DOCSLIB.ORG

Clostridium Species Reported in Stool Analysis at DDI by Chuck Masur, MD and David Quig, Phd

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Clostridium Species Reported in Stool Analysis at DDI by Chuck Masur, MD and David Quig, Phd SPRING 2010 dialog Scientific Support Clostridium Species Reported in Stool Analysis at DDI by Chuck Masur, MD and David Quig, PhD any DDI clients have responsiveness. Rao AV et al with a diagnosis of regressive- asked for more (2009) reported that, in patients onset autism, and who had a information on the with chronic fatigue syndrome, history of antimicrobial therapy, M various clostridium there was a significant decrease with vancomycin 500 mg/d species that may occupy large in anxiety symptoms (Beck for 8 weeks. Communication David Quig, PhD portions of the ecosystem that Anxiety Inventories) in patients and behavior improved but, Vice President is the human gastrointestinal taking probiotics compared to unfortunately, did not endure— tract. In response, DDI will controls (p=0.01). two weeks after the trial ended, assist the clinician with a Members of the clostridium most had regressed and by 8 stepped approach to addressing species may be shown to play months all but one had returned this issue. Non-pathogenic yet-to-be-elucidated roles in to baseline levels. clostridium species now are health and disease, for example, Clostridium is an anerobic reported in the “beneficial/ as mediators in the gut-brain genus of bacteria and, as such, expected” section of our connection, in the evolution of does not grow in the more standard microbiology panel. psychiatric illness (e.g. anxiety aerobic environment found We will continue to offer our disorders), in the prevention in the distal colon. However, Clostridium difficile Toxins A of immune dysfunction and in all clostridia do produce and B panel as an accurate acquired neurodevelopmental endospores, many of which can Chuck Masur, MD assessment for the presence of delay (e.g. autism and the survive for long periods under C. difficiledisease. In addition, autism spectrum disorders, or aerobic conditions. The new DDI is pleased to announce the ASD). The basic fact remains, DDI Comprehensive Clostridium roll-out of the Comprehensive however, that most clostridia Culture uses special media and Clostridium Culture panel that are non-pathogenic and are a anaerobic culture conditions to includes identification of more “commensal” component of the isolate and identify over twenty than twenty expected and gastrointestinal microbiota. clostridium species. Clostridia dysbiotic clostridium species. Some authors (e.g. Bolte also produce specific toxins, These cultures are performed E, 1998) believe that certain two of which (C. difficile toxins under anerobic conditions using species of clostridium produce A and B) are specifically special media optimally suited one or more toxins that may analyzed at DDI. for the growth of clostridia. be factors in the development There are approximately Barb Berta, MS, RD Non-pathogenic (commensal) of some cases of autism. 100 different clostridium bacteria in the human gut Interestingly, clostridia code for species, most of which are play significant roles in the their toxins on genes located — continued on next page Doctor’s Data, Inc. maintenance of health as in plasmids; these short bits of 3755 Illinois Avenue well as in protecting the body DNA can be easily transferred CONTENTS St. Charles, IL 60174-2420 against disease. For example, from one organism to another Clostridium Species Reported 1 800.323.2784 (US & Canada) Huang et al (2005) showed and can thereby confer on a new 630.377.8139 (Elsewhere) that commensal microbiota organism the ability to make Behind the Scenes at DDI 3 44.(0)8712.180.052 (UK) influence steps in CD4 T cell toxins where no such ability What’s New at DDI 3 630.587.7860 (fax) differentiation moderating basal existed previously. Sandler et [email protected] TCR signaling and immune al (2000) treated 11 children Frequently Asked Questions 4 www.doctorsdata.com SPRING 2010 DOCTOR’S DATA INC. Clostridium Species Reported — continued from page 1 benign inhabitants of the C. difficile can be a C. bolteae, C. histolyticum, normal human gut, although a commensal organism in up C. limosum, C. bifermentans, few are well-known pathogens. to 5% of the population; long- C. novyi A, C. sordellii, C. Clostridia are best known for term institutional care is an subterminale and others their pathogenicity in disease independent risk factor for that are included in the DDI entities such as food-borne colonization. Pathogenic C. Comprehensive Clostridium illnesses, wound infections, difficile strains produce several Culture. For further pseudomembranous colitis and toxins, the best known being discussion regarding the gas gangrene. The four main toxins A and B, both of which potential role of clostridium species that are pathogenic in cause diarrhea and inflammation species in autism and the humans are: and both of which can be tested autism spectrum disorders, • C. botulinum—produces a for at DDI by using the “C. the work of Finegold SM toxin found in food and in difficile toxins A and B” test as et al (e.g. 2003. 2004, wounds; causes botulism; a stand-alone or as an add-on 2008) provides excellent Non-pathogenic • C. difficile—found normally to other stool tests. background in that regard. in small quantities in the gut C. perfringens (once called Clostridia generally are clostridium but can overgrow, especially C. welchii) is ubiquitous in nature resistant to antibiotics, and, species now are with prolonged use of and is the third most common in most cases, antibiotic some antibiotics; the most cause of food-borne illness in the treatment of an overgrowth reported in the serious cause of antibiotic- US and UK. It also causes gas of clostridium species “beneficial/expected” associated diarrhea; produces gangrene. When present in food is not warranted. Also, toxins that can cause it is very easily killed by heating considering the potential role section of Doctor’s pseudomembranous colitis; to at least 74˚C; the bad news of plasmids in transferring • —can cause is that the spores can withstand various capacities, including Data’s standard C. perfringens a variety of symptoms and cooking temperatures and antibiotic resistance, from microbiology panel. illnesses ranging from food will germinate if cooked foods one organism to another, poisoning to gas gangrene; are left standing. Antibodies the use of antibiotics in the the organism that is used in to the toxins of food-borne C. treatment of clostridium place of yeast when making perfringens are common and overgrowth should be “salt rising” bread; and most infections are sub-clinical. considered cautiously. Some • C. tetani—found in soil and C. tetani is common in soil strains of probiotics such as wounds; produces toxins that and usually enters the host lactobacillus acidophilus may causes tetanus (tetanus is through a wound in the skin be useful in inhibiting such an the only vaccine-preventable where, once established, it overgrowth; sacharomyces illness that is infectious but produces the toxins that cause boulardi, a non-pathogenic not contagious from person tetanus. Eleven strains of C. yeast, may be of some to person). tetani have been identified and additional utility in this all strains that produce toxin same regard. For further C. botulinum produces seven produce the same neurotoxins information about the role of types of neurotoxins (A-G) with (by weight tetanospasmin is clostridium species in human most strains producing only one of the most potent toxins health and disease, or for one type but some strains known – only botulinum toxin complete citations on any of may produce several toxins. and the exotoxin produced by the publications mentioned Importantly, C. botulinum may Corynebacterium diphtheriae are in this article, please contact transfer neurotoxin genes to more toxic). the Scientific Support other clostridia—this is of Several other species are department at DDI. concern because methods of interest especially to those designed to kill or inhibit C. clinicians treating patients with botulinum may not always work neurodevelopmental disorders well with other clostridium such as those on the autism species. spectrum. These species include 2 O dialog OH Behind the Scenes at DDI— NH2 Meet Dean Bass, Assistant Laboratory Director HO r. Dean Bass’ career has into the environment via feces. polyaromatic hydrocarbon focused on research Dr. Bass’ current projects at DDI compounds in coal using and operations in include improving laboratory high performance liquid Dthe areas of atomic accuracy and automation plus chromatography. He received spectroscopy, including trace developing reference ranges his Master’s and Doctorate at metal analysis, metal speciation, for trace metals in animals. He the University of Texas at Austin and neutron activation. He has has presented his findings in studying trace metal analysis used his expertise in a variety clinical journals and at numerous using thermal desorption of projects to improve the scientific meetings. In addition to mass spectrometry. As an analysis of hair, urine, blood and his role at Doctor’s Data, Dean applications scientist for Hitachi fecal testing for trace metals. also is part of the research team Instruments, he worked on trace He has developed a program at Argonne National Laboratory metal analysis applications to test water for the presence where his projects have been and contributed to the design of toxic metals which supports used to support the Department of trace metal analysis and enhances doctors’ clinical of Energy, the Environmental instruments. He also teaches findings related to metal toxicity. Protection Agency, the Army, the graduate and undergraduate Dean also has been involved with Navy, the Centers for Disease level chemistry at the Illinois the development of programs to Control and prevention, and Institute of Technology. He has test special samples, other than Homeland Security. 26 publications and has given in blood, urine or stool. He has Dr. Bass’ undergraduate over 60 presentations. studied dental amalgams and research at the University the resultant release of mercury of Iowa looked at analyzing What’s New at DDI— by David Quig, PhD DNA Oxidative Damage the damaged residues which a sensitive indicator of overall (urinary 8-hydroxy- are then excreted in urine.
Load more

Recommended publications
  • Appendix III: OTU's Found to Be Differentially Abundant Between CD and Control Patients Via Metagenomeseq Analysis
    Appendix III: OTU's found to be differentially abundant between CD and control patients via metagenomeSeq analysis OTU Log2 (FC CD / FDR Adjusted Phylum Class Order Family Genus Species Number Control) p value 518372 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.16 5.69E-08 194497 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.15 8.93E-06 175761 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 5.74 1.99E-05 193709 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.40 2.14E-05 4464079 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 7.79 0.000123188 20421 Firmicutes Clostridia Clostridiales Lachnospiraceae Coprococcus NA 1.19 0.00013719 3044876 Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] gnavus -4.32 0.000194983 184000 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.81 0.000306032 4392484 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 5.53 0.000339948 528715 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.17 0.000722263 186707 Firmicutes Clostridia Clostridiales NA NA NA 2.28 0.001028539 193101 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.90 0.001230738 339685 Firmicutes Clostridia Clostridiales Peptococcaceae Peptococcus NA 3.52 0.001382447 101237 Firmicutes Clostridia Clostridiales NA NA NA 2.64 0.001415109 347690 Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira NA 3.18 0.00152075 2110315 Firmicutes Clostridia
    [Show full text]
  • Clostridioides Difficileinfections
    bioMérieux In vitro diagnostics serving CLOSTRIDIOIDES public health DIFFICILE INFECTIONS A major player in in vitro diagnostics for more than 50 years, From Diagnosis to bioMérieux has always been driven by a pioneering spirit and unrelenting commitment to improve public health worldwide. Outbreak Management Our diagnostic solutions bring high medical value to healthcare professionals, providing them with the most relevant and reliable information, as quickly as possible, to support treatment decisions and better patient care. bioMérieux’s mission entails a commitment to support medical education, by promoting access to diagnostic knowledge for as many people as possible. Focusing on the medical value of diagnostics, our collection of educational booklets aims to raise awareness of the essential role that diagnostic test results play in healthcare decisions. Other educational booklets are available. Consult your local bioMérieux representative. The information in this booklet is for educational purposes only and is not intended to be exhaustive. It is not intended to be a substitute for professional medical advice. Always consult a medical director, physician, or other qualified health provider regarding processes and/or protocols for diagnosis and treatment of a medical condition. bioMérieux assumes no responsibility or liability for any diagnosis established or treatment prescribed by the physician. bioMérieux, Inc. • 100 Rodolphe Street • Durham, NC 27712 • USA • Tel: (800) 682 2666 • Fax: (800) 968 9494 © 2019 bioMérieux, Inc. • BIOMERIEUX and the BIOMERIEUX logo, are used pending and/or registered trademarks belonging to bioMérieux, or one of its subsidiaries, or one of its companies. companies. its or one of subsidiaries, its or one of bioMérieux, belonging to trademarks registered pending and/or used are logo, and the BIOMERIEUX • BIOMERIEUX Inc.
    [Show full text]
  • Staphylococcus Aureus Kentaro Iwata1*, Asako Doi2, Takahiko Fukuchi1, Goh Ohji1, Yuko Shirota3, Tetsuya Sakai4 and Hiroki Kagawa5
    Iwata et al. BMC Infectious Diseases 2014, 14:247 http://www.biomedcentral.com/1471-2334/14/247 RESEARCH ARTICLE Open Access A systematic review for pursuing the presence of antibiotic associated enterocolitis caused by methicillin resistant Staphylococcus aureus Kentaro Iwata1*, Asako Doi2, Takahiko Fukuchi1, Goh Ohji1, Yuko Shirota3, Tetsuya Sakai4 and Hiroki Kagawa5 Abstract Background: Although it has received a degree of notoriety as a cause for antibiotic-associated enterocolitis (AAE), the role of methicillin resistant Staphylococcus aureus (MRSA) in the pathogenesis of this disease remains enigmatic despite a multitude of efforts, and previous studies have failed to conclude whether MRSA can cause AAE. Numerous cases of AAE caused by MRSA have been reported from Japan; however, due to the fact that these reports were written in the Japanese language and a good portion lacked scientific rigor, many of these reports went unnoticed. Methods: We conducted a systematic review of pertinent literatures to verify the existence of AAE caused by MRSA. We modified and applied methods in common use today and used a total of 9 criteria to prove the existence of AAE caused by Klebsiella oxytoca. MEDLINE/Pubmed, Excerpta Medica Database (EMBASE), the Cochrane Database of Systematic Reviews, and the Japan Medical Abstract Society database were searched for studies published prior to March 2013. Results: A total of 1,999 articles were retrieved for evaluation. Forty-five case reports/series and 9 basic studies were reviewed in detail. We successfully identified articles reporting AAE with pathological and microscopic findings supporting MRSA as the etiological agent. We also found comparative studies involving the use of healthy subjects, and studies detecting probable toxins.
    [Show full text]
  • Identification and Antimicrobial Susceptibility Testing of Anaerobic
    antibiotics Review Identification and Antimicrobial Susceptibility Testing of Anaerobic Bacteria: Rubik’s Cube of Clinical Microbiology? Márió Gajdács 1,*, Gabriella Spengler 1 and Edit Urbán 2 1 Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary; [email protected] 2 Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, 6725 Szeged, Hungary; [email protected] * Correspondence: [email protected]; Tel.: +36-62-342-843 Academic Editor: Leonard Amaral Received: 28 September 2017; Accepted: 3 November 2017; Published: 7 November 2017 Abstract: Anaerobic bacteria have pivotal roles in the microbiota of humans and they are significant infectious agents involved in many pathological processes, both in immunocompetent and immunocompromised individuals. Their isolation, cultivation and correct identification differs significantly from the workup of aerobic species, although the use of new technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, whole genome sequencing) changed anaerobic diagnostics dramatically. In the past, antimicrobial susceptibility of these microorganisms showed predictable patterns and empirical therapy could be safely administered but recently a steady and clear increase in the resistance for several important drugs (β-lactams, clindamycin) has been observed worldwide. For this reason, antimicrobial susceptibility testing of anaerobic isolates for surveillance
    [Show full text]
  • Characterization of an Endolysin Targeting Clostridioides Difficile
    International Journal of Molecular Sciences Article Characterization of an Endolysin Targeting Clostridioides difficile That Affects Spore Outgrowth Shakhinur Islam Mondal 1,2 , Arzuba Akter 3, Lorraine A. Draper 1,4 , R. Paul Ross 1 and Colin Hill 1,4,* 1 APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; [email protected] (S.I.M.); [email protected] (L.A.D.); [email protected] (R.P.R.) 2 Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh 3 Biochemistry and Molecular Biology Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh; [email protected] 4 School of Microbiology, University College Cork, T12 K8AF Cork, Ireland * Correspondence: [email protected] Abstract: Clostridioides difficile is a spore-forming enteric pathogen causing life-threatening diarrhoea and colitis. Microbial disruption caused by antibiotics has been linked with susceptibility to, and transmission and relapse of, C. difficile infection. Therefore, there is an urgent need for novel therapeutics that are effective in preventing C. difficile growth, spore germination, and outgrowth. In recent years bacteriophage-derived endolysins and their derivatives show promise as a novel class of antibacterial agents. In this study, we recombinantly expressed and characterized a cell wall hydrolase (CWH) lysin from C. difficile phage, phiMMP01. The full-length CWH displayed lytic activity against selected C. difficile strains. However, removing the N-terminal cell wall binding domain, creating CWH351—656, resulted in increased and/or an expanded lytic spectrum of activity. C. difficile specificity was retained versus commensal clostridia and other bacterial species.
    [Show full text]
  • Synergistic Haemolysis Test for Presumptive Identification and Differentiation of Clostridium Perfringens, C
    J Clin Pathol: first published as 10.1136/jcp.33.4.395 on 1 April 1980. Downloaded from J Clin Pathol 1980; 33: 395-399 Synergistic haemolysis test for presumptive identification and differentiation of Clostridium perfringens, C. bifermentans, C. sordeilhi, and C. paraperfringens STEVAN M GUBASH From the Department ofPathology, Division of Medical Microbiology, Kingston General Hospital, Kingston, Ontario, Canada K7L 2 V7, and the Department of Microbiology and Immunology, Queen's University, Kingston, Ontario, Canada K7L 3N6 SUMMARY A new test for the presumptive identification of Clostridium perfringens, C. bifermentans, C. sordellii, and C. paraperfringens is described. The test is based on the synergistic haemolysis shown by the clostridia and group B streptococci on sheep and human and CaCl2-supplemented human blood agar. C. perfringens gave crescent-shaped synergistic lytic zones (7 to over 10 mm in length), and C. paraperfringens usually small-sized (3 mm), bullet-shaped reactions on all three types of media. C. bifermentans showed a horseshoe-shaped synergistic reaction only on human blood containing media, and C. sordellii only on CaCl2-supplemented human blood agar. C. perfringens type A antiserum inhibited synergistic lytic activities of the four species. The test provided a reliable method for presumptive identification and differentiation of the four clostridial species and may obviate the need for the Nagler test. http://jcp.bmj.com/ Most clinical microbiology laboratories use the genically related phospholipase C. The test is based Nagler test 2 3 for presumptive identification of on the synergistic haemolysis due to the interaction Clostridium perfringens and other phospholipase C of the CAMP-factor of group B streptococci and (lecithinase C) producing clostridia.
    [Show full text]
  • Clostridial Diseases of Cattle
    Clostridial Diseases of Cattle Item Type text; Book Authors Wright, Ashley D. Publisher College of Agriculture, University of Arizona (Tucson, AZ) Download date 01/10/2021 18:20:24 Item License http://creativecommons.org/licenses/by-nc-sa/4.0/ Link to Item http://hdl.handle.net/10150/625416 AZ1712 September 2016 Clostridial Diseases of Cattle Ashley Wright Vaccinating for clostridial diseases is an important part of a ranch health program. These infections can have significant Sporulating bacteria, such as Clostridia and Bacillus, economic impacts on the ranch due to animal losses. There form endospores that protect bacterial DNA from extreme are several diseases caused by different organisms from the conditions such as heat, cold, dry, UV radiation, and some genus Clostridia, and most of these are preventable with a disinfectants. Unlike fungal spores, these spores cannot sound vaccination program. Many of these infections can proliferate; they are dormant forms of the bacteria that allow progress very rapidly; animals that were healthy yesterday survival until environmental conditions are ideal for growth. are simply found dead with no observed signs of sickness. In most cases treatment is difficult or impossible, therefore we absence of oxygen to survive. Clostridia are one genus of rely on vaccination to prevent infection. The most common bacteria that have the unique ability to sporulate, forming organisms included in a 7-way or 8-way clostridial vaccine microscopic endospores when conditions for growth and are discussed below. By understanding how these diseases survival are less than ideal. Once clostridial spores reach a occur, how quickly they can progress, and which animals are suitable, oxygen free, environment for growth they activate at risk you will have a chance to improve your herd health and return to their bacterial (vegetative) state.
    [Show full text]
  • Clostridioides Difficile Infection in Adults and Children
    Guidelines for Clinical Care Quality Department Clostridioides difficile Infection Guideline Team Clostridioides difficile Infection Team Leads in Adults and Children Tejal N Gandhi MD Infectious Diseases Patient population: Adults and children with a primary or recurrent episode of Clostridioides Krishna Rao, MD difficile infection (CDI). Infectious Diseases Team Members Objectives: Gregory Eschenauer, PharmD 1. Provide a brief overview of the epidemiology of, and risk factors for development Pharmacy of CDI. John Y Kao, MD 2. Provide guidance regarding which patients should be tested for CDI, summarize merits and Gastroenterology limitations of available diagnostic tests, and describe the optimal approach to laboratory diagnosis. Lena M Napolitano, MD 3. Review the most effective treatment strategies for patients with CDI including patients with Surgery recurrences or complications. F Jacob Seagull, PhD Leaning Heath Sciences Key Points for Adult Patients: David M Somand, MD Emergency Medicine Diagnosis Alison C Tribble, MD Definitive diagnosis of CDI requires either the presence of toxigenic C. difficile in stool with Pediatric Infectious Diseases compatible symptoms, or clinical evidence of pseudomembranous colitis (Table 2, Figure 4). Amanda M Valyko, MPH, CIC Once identified, CDI should be classified according to severity (Table 3). Infection Control Although risk factors for CDI (Table 1) should guide suspicion for CDI, testing should be ordered Michael E Watson Jr, MD, only when indicated (Figure 1). Use judgment and consider not testing in patients that have PhD recently started tube feeds, are taking a laxative medication, or have recently received oral Pediatric Infectious Diseases radiologic contrast material. [IC] Consultants: Choice of test should be guided by a multi-step algorithm for the rapid diagnosis of CDI (Figure 2).
    [Show full text]
  • Porphyromonas Gingivalis and Treponema Denticola Exhibit Metabolic Symbioses
    Porphyromonas gingivalis and Treponema denticola Exhibit Metabolic Symbioses Kheng H. Tan1., Christine A. Seers1., Stuart G. Dashper1., Helen L. Mitchell1, James S. Pyke1, Vincent Meuric1, Nada Slakeski1, Steven M. Cleal1, Jenny L. Chambers2, Malcolm J. McConville2, Eric C. Reynolds1* 1 Oral Health CRC, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia, 2 Department of Biochemistry and Molecular Biology, Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia Abstract Porphyromonas gingivalis and Treponema denticola are strongly associated with chronic periodontitis. These bacteria have been co-localized in subgingival plaque and demonstrated to exhibit symbiosis in growth in vitro and synergistic virulence upon co-infection in animal models of disease. Here we show that during continuous co-culture a P. gingivalis:T. denticola cell ratio of 6:1 was maintained with a respective increase of 54% and 30% in cell numbers when compared with mono- culture. Co-culture caused significant changes in global gene expression in both species with altered expression of 184 T. denticola and 134 P. gingivalis genes. P. gingivalis genes encoding a predicted thiamine biosynthesis pathway were up- regulated whilst genes involved in fatty acid biosynthesis were down-regulated. T. denticola genes encoding virulence factors including dentilisin and glycine catabolic pathways were significantly up-regulated during co-culture. Metabolic labeling using 13C-glycine showed that T. denticola rapidly metabolized this amino acid resulting in the production of acetate and lactate. P. gingivalis may be an important source of free glycine for T. denticola as mono-cultures of P. gingivalis and T. denticola were found to produce and consume free glycine, respectively; free glycine production by P.
    [Show full text]
  • Type of the Paper (Article
    Supplementary Materials S1 Clinical details recorded, Sampling, DNA Extraction of Microbial DNA, 16S rRNA gene sequencing, Bioinformatic pipeline, Quantitative Polymerase Chain Reaction Clinical details recorded In addition to the microbial specimen, the following clinical features were also recorded for each patient: age, gender, infection type (primary or secondary, meaning initial or revision treatment), pain, tenderness to percussion, sinus tract and size of the periapical radiolucency, to determine the correlation between these features and microbial findings (Table 1). Prevalence of all clinical signs and symptoms (except periapical lesion size) were recorded on a binary scale [0 = absent, 1 = present], while the size of the radiolucency was measured in millimetres by two endodontic specialists on two- dimensional periapical radiographs (Planmeca Romexis, Coventry, UK). Sampling After anaesthesia, the tooth to be treated was isolated with a rubber dam (UnoDent, Essex, UK), and field decontamination was carried out before and after access opening, according to an established protocol, and shown to eliminate contaminating DNA (Data not shown). An access cavity was cut with a sterile bur under sterile saline irrigation (0.9% NaCl, Mölnlycke Health Care, Göteborg, Sweden), with contamination control samples taken. Root canal patency was assessed with a sterile K-file (Dentsply-Sirona, Ballaigues, Switzerland). For non-culture-based analysis, clinical samples were collected by inserting two paper points size 15 (Dentsply Sirona, USA) into the root canal. Each paper point was retained in the canal for 1 min with careful agitation, then was transferred to −80ºC storage immediately before further analysis. Cases of secondary endodontic treatment were sampled using the same protocol, with the exception that specimens were collected after removal of the coronal gutta-percha with Gates Glidden drills (Dentsply-Sirona, Switzerland).
    [Show full text]
  • The American Society of Colon and Rectal Surgeons Clinical Practice
    CLINICAL PRACTICE GUIDELINES 05/18/2021 on m7j+Lz0A3Xux7u8LH54Mj5YEKJ1nYV8VK4orUjhbpk89GhwzOnar+8anRBK3LfF1V2zEXE1u0nGxPGdFl1M3hEeUEtFEphcxy9cz7yeir/pEV8b5POc6vbIuuK2BN7bKd/4WfXOBO9Zdt9xCqbLQaKAuqUBNPYvKIxVC/YioDhw= by http://journals.lww.com/dcrjournal from Downloaded The American Society of Colon and Rectal Surgeons Downloaded Clinical Practice Guidelines for the Management of from http://journals.lww.com/dcrjournal Clostridioides difficile Infection Vitaliy Poylin, M.D.1 • Alexander T. Hawkins, M.D., M.P.H.2 • Anuradha R. Bhama, M.D.3 Marylise Boutros, M.D.4 • Amy L. Lightner, M.D.5 • Sahil Khanna, M.B.B.S., M.S.6 Ian M. Paquette, M.D.7 • Daniel L. Feingold, M.D.8 by m7j+Lz0A3Xux7u8LH54Mj5YEKJ1nYV8VK4orUjhbpk89GhwzOnar+8anRBK3LfF1V2zEXE1u0nGxPGdFl1M3hEeUEtFEphcxy9cz7yeir/pEV8b5POc6vbIuuK2BN7bKd/4WfXOBO9Zdt9xCqbLQaKAuqUBNPYvKIxVC/YioDhw= Prepared by the Clinical Practice Guidelines Committee of The American Society of Colon and Rectal Surgeons 1 Division of Gastrointestinal Surgery, Northwestern Medicine, Chicago, Illinois 2 Department of Surgery, Section of Colon & Rectal Surgery, Vanderbilt University Medical Center, Nashville, Tennessee 3 Department of Surgery, Division of Colon & Rectal Surgery, Rush University Medical Center, Chicago, Illinois 4 Jewish General Hospital, McGill University, Montreal, Quebec, Canada 5 Department of Colorectal Surgery, Digestive Disease Surgery Institute, Cleveland Clinic, Cleveland, Ohio 6 Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 7 Department of Surgery, University of Cincinnati,
    [Show full text]
  • Method Comparison for the Direct Enumeration of Bacterial Species Using a Chemostat Model of the Human Colon Ines B
    Moura et al. BMC Microbiology (2020) 20:2 https://doi.org/10.1186/s12866-019-1669-2 METHODOLOGY ARTICLE Open Access Method comparison for the direct enumeration of bacterial species using a chemostat model of the human colon Ines B. Moura1* , Charmaine Normington1, Duncan Ewin1, Emma Clark1, Mark H. Wilcox1,2, Anthony M. Buckley1† and Caroline H. Chilton1† Abstract Background: Clostridioides difficile infection (CDI) has a high recurrent infection rate. Faecal microbiota transplantation (FMT) has been used successfully to treat recurrent CDI, but much remains unknown about the human gut microbiota response to replacement therapies. In this study, antibiotic-mediated dysbiosis of gut microbiota and bacterial growth dynamics were investigated by two quantitative methods: real-time quantitative PCR (qPCR) and direct culture enumeration, in triple-stage chemostat models of the human colon. Three in vitro models were exposed to clindamycin to induce simulated CDI. All models were treated with vancomycin, and two received an FMT. Populations of total bacteria, Bacteroides spp., Lactobacillus spp., Enterococcus spp., Bifidobacterium spp., C. difficile, and Enterobacteriaceae were monitored using both methods. Total clostridia were monitored by selective culture. Using qPCR analysis, we additionally monitored populations of Prevotella spp., Clostridium coccoides group, and Clostridium leptum group. Results: Both methods showed an exacerbation of disruption of the colonic microbiota following vancomycin (and earlier clindamycin) exposure, and a quicker recovery (within 4 days) of the bacterial populations in the models that received the FMT. C. difficile proliferation, consistent with CDI, was also observed by both qPCR and culture. Pearson correlation coefficient showed an association between results varying from 98% for Bacteroides spp., to 62% for Enterobacteriaceae.
    [Show full text]