help public health policy makers control these isolates in drinking water supplies in Kermanshah.

Mycobacterium tuberculosis Beijing Genotype in Western Iran: Distribution and Drug Resistance.

INTRODUCTION: Mycobacterium tuberculosis Beijing genotype is gaining importance all over the world because this genotype is highly prevalent in several areas and is also frequently associated with drug resistance. AIM: To identify and determine the frequency of Beijing genotype and mix infection with Beijing and non-Beijing in west of Iran and analyse the association between Beijing genotype and drug resistance. MATERIALS AND METHODS: This cross-sectional study was conducted on 146 Tuberculosis (TB) samples collected at the TB reference laboratory in Kermanshah west of Iran from January 2014 to February 2015, Mycobacterium tuberculosis isolates from sputum samples, detected by microcopy, biochemical tests and solid culture were included and then the confirmed samples with Cepheid Xpert MTB/RIF assay were subjected to drug susceptibility tests for rifampicin, isoniazid, ethambutol using proportional method. The prevalence rate of Beijing and non-Beijing genotype was determined by Multiplex- Polymerase Chain Reaction (PCR). RESULT: A total of 15/146 (10%) isolates were diagnosed as Beijing genotypes and the remaining 131/146(90%) isolates were non-Beijing genotypes by Multiplex PCR method. Among the 15 Beijing cases, 14 samples have shown mix infection indicating the presence of both Beijing and non-Beijing strains in samples. Three isolates from all cases were drug resistant. Interestingly all drug resistance isolates were from Beijing genotype which shows strong association between drug resistance and Beijing genotype. Also this genotype was more prevalent in younger age-group people (p=0.035). CONCLUSION: Frequency of Beijing genotype in west of Iran is more than other sites of Iran but less than Asia. According to our result, mix infections with Beijing and non-Beijing, had the most prevalence therefore we should be concerned more about mix infections. Multiplex-PCR method is feasible, trustworthy and can distinguish mix infections. It is suggested to perform spoligotyping in addition to multiplex PCR method to discriminate mix infections.

Magnetic Resonance Enterography in 300 Known Cases of Crohn's Disease: An Initial Report from a Referral Center in Iran.

BACKGROUND Magnetic resonance enterography (MRE) has become the modality of choice in assessment of patients with Crohn's disease (CD). We aimed to present our experience on 300 patients with CD who underwent MRE during the first 30 months after setting up MRE for the first time in a referral center in Iran. METHODS Patients with a definite diagnosis of CD based on either ileocolonoscopy or histopathological studies were included in the final report and categorized into four phenotypes of inactive, active, stricturing, and penetrating disease. RESULTS This was a case series study on 300 patients with known CD out of 594 referred subjects. The most prevalent phenotype was inactive observed in 162 (54.0%) patients followed by stricturing in 44 (14.7%), active in 40 (13.3%), penetrating in 27(9%), and active on chronic in 27 (9%) cases. The number of referred patients increased from 51 cases in the first 6 months to 165 in the last 6 months. CONCLUSION This study presents the first report on the application of MRE in Iran as superb modality for management of CD. The growing number of referred patients indicates that MRE has been successful in addressing the most critical concerns of clinicians on determining the dominant disease phenotype.

Frequency of Mutations Associated with Rifampicin Resistance in Mycobacterium tuberculosis Strains Isolated from Patients in West of Iran.

BACKGROUND AND OBJECTIVE: Tuberculosis (TB) is a devastating infectious disease causing high mortality and morbidity worldwide. The most serious threat related to tuberculosis control is the recent emergence of drug-resistant tuberculosis strains. The aim of the present study was to identify various types of mutations in the rpoB region in rifampicin-resistant strains isolated from sputum of tuberculosis patients. MATERIALS AND METHODS: Drug susceptibility of 125 Mycobacterium tuberculosis isolates was determined using the CDC standard conventional proportional method. Target DNA of M. tuberculosis was amplified by polymerase chain reaction, hybridized, and scanned. We used the low cost density array (LCD-array) to detect mutations within the 90-bp rpoB region. Each array is a transparent, prestructured polymer support using a nonfluorescent detection principle based on the precipitation of a clearly visible dark substrate. RESULTS: Of the 125 M. tuberculosis isolates, 35 (28%) were found to be rifampicin-resistant and using the LCD array revealed point mutations at nine different codons as follows: S512T (AGC→ACC) (20%), D516V (GAC→GTC) (20%), H526D (CAC→GAC) (6%), H526R (CAC→CGC) (20%), H526Y (CAC→TAC) (23%), and S531W (TCG→TGG) (8%), and the most frequent site mutations were L511P (CCG→CTG) (46%), followed by S531l (TCG→TTG) (40%) and D516Y (GAC→TAC) (26%). CONCLUSION: Our data significantly differs from previously reported mutation frequencies for codon 526 (CAC to GAC) among Italian isolates (40.1%) and Greek isolates (17.6%). Phenotypic testing is time-consuming and requires laboratory resources. Microarray rpoB is useful in detecting rifampicin resistance-determining region-associated site mutations of rifampicin-resistant M. tuberculosis isolates.

Anti tuberculosis drug resistance in west of iran.

BACKGROUND AND OBJECTIVE: Mycobacterium tuberculosis has developed resistance to antituberculosis drugs and becoming a major and alarming public health problem in worldwide. This study was aimed to determine antituberculosis drug resistance rate and to identify multidrug resistant tuberculosis (MDR-TB) in West of Iran. MATERIALS AND METHODS: Of 130 samples were included between December 2011 and July 2012 in the study from that 112 cases were M. tuberculosis. The proportional method was carried out according to the Clinical and Laboratory Standards Institute on Lowenstein-Jensen against isoniazid, rifampicin, streptomycin, ethambutol, pyrazinamide, para aminosalicylic acid, ethionamide, cycloserine (CYC). The microdilution method was carried out using 7H9 broth with 96 well-plates. RESULTS: From 112 isolates, resistance was observed to isoniazid 18 (16.07%), rifampicin 16 (14.28%), streptomycin 25 (22.32%), ethambutol 15 (13.39%), pyrazinamide 27 (24.10%), para aminosalicylic acid 19 (16.96%), CYC 4 (3.57%), and ethionamide 14 (12.5%) cases. 16 isolates were MDR. CONCLUSION: The high prevalence of MDR-TB in our study is assumed to be due to recent transmission of drug-resistant strains. Overall, the rate of drug resistance in our study was high, which is in line with findings of some high-burden countries. Hence that early case detection, rapid drug susceptibility testing, and effective anti-TB treatment is necessary.