scholarly journals A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples

2019 ◽  
Vol 9 ◽  
Author(s):  
Chao Zhang ◽  
Prashant V. Thakkar ◽  
Sarah Ellen Powell ◽  
Prateek Sharma ◽  
Sreekar Vennelaganti ◽  
...  
Keyword(s):  
Endoscopic Biopsy ◽  
Tissue Samples ◽  
Biopsy Tissue ◽  
Enzymatic Lysis ◽  
Microbiome Profiling

scholarly journals Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer

2021 ◽  
Vol 9 ◽  
Author(s):  
Yumeng Yuan ◽  
Yihuan Chen ◽  
Fen Yao ◽  
Mi Zeng ◽  
Qingdong Xie ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gut Microbiome ◽  
Laboratory Data ◽  
Antibiotic Resistance Genes ◽  
Lavage Fluid ◽  
Tissue Samples ◽  
Shotgun Metagenomics ◽  
Paired Samples ◽  
Biopsy Tissue ◽  
Cluster 2

Aim: The gut microbiome plays a crucial role in colorectal cancer (CRC) tumorigenesis, but compositions of microorganisms have been inconsistent in previous studies due to the different types of specimens. We investigated the microbiomes and resistomes of CRC patients with colonic biopsy tissue and intestinal lavage fluid (IVF).Methods: Paired samples (biopsy tissue and IVF) were collected from 20 patients with CRC, and their gut microbiomes and resistomes were measured by shotgun metagenomics. Clinical and laboratory data were recorded. Bioinformatics (KneadData, Kraken2, and FMAP) and statistical analysis were done using the R (v4.0.2) software.Results: Bacterial diversity in IVF was higher than in tissue samples, and bacterial operational taxonomic units (OTUs) were 2,757 in IVF vs. 197 in tissue. β-diversity showed distinct clusters in paired samples. The predominant bacteria in IVF were phylum Proteobacteria, while the predominant bacteria of tissue were phylum Actinobacteria. Twenty-seven representative bacteria were selected to form six bacterial clusters, which showed only Firmicutes Cluster 1, and the Bacteroidetes Cluster 1 were significantly more abundant in the IVF group than those in the tissue group (p < 0.05). The Firmicutes Cluster 2, Bacteroidetes Cluster 2, Pathogen Cluster, and Prevotella Cluster were not significantly different between IVF and tissue (p > 0.05). Correlation analysis revealed that some bacteria could have effects on metabolic and inflammatory parameters of CRC patients. A total of 1,295 antibiotic resistance genes (ARGs) were detected in the gut microbiomes, which conferred multidrug resistance, as well as resistance to tetracycline, aminoglycoside, and more. Co-occurrence patterns revealed by the network showed mainly ARG-carrying bacteria to be similar between IVF and tissue, but leading bacteria located in the hub differed between IVF and tissue.Conclusion: Heterogeneity of microbiota is particularly evident when studied with IVF and tissue samples, but bacterial clusters that have close relationships with CRC carcinogenesis are not significantly different, using IVF as an alternative to tissue for gut microbiome, and resistome assessment may be a feasible method.

scholarly journals Application value of tissue tuberculosis antigen combined with Xpert MTB/RIF detection in differential diagnosis of intestinal tuberculosis and Crohn’s disease

2020 ◽  
Author(s):  
Baoying Fei ◽  
Lin Zhou ◽  
Yu Zhang ◽  
Linhe Luo ◽  
Yuanyuan Chen
Keyword(s):  
Differential Diagnosis ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Intestinal Tuberculosis ◽  
Surgical Excision ◽  
Endoscopic Biopsy ◽  
Detection Sensitivity ◽  
Intestinal Tissue ◽  
Tissue Samples ◽  
Tuberculosis Antigen

Abstract Background: The purpose of this study was to evaluate the value of Xpert MTB/RIF detection and tuberculosis antigen detection of Mycobacterium tuberculosis cluster (MTBC) in intestinal tissues for differentiating intestinal tuberculosis (ITB) from Crohn’s disease (CD). Methods: A total of 110 patients who were clinically diagnosed with CD or ITB were monitored. Several specimens of intestinal tissue from endoscopic biopsy or surgical excision were used for culture and Xpert MTB/RIF for detection of MTBC, respectively. Four antigens (38KDa, ESAT-6, MPT64, Ag85 complex) of MTBC in intestinal tissue were detected by immunohistochemistry. Results: A total of 42 cases of intestinal tuberculosis and 46 cases of CD were included in the experimental analysis. Perianal lesions and longitudinal ulcers were more common in CD patients (p < 0.05), while caseous granuloma and annular ulcers were more common in ITB patients (P < 0.05). The positive rate of MTBC detected by Xpert MTB/RIF in intestinal tissue samples of ITB patients was 33.33%, which was significantly higher compared to CD patients (p < 0.05) and compared to acid-fast staining smears (9.52%) (p < 0.05). The positive MPT64 expression rate in patients with intestinal tuberculosis was 40.48%, which was significantly higher than that observed in CD patients, which was 19.56% (p<0.05). Conclusions: The detection of Xpert MTB/RIF in intestinal tissue is a rapid and useful method for establishing an early diagnosis of intestinal tuberculosis. The detection of Xpert MTB/RIF and MPT64 antigen in intestinal tissues have definitive value in the differential diagnosis of intestinal tuberculosis and Crohn’s disease. The combination of these two methods could improve detection sensitivity.

scholarly journals Application value of tissue tuberculosis antigen combined with Xpert MTB/RIF detection in differential diagnosis of intestinal tuberculosis and Crohn’s disease

2019 ◽  
Author(s):  
baoying fei ◽  
lin zhou ◽  
yu zhang ◽  
Linhe Luo ◽  
Yuanyuan Chen
Keyword(s):  
Differential Diagnosis ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Intestinal Tuberculosis ◽  
Surgical Excision ◽  
Endoscopic Biopsy ◽  
Detection Sensitivity ◽  
Intestinal Tissue ◽  
Tissue Samples ◽  
Tuberculosis Antigen

Abstract Abstract Background: The purpose of this study was to evaluate the value of Xpert MTB/RIF detection and tuberculosis antigen detection of Mycobacterium tuberculosis (MTB) in intestinal tissues for differentiating intestinal tuberculosis (ITB) from Crohn’s disease (CD). Materials and Methods: A total of 110 patients who were clinically diagnosed with CD or ITB were monitored. Several specimens of intestinal tissue from endoscopic biopsy or surgical excision were used for MTB culture and Xpert MTB/RIF detection, respectively. Four antigens (38KDa, ESAT-6, MPT64, Ag85 complex) of MTB in intestinal tissue were detected by immunohistochemistry. Results: A total of 42 cases of intestinal tuberculosis and 46 cases of CD were included in the experimental analysis. Perianal lesions and longitudinal ulcers were more common in CD patients (p < 0.05), while caseous granuloma and annular ulcers were more common in ITB patients (P < 0.05). The positive rate of M. tuberculosis detected by Xpert MTB/RIF in intestinal tissue samples of ITB patients was 33.33%, which was significantly higher compared to CD patients (p < 0.05) and compared to acid-fast staining smears (9.52%) (p < 0.05). The positive MPT64 expression rate in patients with intestinal tuberculosis was 40.48%, which was significantly higher than that observed in CD patients, which was 19.56% (p<0.05). Conclusions: The detection of Xpert MTB/RIF in intestinal tissue was conducive to the quick and early diagnosis of intestinal tuberculosis. Xpert MTB/RIF and MPT64 antigen in intestinal tissues had certain value in the differential diagnosis of intestinal tuberculosis and Crohn’s disease. The combination of these two methods could improve detection sensitivity.

scholarly journals Glutamine oxidation and utilization by rat and human oesophagus and duodenum

1999 ◽  
Vol 81 (4) ◽  
pp. 323-329 ◽  
Author(s):  
L. A. James ◽  
P. G. Lunn ◽  
S. Middleton ◽  
M. Elia
Keyword(s):  
Oxidative Metabolism ◽  
Glucose Utilization ◽  
Human Subjects ◽  
The Other ◽  
Tissue Samples ◽  
Biopsy Tissue ◽  
Human Biopsy

The rates of utilization and oxidation of glutamine and glucose by oesophageal and duodenal tissues have been investigated in both rats and human subjects. In the rat, glutamine utilization by oesophageal tissue was 2–3-fold lower than that in the duodenum, and this substrate contributed less than 10 % to the total oxidative metabolism of the tissue, even when glutamine was the only substrate provided. In contrast, rat duodenal tissue derived about 34 % of the total CO2 production from glutamine-C, and this contribution was not suppressed by the addition of either glucose or a mixture of the other substrates. Rates of glucose utilization and oxidation by the duodenum were lower than those for glutamine, and were significantly (P<0·001) suppressed by addition of glutamine. In both oesophageal and duodenal tissues, less than 10 % of the glutamine-C utilized was fully oxidized, approximately 60–70 % was converted to glutamate, and 30–40 % to alanine. Results obtained using human biopsy tissue samples were similar to those observed in the rat. Glutamine oxidation contributed 34 (sd 4) % of the total CO2 production by the duodenal tissue, but only 8 (sd 4) % to oesophageal tissue oxidation. The findings suggest that glutamine is not an important or preferred fuel for oesophageal tissue, whereas it is for duodenal tissue. Thus, these tissues can be expected to respond differently to glutamine administration.

Submucosal Endoscopic Sampling for Indefinite Gastric Linitis Plastica Infiltrating into the Submucosal Layer

2015 ◽  
Vol 24 (3) ◽  
pp. 375-378 ◽  
Author(s):  
Taiga Chiyo ◽  
Hideki Kobara ◽  
Hirohito Mori ◽  
Naomi Katsuki ◽  
Reiji Haba ◽  
...  
Keyword(s):  
Diagnostic Yield ◽  
False Negative ◽  
Linitis Plastica ◽  
Needle Aspiration ◽  
Endoscopic Biopsy ◽  
Direct Vision ◽  
Tissue Samples ◽  
Submucosal Tumors ◽  
Negative Results ◽  
Multiple Biopsies

The diagnosis of diffuse-type gastric cancer, named linitis plastica (LP), is difficult because of its infiltration into the submucosa. Conventional endoscopic biopsy sampling may show false-negative results because the superficial mucosa is often normal. These macroscopic features do not often permit the distinction between benign and malignant lesions, and sampling methods have some limitations. Accordingly, a secure sampling method is required in order to increase the diagnostic yield. We have developed a submucosal tunneling technique for sampling submucosal tumors, which can visualize tumor surfaces and obtain tissue samples under direct vision. We report a rare case of indefinite gastric LP that could be diagnosed by this method. As multiple biopsies and endoscopic ultrasound (EUS)-guided fine needle aspiration (FNA) did not help us histologically diagnose the lesion, our new method of submucosal endoscopy which has advantages of visualizing tumor surfaces and obtaining tissue samples under direct vision in the submucosa was introduced. Histological examination of all acquired samples confirmed the presence of a poorly differentiated adenocarcinoma. The present case demonstrates that this method is a reasonable option for indefinite LP with features inflating into submucosa, providing an update on the contemporary concepts. 

Efficacy of simultaneous single-trajectory endoscopic tumor biopsy and endoscopic cerebrospinal fluid diversion procedures in intra- and paraventricular tumors

2011 ◽  
Vol 30 (4) ◽  
pp. E4 ◽  
Author(s):  
Aaron Mohanty ◽  
Vani Santosh ◽  
B. Indira Devi ◽  
Satyanarayana Satish ◽  
Arundhati Biswas
Keyword(s):  
Tumor Location ◽  
Endoscopic Biopsy ◽  
Third Ventriculostomy ◽  
Success Rates ◽  
Tumor Biopsy ◽  
Tissue Samples ◽  
Biopsy Procedure ◽  
Cerebrospinal Fluid Diversion ◽  
Csf Diversion ◽  
Rigid Rod

Object Intraventricular and paraventricular tumors resulting in hydrocephalus commonly require a CSF diversion procedure. A tumor biopsy can often be performed concurrently. Although the tissue samples obtained during endoscopic biopsy procedures are small, a diagnosis can be made in most cases. In the present study the authors analyzed the efficacy of concurrent endoscopic biopsy and CSF diversion procedures using a single bur hole and trajectory. Methods Eighty-seven patients with intraventricular and paraventricular tumors were treated with endoscopic biopsy and CSF diversion procedures using a rigid rod-lens endoscope or a rigid fiberscope during a 10-year period. All patients underwent a tumor biopsy and an endoscopic third ventriculostomy (ETV), aqueductal stenting (AS), or ventriculoperitoneal (VP) shunting, depending on the tumor location and site of obstruction. A single bur hole for both procedures was used in all patients. Results Among the 87 patients, the biopsy was diagnostic in 72 (83%) and merely suggestive in 7 (8%); in 8 patients (9%) the sample was nondiagnostic. Among the 22 patients who underwent an initial endoscopic biopsy and subsequent procedures, the specimen obtained at the second surgery was concordant with the initial endoscopic biopsy sample in 13 patients; it was somewhat similar in 4 patients. In the other 5 patients, either a microsurgical or stereotactic approach was used to correctly diagnose the pathology. Fifty-five patients were considered for endoscopic CSF diversion procedures; an ETV was performed in 52 patients and AS in 2. An ETV could not be performed in 3 patients for technical reasons. A VP shunt was inserted in 32 patients, with 25 undergoing shunt placement at the same time as the ETV and 7 at a later date. Significant bleeding was encountered in 3 patients during the tumor biopsy and in 1 patient during the ETV. The ETV failed in 1 patient during the follow-up, and a repeat ETV was required. Conclusions Endoscopic biopsy sampling and a concurrent CSF diversion procedure through a single bur hole and trajectory can be considered for intraventricular tumors. The overall success rates of 83% for the biopsy procedure and 86% for the ETV indicate that the procedures are beneficial in the majority of cases. A concordance rate of 75% was found in patients who underwent an initial biopsy procedure and a subsequent microsurgical approach for tumor excision.

scholarly journals Application value of tissue tuberculosis antigen combined with Xpert MTB/RIF detection in differential diagnoses of intestinal tuberculosis and Crohn’s disease

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Baoying Fei ◽  
Lin Zhou ◽  
Yu Zhang ◽  
Linhe Luo ◽  
Yuanyuan Chen
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Intestinal Tuberculosis ◽  
Immunohistochemical Analysis ◽  
Surgical Excision ◽  
Endoscopic Biopsy ◽  
Detection Sensitivity ◽  
Intestinal Tissue ◽  
Tissue Samples ◽  
Caseating Granuloma

Abstract Background The purpose of this study was to examine the value of Xpert MTB/RIF assay and detection of additional Mycobacterium tuberculosis complex (MTBC) species antigens from intestinal tissue samples in differentiating intestinal tuberculosis (ITB) from Crohn’s disease (CD). Methods Several clinical specimens of intestinal tissue obtained by either endoscopic biopsy or surgical excision were used for mycobacteriologic solid cultures,Xpert MTB/RIF assays, immunohistochemistry, and histological examinations. Four antigens (38KDa, ESAT-6, MPT64, and Ag85 complex) of MTBC in the intestinal tissue were detected by immunohistochemical analysis. Results The study included 42 patients with ITB and 46 with CD. Perianal lesions and longitudinal ulcers were more common in patients with CD, while caseating granuloma and annular ulcers were more common in patients with ITB. The positive rate of MTBC detected by Xpert MTB/RIF in intestinal tissues of patients with ITB was 33.33%, which was significantly higher than that in patients with CD and that detected using acid-fast staining smears. It was also higher than that detected by tissue MTBC culture, but the difference was not statistically significant. The positive MPT64 expression rate in patients with ITB was 40.48%, which was significantly higher than that observed in patients with CD. The sensitivity of parallelly combined detection of tuberculosis protein MPT64 and Xpert MTB/RIF in diagnosing ITB was 50.0%. Conclusions The detection of Xpert MTB/RIF in intestinal tissue is a rapid and useful method for establishing an early diagnosis of ITB. The detection of MTBC using Xpert MTB/RIF and MPT64 antigen in intestinal tissues has a definitive value in the differential diagnosis ofITB and CD. The combination of these two methods can improve the detection sensitivity.

scholarly journals Application value of tissue tuberculosis antigen combined with Xpert MTB/RIF detection in differential diagnoses of intestinal tuberculosis and Crohn’s disease

2020 ◽  
Author(s):  
Baoying Fei ◽  
Lin Zhou ◽  
Yu Zhang ◽  
Linhe Luo ◽  
Yuanyuan Chen
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Intestinal Tuberculosis ◽  
Immunohistochemical Analysis ◽  
Surgical Excision ◽  
Endoscopic Biopsy ◽  
Detection Sensitivity ◽  
Intestinal Tissue ◽  
Tissue Samples ◽  
Caseating Granuloma

Abstract Background: The purpose of this study was to examine the value of Xpert MTB/RIF assay and detection of additional Mycobacterium tuberculosis complex (MTBC) species antigens from intestinal tissue samples in differentiating intestinal tuberculosis (ITB) from Crohn’s disease (CD).Methods: Several clinical specimens of intestinal tissue obtained by either endoscopic biopsy or surgical excision were used for mycobacteriologic solid cultures ,Xpert MTB/RIF assays , immunohistochemistry, and histological examinations. Four antigens (38KDa, ESAT-6, MPT64, and Ag85 complex) of MTBC in the intestinal tissue were detected by immunohistochemical analysis.Results: The study included 42 patients with ITB and 46 with CD. Perianal lesions and longitudinal ulcers were more common in patients with CD, while caseating granuloma and annular ulcers were more common in patients with ITB. The positive rate of MTBC detected by Xpert MTB/RIF in intestinal tissues of patients with ITB was 33.33%, which was significantly higher than that in patients with CD and that detected using acid-fast staining smears. It was also higher than that detected by tissue MTBC culture, but the difference was not statistically significant.The positive MPT64 expression rate in patients with ITB was 40.48%, which was significantly higher than that observed in patients with CD. The sensitivity of parallelly combined detection of tuberculosis protein MPT64 and Xpert MTB/RIF in diagnosing ITB was 50.0%.Conclusions: The detection of Xpert MTB/RIF in intestinal tissue is a rapid and useful method for establishing an early diagnosis of ITB. The detection of MTBC using Xpert MTB/RIF and MPT64 antigen in intestinal tissues has a definitive value in the differential diagnosis ofITB and CD. The combination of these two methods can improve the detection sensitivity.

ESI detection of titanium in lungs of a spray paint sniffer

1991 ◽  
Vol 49 ◽  
pp. 134-135
Author(s):  
A. F. Tryka ◽  
W. E. Cox ◽  
S. H. Van Devanter
Keyword(s):  
Lung Biopsy ◽  
Substance Abusers ◽  
Acute Onset ◽  
Solid Particles ◽  
Tissue Samples ◽  
Electron Dense Material ◽  
Biopsy Tissue ◽  
History Of ◽  
Electron Energy Loss ◽  
Volatile Materials

Do lungs of inhalation substance abusers contain materials indicative of such abuse, and is it possible to detect these materials by electron energy loss spectroscopy? While most abuse involves only volatile materials, spray paint is one material where when volatile materials evaporate, resultant solid particles may be of respirable size. These particles may contain paint pigments such as titanium dioxide.Lung biopsy tissue was obtained for diagnostic purposes from a 16 year old male who presented with acute onset of progressive respiratory insufficiency. The patient later admitted to a history of significant paint sniffing. Desquamative interstitial pneumonitis was observed by light microscopy, with an unusual additional feature of many alveolar macrophages having dusty cytoplasm. Routine ultrastructural study demonstrated large amounts of electron dense material in these macrophages. To address the question of what materials were present in the cells, additional tissue samples were embedded in Araldite, sectioned at 30 nm, and viewed unstained on a Zeiss 902.

scholarly journals Application value of tissue tuberculosis antigen combined with Xpert MTB/RIF detection in differential diagnosis of intestinal tuberculosis and Crohn’s disease

2019 ◽  
Author(s):  
Baoying Fei ◽  
Lin Zhou ◽  
Yu Zhang ◽  
Linhe Luo ◽  
Yuanyuan Chen
Keyword(s):  
Differential Diagnosis ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Intestinal Tuberculosis ◽  
Surgical Excision ◽  
Endoscopic Biopsy ◽  
Detection Sensitivity ◽  
Intestinal Tissue ◽  
Tissue Samples ◽  
Tuberculosis Antigen

Abstract Background: The purpose of this study was to evaluate the value of Xpert MTB/RIF detection and tuberculosis antigen detection of Mycobacterium tuberculosis (MTB) in intestinal tissues for differentiating intestinal tuberculosis (ITB) from Crohn’s disease (CD). Materials and Methods: A total of 110 patients who were clinically diagnosed with CD or ITB between January 2016 and March 2018 were initially enrolled in this study. The patients were monitored and their clinical, endoscopic and histopathological characteristics were followed up until their final diagnosis was clearly made. Several specimens of intestinal tissue from endoscopic biopsy or surgical excision were collected. One piece was used as paraffin specimen, and the other two pieces were used for MTB culture and Xpert MTB/RIF detection, respectively. Four antigens (38KDa protein, ESAT-6 protein, MPT64, Ag85 complex) of MTB in intestinal tissue were detected by immunohistochemistry. Results: A total of 42 cases of intestinal tuberculosis and 46 cases of CD were included in the experimental analysis. Perianal lesions and longitudinal ulcers were more common in CD patients (p < 0.05), while caseous granuloma and annular ulcers were more common in ITB patients (P < 0.05). The positive rate of M. tuberculosis detected by Xpert MTB/RIF in intestinal tissue samples of ITB patients was 33.33%, which was significantly higher compared to CD patients (p < 0.05) and compared to acid-fast staining smears (9.52%) (p < 0.05). The positive MPT64 expression rate in patients with intestinal tuberculosis was 40.48%, which was significantly higher than that observed in CD patients, which was 19.56% (X2=4.61, p<0.05). Conclusions: The detection of Xpert MTB/RIF in intestinal tissue was conducive to the quick and early diagnosis of intestinal tuberculosis. Xpert MTB/RIF and MPT64 antigen in intestinal tissues had certain value in the differential diagnosis of intestinal tuberculosis and Crohn’s disease. The combination of these two methods could improve detection sensitivity.

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