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https://www.readbyqxmd.com/read/27812352/impact-of-different-fecal-processing-methods-on-assessments-of-bacterial-diversity-in-the-human-intestine
#1
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-disease
#2
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 Dowd, Asaad Assiri, Harland Winter
BACKGROUND & 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 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
#3
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 the September 2014...
October 25, 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
#4
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
#5
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
#6
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
#7
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)...
August 17, 2016: Parasitology Research
https://www.readbyqxmd.com/read/27263967/clostridium-difficile-infections-in-children-impact-of-the-diagnostic-method-on-infection-rates
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/26878755/non-heat-treated-frozen-raspberries-the-most-likely-vehicle-of-a-norovirus-outbreak-in-oslo-norway-november-2013
#12
M Einöder-Moreno, H Lange, M Grepp, E Osborg, K Vainio, L Vold
In November 2013, the Norwegian Institute of Public Health was notified of a gastroenteritis outbreak following two meetings held at a conference centre. Identical food and beverages were served during the meetings. We investigated in order to identify the vehicle of infection and implement control measures. Meeting participants completed an online questionnaire on consumption of foods and beverages. We asked symptomatic participants to provide a stool sample. We defined a case as diarrhoea and/or vomiting in a participant who became ill within 3 days after the meeting...
October 2016: Epidemiology and Infection
https://www.readbyqxmd.com/read/26840470/human-dna-quantification-in-the-stools-of-patients-with-colorectal-cancer
#13
Yolanda Teixeira, Jacqueline Miranda Lima, Maria Luiza Almeida Prado Oliveira Souza, Pedro Aguiar, Tiago Donizetti Silva, Nora Manoukian Forones
BACKGROUND: Colorectal cancer is one of the main cause of cancer in the world. Colonoscopy is the best screen method, however the compliance is less than 50%. Quantification of human DNA (hDNA) in the feces may be a possible screen non-invasive method that is a consequence of the high proliferation and exfoliation of cancer cells. OBJECTIVE: To quantify the human DNA in the stools of patients with colorectal cancer or polyps. METHODS: Fifty patients with CRC, 26 polyps and 53 with normal colonoscopy were included...
December 2015: Arquivos de Gastroenterologia
https://www.readbyqxmd.com/read/26628567/establishing-a-fecal-microbiota-transplant-service-for-the-treatment-of-clostridium-difficile-infection
#14
Samuel P Costello, Emily C Tucker, Justin La Brooy, Mark N Schoeman, Jane M Andrews
Recurrent or refractory Clostridium difficile infection (CDI) has become an increasing problem in the past decade. Fecal microbiota transplant (FMT) is a highly efficacious treatment for recurrent CDI; however, a number of technical, logistical, and regulatory issues have hampered the development of an FMT capability at many hospitals. The development of a frozen stool bank of screened donor stool is an important step in the standardization of the procedure. This gives clinicians rapid access to thoroughly screened donor stool when needed, without the ethical and logistical problems associated with patient-selected donors...
April 1, 2016: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/26360049/use-of-occult-blood-detection-cards-for-real-time-pcr-based-diagnosis-of-schistosoma-mansoni-infection
#15
Mirjam Schunk, Seleshi Kebede Mekonnen, Beyene Wondafrash, Carolin Mengele, Erna Fleischmann, Karl-Heinz Herbinger, Jaco J Verweij, Christof Geldmacher, Gisela Bretzel, Thomas Löscher, Ahmed Zeynudin
BACKGROUND: In Schistosoma mansoni infection, diagnosis and control after treatment mainly rely on parasitological stool investigations which are laborious and have limited sensitivity. PCR methods have shown equal or superior sensitivity but preservation and storage methods limit their use in the field. Therefore, the use of occult blood detection cards (fecal cards) for easy sampling and storage of fecal samples for further PCR testing was evaluated in a pilot study. METHODOLOGY: Stool specimens were collected in a highly endemic area for S...
2015: PloS One
https://www.readbyqxmd.com/read/26341330/use-of-sequence-analysis-of-the-p2-domain-for-characterization-of-norovirus-strains-causing-a-large-multistate-outbreak-of-norovirus-gastroenteritis-in-germany-2012
#16
Marina Höhne, Sandra Niendorf, Andreas Mas Marques, C-Thomas Bock
Human norovirus is the main cause of non-bacterial gastroenteritis worldwide. It is transmitted from person to person, by fecally contaminated food or water or through virus containing aerosols originating during vomiting of infected persons. In September and October 2012, the largest foodborne norovirus outbreak in Germany so far spread over 5 Federal States (Berlin, Brandenburg, Saxony, Saxony-Anhalt, and Thuringia) affecting nearly 11,000 people mainly in schools and child care facilities. Epidemiological and trace-back investigations supported the assumption that a batch of frozen strawberries imported from China was the likely source of the outbreak...
October 2015: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/26269741/collection-media-and-delayed-freezing-effects-on-microbial-composition-of-human-stool
#17
Roberto Flores, Jianxin Shi, Guoqin Yu, Bing Ma, Jacques Ravel, James J Goedert, Rashmi Sinha
BACKGROUND: Different bacteria in stool have markedly varied growth and survival when stored at ambient temperature. It is paramount to develop optimal biostabilization of stool samples during collection and assess long-term storage for clinical specimens and epidemiological microbiome studies. We evaluated the effect of collection media and delayed freezing up to 7 days on microbial composition. Ten participants collected triplicate stool samples each into no media as well as RNAlater® with and without kanamycin or ciprofloxacin...
2015: Microbiome
https://www.readbyqxmd.com/read/26268821/heavy-hematuria-requiring-cystectomy-in-a-patient-with-hemophilia-a-a-case-report-and-literature-review
#18
REVIEW
Satoshi Washino, Masaru Hirai, Yutaka Kobayashi, Kimitoshi Saito, Tomoaki Miyagawa
BACKGROUND: Hemophilia A is an X-linked recessive disorder caused by a deficiency in factor VIII. Hemophilia A affects 1 in 5,000-10,000 males. Hematuria is frequent in hemophilia. Hematuria in hemophilia is generally considered benign and manageable with conservative therapy; however, severe hematuria requiring surgical therapy has rarely been reported. CASE PRESENTATION: A 60-year-old male with hemophilia A presented with persistent gross hematuria of unknown cause...
2015: BMC Urology
https://www.readbyqxmd.com/read/26264455/faecal-microbiota-transplant-for-recurrent-clostridium-difficile-infection-using-long-term-frozen-stool-is-effective-clinical-efficacy-and-bacterial-viability-data
#19
S P Costello, M A Conlon, M S Vuaran, I C Roberts-Thomson, J M Andrews
BACKGROUND: Faecal microbial transplant (FMT) for recurrent Clostridium difficile infection (rCDI) is greatly facilitated by frozen stool banks. However, the effect of frozen storage of stool for greater than 2 months on the viability of stool bacteria is unknown and the efficacy of FMT is not clear. AIM: To evaluate the viability of bacteria in stool frozen for up to 6 months, and the clinical efficacy of FMT with stool frozen for 2-10 months, for the treatment of rCDI...
October 2015: Alimentary Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/26252519/methods-for-improving-human-gut-microbiome-data-by-reducing-variability-through-sample-processing-and-storage-of-stool
#20
Monika A Gorzelak, Sandeep K Gill, Nishat Tasnim, Zahra Ahmadi-Vand, Michael Jay, Deanna L Gibson
Gut microbiome community analysis is used to understand many diseases like inflammatory bowel disease, obesity, and diabetes. Sampling methods are an important consideration for human microbiome research, yet are not emphasized in many studies. In this study, we demonstrate that the preparation, handling, and storage of human faeces are critical processes that alter the outcomes of downstream DNA-based bacterial community analyses via qPCR. We found that stool subsampling resulted in large variability of gut microbiome data due to different microenvironments harbouring various taxa within an individual stool...
2015: PloS One
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