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https://www.readbyqxmd.com/read/28412936/-1-h-nmr-analysis-of-feces-new-possibilities-in-the-helminthes-infections-research
#1
Sarantos Kostidis, Daria Kokova, Natalia Dementeva, Irina V Saltykova, Hye Kyong Kim, Young Hae Choi, Oleg A Mayboroda
BACKGROUND: Analysis of the stool samples is an essential part of routine diagnostics of the helminthes infections. However, the standard methods such Kato and Kato-Katz utilize only a fraction of the information available. Here we present a method based on the nuclear magnetic resonance spectroscopy (NMR) which could be auxiliary to the standard procedures by evaluating the complex metabolic profiles (or phenotypes) of the samples. METHOD: The samples were collected over the period of June-July 2015, frozen at -20 °C at the site of collection and transferred within four hours for the permanent storage at -80 °C...
April 17, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28359329/comparison-of-stool-versus-rectal-swab-samples-and-storage-conditions-on-bacterial-community-profiles
#2
Christine M Bassis, Nicholas M Moore, Karen Lolans, Anna M Seekatz, Robert A Weinstein, Vincent B Young, Mary K Hayden
BACKGROUND: Sample collection for gut microbiota analysis from in-patients can be challenging. Collection method and storage conditions are potential sources of variability. In this study, we compared the bacterial microbiota from stool stored under different conditions, as well as stool and swab samples, to assess differences due to sample storage conditions and collection method. METHODS: Using bacterial 16S rRNA gene sequence analysis, we compared the microbiota profiles of stool samples stored and collected under various conditions...
March 31, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28290266/improved-diagnosis-of-trichuris-trichiura-by-using-a-bead-beating-procedure-on-ethanol-preserved-stool-samples-prior-to-dna-isolation-and-the-performance-of-multiplex-real-time-pcr-for-intestinal-parasites
#3
Maria M M Kaisar, Eric A T Brienen, Yenny Djuardi, Erliyani Sartono, Maria Yazdanbakhsh, Jaco J Verweij, Taniawati Supali, Lisette VAN Lieshout
For the majority of intestinal parasites, real-time PCR-based diagnosis outperforms microscopy. However, the data for Trichuris trichiura have been less convincing and most comparative studies have been performed in populations with low prevalence. This study aims to improve detection of T. trichuria DNA in human stool by evaluating four sample preparation methods. Faecal samples (n = 60) were collected at Flores island, Indonesia and examined by microscopy. Aliquots were taken and a bead-beating procedure was used both on directly frozen stool and on material preserved with 96% ethanol...
March 14, 2017: Parasitology
https://www.readbyqxmd.com/read/28260999/gut-microbiota-analysis-results-are-highly-dependent-on-the-16s-rrna-gene-target-region-whereas-the-impact-of-dna-extraction-is-minor
#4
Anniina Rintala, Sami Pietilä, Eveliina Munukka, Erkki Eerola, Juha-Pekka Pursiheimo, Asta Laiho, Satu Pekkala, Pentti Huovinen
Next-generation sequencing (NGS) is currently the method of choice for analyzing gut microbiota composition. As gut microbiota composition is a potential future target for clinical diagnostics, it is of utmost importance to enhance and optimize the NGS analysis procedures. Here, we have analyzed the impact of DNA extraction and selected 16S rDNA primers on the gut microbiota NGS results. Bacterial DNA from frozen stool specimens was extracted with 5 commercially available DNA extraction kits. Special attention was paid to the semiautomated DNA extraction methods that could expedite the analysis procedure, thus being especially suitable for clinical settings...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28220514/randomised-clinical-trial-faecal-microbiota-transplantation-for-recurrent-clostridum-difficile-infection-fresh-or-frozen-or-lyophilised-microbiota-from-a-small-pool-of-healthy-donors-delivered-by-colonoscopy
#5
Z D Jiang, N J Ajami, J F Petrosino, G Jun, C L Hanis, M Shah, L Hochman, V Ankoma-Sey, A W DuPont, M C Wong, A Alexander, S Ke, H L DuPont
BACKGROUND: Faecal microbiota transplantation (FMT) has become routine in managing recurrent C. difficile infection (CDI) refractory to antibiotics. AIM: To compare clinical response and improvements in colonic microbiota diversity in subjects with recurrent CDI using different donor product. METHODS: Seventy-two subjects with ≥3 bouts of CDI were randomised in a double-blind study to receive fresh, frozen or lyophilised FMT product via colonoscopy from 50 g of stool per treatment from eight healthy donors...
February 21, 2017: Alimentary Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28121648/changes-in-the-gut-microbiota-after-early-administration-of-oral-synbiotics-to-young-infants-in-india
#6
Dinesh S Chandel, Maria E Perez-Munoz, Fang Yu, Robert Boissy, Radhanath Satpathy, Pravas R Misra, Nidhi Sharma, Rama Chaudhry, Sailajanandan Parida, Daniel A Peterson, Ira H Gewolb, Pinaki Panigrahi
OBJECTIVES: We examined the changes in the developing gut microbiota of Indian infants enrolled in a colonization study of an oral synbiotic (L. plantarum and fructo-oligosaccharides) preparation. METHODS: Frozen stool samples were available from a previously published clinical study of the synbiotic preparation administered daily for seven days to full term Indian infants delivered by C-section. 16S rRNA gene sequencing of fecal bacterial community-DNA was done in 11 infants sampled at Day-7 and Day-60 of life...
January 25, 2017: Journal of Pediatric Gastroenterology and Nutrition
https://www.readbyqxmd.com/read/28103236/impact-of-cd4-t-cell-responses-on-clinical-outcome-following-oral-administration-of-wild-type-enterotoxigenic-escherichia-coli-in-humans
#7
Monica A McArthur, Wilbur H Chen, Laurence Magder, Myron M Levine, Marcelo B Sztein
Enterotoxigenic Escherichia coli (ETEC) is a non-invasive enteric pathogen of considerable public health importance, being one of the most common attributable causes of diarrheal illness in infants and young children in developing countries and the most common cause of traveler's diarrhea. To enhance study-to-study consistency of our experimental challenge model of ETEC in volunteers, and to allow concomitant multi-site trials to evaluate anti-ETEC immunoprophylactic products, hundreds of vials, each containing a standardized inoculum of virulent wild-type (wt) ETEC strain H10407 (serotype O78:H11 expressing colonization factor antigen I and heat-labile and heat-stable enterotoxins), were prepared under current Good Manufacturing Practices (cGMP) and frozen...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28000190/-short-term-efficacy-on-fecal-microbiota-transplantation-combined-with-soluble-dietary-fiber-and-probiotics-in-the-treatment-of-slow-transit-constipation
#8
Xiaolong Ge, Chao Ding, Jianfeng Gong, Hongliang Tian, Yao Wei, Qiyi Chen, Lili Gu, Ning Li
OBJECTIVE: To evaluate the efficacy and safety of fecal microbiota transplantation (FMT) combined with soluble dietary fiber and probiotics for slow transit constipation(STC). METHODS: Twenty-three patients with STC from Jinling Hospital, Medical School of Nanjing University were prospectively enrolled between April 2015 and January 2016. STC patients received FMT combined with soluble dietary fiber and probiotics. Fresh stool(100 g) was immediately mixed in a blender with 500 ml of 0...
December 25, 2016: Zhonghua Wei Chang Wai Ke za Zhi, Chinese Journal of Gastrointestinal Surgery
https://www.readbyqxmd.com/read/27927919/clinical-evaluation-and-cost-analysis-of-great-basin-shiga-toxin-direct-molecular-assay-for-detection-of-shiga-toxin-producing-escherichia-coli-in-diarrheal-stool-specimens
#9
Matthew L Faron, Nathan A Ledeboer, Jessica Connolly, Paul A Granato, Brenda R Alkins, Jennifer Dien Bard, Judy A Daly, Stephen Young, Blake W Buchan
The Shiga Toxin Direct molecular assay (ST Direct) relies on nucleic acid amplification and solid array-based amplicon detection to identify Shiga toxin-producing Escherichia coli (STEC) in preserved stool specimens. Genes encoding Shiga toxin (stx1 and stx2), as well as the E. coli serotype O:157-specific marker rfbE, are simultaneously detected within 2 h. ST Direct was evaluated using 1,084 prospectively collected preserved stool specimens across five clinical centers. An additional 55 retrospectively collected, frozen specimens were included to increase the number of positive specimens evaluated...
February 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27812352/impact-of-different-fecal-processing-methods-on-assessments-of-bacterial-diversity-in-the-human-intestine
#10
Yu-Hsin Hsieh, Courtney M Peterson, Anne Raggio, Michael J Keenan, Roy J Martin, Eric Ravussin, Maria L Marco
The intestinal microbiota are integral to understanding the relationships between nutrition and health. Therefore, fecal sampling and processing protocols for metagenomic surveys should be sufficiently robust, accurate, and reliable to identify the microorganisms present. We investigated the use of different fecal preparation methods on the bacterial community structures identified in human stools. Complete stools were collected from six healthy individuals and processed according to the following methods: (i) randomly sampled fresh stool, (ii) fresh stool homogenized in a blender for 2 min, (iii) randomly sampled frozen stool, and (iv) frozen stool homogenized in a blender for 2 min, or (v) homogenized in a pneumatic mixer for either 10, 20, or 30 min...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27811291/fungal-microbiota-profile-in-newly-diagnosed-treatment-na%C3%A3-ve-children-with-crohn-s-disease
#11
Mohammad El Mouzan, Feng Wang, Mohammad Al Mofarreh, Rajita Menon, Ahmad Al Barrag, Kirill S Korolev, Ahmad Al Sarkhy, Mona Al Asmi, Yassin Hamed, Anjum Saeed, Scot E Dowd, Asaad Assiri, Harland Winter
BACKGROUND AND AIMS: Although increasing evidence suggests a role for fungi in inflammatory bowel disease [IBD], data are scarce and mostly from adults. Our aim was to define the characteristics of fungal microbiota in newly diagnosed treatment-naïve children with Crohn's disease [CD]. METHODS: The children referred for colonoscopy were prospectively enrolled in the study at King Khalid University Hospital, King Saud University, and Al Mofarreh Polyclinics in Riyadh...
November 3, 2016: Journal of Crohn's & Colitis
https://www.readbyqxmd.com/read/27793749/fresh-vs-frozen-samples-and-ambient-temperature-have-little-effect-on-detection-of-colorectal-cancer-or-adenomas-by-a-fecal-immunochemical-test-in-a-colorectal-cancer-screening-cohort-in-germany
#12
Hongda Chen, Simone Werner, Hermann Brenner
BACKGROUND & AIMS: Fecal immunochemical tests (FITs) are used in colorectal cancer (CRC) screening. We compared detection of CRCs and colorectal neoplasms by FITs using fresh samples (collected into buffer-filled tubes) vs frozen samples, and we assessed the effects of seasonal variations in ambient temperature on test performance. METHODS: We performed a prospective study of 3466 individuals (50% male; mean age, 62 years) undergoing screening colonoscopies at 20 gastroenterology practices in southern Germany from November 2008 through September 2014...
October 26, 2016: Clinical Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/27558918/a-robust-ambient-temperature-collection-and-stabilization-strategy-enabling-worldwide-functional-studies-of-the-human-microbiome
#13
Ericka L Anderson, Weizhong Li, Niels Klitgord, Sarah K Highlander, Mark Dayrit, Victor Seguritan, Shibu Yooseph, William Biggs, J Craig Venter, Karen E Nelson, Marcus B Jones
As reports on possible associations between microbes and the host increase in number, more meaningful interpretations of this information require an ability to compare data sets across studies. This is dependent upon standardization of workflows to ensure comparability both within and between studies. Here we propose the standard use of an alternate collection and stabilization method that would facilitate such comparisons. The DNA Genotek OMNIgene∙Gut Stool Microbiome Kit was compared to the currently accepted community standard of freezing to store human stool samples prior to whole genome sequencing (WGS) for microbiome studies...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27544433/the-impact-of-handling-and-storage-of-human-fecal-material-on-bacterial-activity
#14
Eleni Karatza, Maria Vertzoni, Uwe Muenster, Christos Reppas
Fecal material prepared from human stools is frequently used for the assessment of bacterial degradation of active pharmaceutical ingredients as relevant data are useful for evaluating the potential for colonic drug delivery. The impact of handling and storage of human fecal material on bacterial activity was assessed by evaluating the degradation characteristics of metronidazole and olsalazine. Multiple freeze (-70°C)-thaw cycles should be avoided. Incubation of frozen material for about 2 h in the anaerobic workstation ensures regeneration of the highest possible bacterial activity...
November 2016: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27534405/physical-pre-treatment-improves-efficient-dna-extraction-and-qpcr-sensitivity-from-clostridium-difficile-spores-in-faecal-swine-specimens
#15
Łukasz Grześkowiak, Jürgen Zentek, Wilfried Vahjen
A considerable fraction of the faecal microbiota is spore-forming. Molecular quantification of bacteria may be underestimated if preceded with nucleic acid extraction without special treatment to extract recalcitrant bacterial spores. The objective of this study was to improve the DNA extraction regarding the presence of Clostridium difficile spores in faecal swine specimens. Sow faeces were inoculated with spores of C. difficile (10(6) CFU), frozen at - 30 °C overnight and subjected to DNA extraction. As a preceding step to a standard DNA extraction method (QIAamp DNA stool Mini kit), different physical treatments such as microwave oven heating and repeated bead-beating techniques and a combination of both were applied and compared with each other by means of qPCR...
November 2016: Current Microbiology
https://www.readbyqxmd.com/read/27530517/is-dried-stool-spots-on-filter-paper-method-dssfp-more-sensitive-and-effective-for-detecting-blastocystis-spp-and-their-subtypes-by-pcr-and-sequencing
#16
Ayse Seyer, Djursun Karasartova, Emrah Ruh, Ayse Semra Güreser, Turgut Imir, Aysegul Taylan-Ozkan
PCR and DNA sequencing are currently the diagnostic methods of choice for detection of Blastocystis spp. and their suptypes. Fresh or frozen stool samples have disadvantages in terms of several aspects such as transportation, storage, and existence of PCR inhibitors. Filter paper technology may provide a solution to these issues. The aim of the present study was to detect Blastocystis spp. and their subtypes by employing two different preservation methods: conventional frozen stool (FS) and dried stool spots on filter paper (DSSFP)...
December 2016: Parasitology Research
https://www.readbyqxmd.com/read/27263967/clostridium-difficile-infections-in-children-impact-of-the-diagnostic-method-on-infection-rates
#17
Mohammad AlGhounaim, Yves Longtin, Milagros Gonzales, Joanna Merckx, Nicholas Winters, Caroline Quach
BACKGROUND Polymerase chain reaction (PCR) assays based on the detection of the toxin B gene are replacing enzyme-linked immunosorbent assay (ELISA)-based toxin production detection or cell cytotoxicity assay in most laboratories. OBJECTIVE To determine the proportion of pediatric patients diagnosed with Clostridium difficile infection by PCR who would have also been diagnosed by ELISA and to compare the clinical characteristics of PCR+/ELISA+ vs PCR+/ELISA- patients. METHODS Using the microbiology laboratory information system, stool samples positive for C...
September 2016: Infection Control and Hospital Epidemiology
https://www.readbyqxmd.com/read/27171433/incidence-etiology-and-risk-factors-for-travelers-diarrhea-during-a-hospital-ship-based-military-humanitarian-mission-continuing-promise-2011
#18
Jessica M Hameed, Ramona L McCaffrey, Andrea McCoy, Tracy Brannock, Gregory J Martin, William T Scouten, Krista Brooks, Shannon D Putnam, Mark S Riddle
Travelers' diarrhea (TD) is the most common ailment affecting travelers, including deployed U.S. military. Continuing Promise 2011 was a 5-month humanitarian assistance/disaster response (HA/DR) military and non-governmental organization training mission aboard the hospital ship USNS Comfort, which deployed to Central and South America and the Caribbean between April and September 2011. Enhanced TD surveillance was undertaken during this mission for public health purposes. Passive surveillance (clinic visits), active surveillance (self-reported questionnaires), and stool samples were collected weekly from shipboard personnel...
2016: PloS One
https://www.readbyqxmd.com/read/27098621/evaluation-of-the-performance-of-a-fecal-tumor-m2-pk-rapid-kit-using-stool-specimens-for-detection-of-colorectal-tumors
#19
Chi Hyun Cho, Jeeyong Kim, Mi Ae Jang, Beom Jae Lee, Jong-Jae Park, Chae Seung Lim
BACKGROUND: In gastrointestinal tumors, only subunits of pyruvate kinase isoenzyme type M2 are detectable, and mainly in the dimeric form termed tumor M2-PK. A rapid test for the detection of M2-PK in stool has been developed. We evaluated the performance of the M2-PK rapid kit for the detection of colorectal tumors compared with colonoscopy DESIGN: Stool specimens (n=268) were obtained from patients who had a fecal occult blood test and colonoscopy performed for clinical evaluation or routine health checkup...
2016: Annals of Clinical and Laboratory Science
https://www.readbyqxmd.com/read/27065191/optimized-sample-handling-strategy-for-metabolic-profiling-of-human-feces
#20
Jasmine Gratton, Jutarop Phetcharaburanin, Benjamin H Mullish, Horace R T Williams, Mark Thursz, Jeremy K Nicholson, Elaine Holmes, Julian R Marchesi, Jia V Li
Fecal metabolites are being increasingly studied to unravel the host-gut microbial metabolic interactions. However, there are currently no guidelines for fecal sample collection and storage based on a systematic evaluation of the effect of time, storage temperature, storage duration, and sampling strategy. Here we derive an optimized protocol for fecal sample handling with the aim of maximizing metabolic stability and minimizing sample degradation. Samples obtained from five healthy individuals were analyzed to assess topographical homogeneity of feces and to evaluate storage duration-, temperature-, and freeze-thaw cycle-induced metabolic changes in crude stool and fecal water using a (1)H NMR spectroscopy-based metabolic profiling approach...
May 3, 2016: Analytical Chemistry
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