edodontic microbiology

Endodontic Microbiology Endodontic Microbiology Second Edition Edited by Ashraf F Fouad Freedland Distinguished Professor and Chair Department of Endodontics School of Dentistry, University of North Carolina Chapel Hill, NC, USA This edition first published 2017 © 2017 by John Wiley & Sons, Inc All rights reserved No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by law Advice on how to obtain permission to reuse material from this title is available at http://www.wiley.com/go/permissions The right of Ashraf F Fouad to be identified as the author of the editorial material in this work has been asserted in accordance with law Registered Office John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, USA For details of our global editorial offices, customer services, and more information about Wiley products visit us at www.wiley.com Wiley also publishes its books in a variety of electronic formats and by print-on-demand Some content that appears in standard print versions of this book may not be available in other formats Limit of Liability/Disclaimer of Warranty The contents of this work are intended to further general scientific research, understanding, and discussion only and are not intended and should not be relied upon as recommending or promoting scientific method, diagnosis, or treatment by physicians for any particular patient The publisher and the authors make no representations or warranties with respect to the accuracy and completeness of the contents of this work and specifically disclaim all warranties, including without limitation any implied warranties of fitness for a particular purpose In view of ongoing research, equipment modifications, changes in governmental regulations, and the constant flow of information relating to the use of medicines, equipment, and devices, the reader is urged to review and evaluate the information provided in the package insert or instructions for each medicine, equipment, or device for, among other things, any changes in the instructions or indication of usage and for added warnings and precautions Readers should consult with a specialist where appropriate The fact that an organization or website is referred to in this work as a citation and/or potential source of further information does not mean that the author or the publisher endorses the information the organization or website may provide or recommendations it may make Further, readers should be aware that websites listed in this work may have changed or disappeared between when this works was written and when it is read No warranty may be created or extended by any promotional statements for this work Neither the publisher nor the author shall be liable for any damages arising herefrom Library of Congress Cataloging-in-Publication Data Names: Fouad, Ashraf F., editor Title: Endodontic microbiology / edited by Ashraf F Fouad Description: Second edition | Hoboken, NJ : John Wiley & Sons Inc., 2017 | Includes bibliographical references and index Identifiers: LCCN 2016042792 | ISBN 9781118758243 (cloth) | ISBN 9781118975497 (Adobe PDF) | ISBN 9781118975503 (epub) Subjects: | MESH: Dental Pulp Diseases–microbiology | Dental Pulp Diseases–drug therapy | Periapical Diseases–microbiology | Periapical Diseases–drug therapy | Anti-Infective Agents–therapeutic use | Root Canal Therapy Classification: LCC RK351 | NLM WU 230 | DDC 617.6/342–dc23 LC record available at https://lccn.loc.gov/2016042792 Cover images courtesy of the author Set in 9.5/11.25pt TimesLTStd by Aptara Inc., New Delhi, India 10 Dedication To Amal, Fikry, Lori, Amani, George, Anthony Gade, and Edward; thank you for providing me the opportunity, the inspiration, the motivation, and the love Ashraf F Fouad Contents Contributors Preface Preface to the First Edition Microbial Perspectives in the Twenty-First Century William Wade Diagnosis, Epidemiology, and Global Impact of Endodontic Infections Dag Ørstavik Microbiology of Dental Caries and Dentinal Tubule Infection Robert M Love and Anne C.R Tanner ix xi xiii 11 25 Fungi in Endodontic Infections Bilge Hakan Sen and B Găuniz Baksi 197 10 Severe Head and Neck Infections Jaime S Brahim and Robert A Ord 231 11 Endodontic Infections and Pain Anibal Diogenes and Ken M Hargreaves 251 12 Systemic Antibiotics in Endodontic Infections Ashraf F Fouad 13 Topical Antimicrobials in Endodontics Anil Kishen 269 287 Culture-Based Analysis of Endodontic Infections Gunnar Dahl´en 51 14 Endodontic Infections in Incompletely Developed Teeth George T.J Huang, Domenico Ricucci, and Louis M Lin Molecular Analysis of Endodontic Infections Jos´e F Siqueira, Jr, and Isabela N Rˆoc¸as 341 81 15 Prognosis of Healing in Treated Teeth with Endodontic Infections Shimon Friedman 16 Endodontic Infections and Systemic Disease Ashraf F Fouad 385 Glossary Index 409 413 Extraradicular Endodontic Infections 129 Brenda P F A Gomes and Ericka T Pinheiro Virulence of Endodontic Bacterial Pathogens Christine Sedgley Viruses in Endodontic Pathosis Mohamed Sabeti 149 311 179 vii Contributors Editor Ashraf F Fouad, DDS, MS Freedland Distinguished Professor and Chair Department of Endodontics School of Dentistry, University of North Carolina Chapel Hill, NC, USA Anibal Diogenes, DDS, PhD Diplomate, American Board of Endodontics Director, Advanced Program in Endodontics Department of Endodontics University of Texas Health Science Center at San Antonio Dental School San Antonio, TX, USA Authors ă B Guniz Baksi, DDS, PhD Professor Department of Oral Diagnosis and Radiology School of Dentistry Ege University Izmir, Turkey Shimon Friedman, DMD Professor, MSc Endodontics Program University of Toronto Faculty of Dentistry Toronto, Ontario, Canada Jaime S Brahim, DDS, MS Professor, Undergraduate Director Oral and Maxillofacial Surgery Department University of Maryland Dental School and Hospital Baltimore, MD, USA Gunnar Dahl´en, DDS, PhD (Dr Odont) Professor and Chairman Department of Oral Microbiology and Immunology Institute of Odontology Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden Brenda P.F.A Gomes, MSc, PhD, BDS Professor, Endodontics Piracicaba Dental School State University of Campinas Piracicaba, SP, Brazil Ken M Hargreaves, DDS, PhD Professor and Chair Department of Endodontics University of Texas Health Science Center at San Antonio Dental School San Antonio, TX, USA George T.J Huang, DDS, MSD, DSc Professor Director for Stem Cells and Regenerative Therapies Department of Bioscience Research College of Dentistry University of Tennessee Health Science Center Memphis, TN, USA Anil Kishen, PhD, MDS, BDS Professor and Head Discipline of Endodontics Faculty of Dentistry, University of Toronto Toronto, Ontario, Canada Louis M Lin, BDS, DMD, PhD Professor of Department of Endodontics College of Dentistry New York University New York, NY, USA Robert M Love, BDS, MDS, PhD, FRACDS Professor, Dean and Head of School School of Dentistry and Oral Health Griffith University Queensland, Australia Robert A Ord, DDS, MD, FRCS, FACS, MS Chairman and Professor Department of Oral and Maxillofacial Surgery University of Maryland Medical Center ix x Contributors University of Maryland School of Dentistry Baltimore, MD, USA Faculty of Dentistry, Est´acio de S´a University Rio de Janeiro, Brazil Faculty of Dentistry, Est´acio de S´a University Rio de Janeiro, Brazil Dag Ørstavik, Cand Odont, Dr Odont Professor and Head, Department of Endodontics Institute for Clinical Dentistry University of Oslo Oslo, Norway Mohamed Sabeti, DDS, MA Diplomate, American Board of Endodontics Associate Professor Loma Linda University Los Angeles, CA, USA Anne C.R Tanner, BDS, PhD Senior Member of Staff Department of Microbiology The Forsyth Institute Cambridge, MA, USA; Associate Clinical Professor Harvard School of Dental Medicine Boston, MA, USA Ericka T Pinheiro, MSc, PhD, BDS Assistant Professor Department of Dentistry University of S˜ao Paulo S˜ao Paulo, Brazil Domenico Ricucci, MD, DDS Laboratory Head Private practice Cetraro, CS, Italy Isabela N Rˆoc¸as, DDS, MSc, PhD Professor, Department of Endodontics; Head, Molecular Microbiology Laboratory Christine Sedgley, MDS, MDSc, FRACDS, MRACDS(ENDO), PhD Professor and Chair Department of Endodontology School of Dentistry, Oregon Health & Science University Portland, OR, USA Bilge Hakan Sen, DDS, PhD Ege University Izmir, Turkey Jos´e F Siqueira, Jr, DDS, MSc, PhD Chairman and Director PostGraduate Program in Endodontics William Wade, BSc, PhD Professor of Oral Microbiology Centre for Immunology and Infectious Disease Blizard Institute Barts and The London School of Medicine and Dentistry Queen Mary University of London London, UK Preface Much has happened in endodontic microbiology since the publication of the first edition of this book Hundreds of important research studies and reviews have been added to the literature in this important field We now have many better epidemiologic studies on the prevalence of endodontic disease, its association with systemic disease, and its potential contributions to major morbidity and mortality of patients The area of polymicrobial infections is now recognized as a major public health problem In the last decade it has seen innovations in research methodologies as well as the conceptual descriptions of how these infections can produce disease In the field of endodontic microbiology, next generation sequencing is now commonly used in research, revealing hundreds if not thousands of microbial taxa that are involved in endodontic pathosis The study of microbial virulence has also seen major advances These include the interplay of different pathogens, such as bacteria, viruses, and fungi, to increase the pathogenicity of either, the host–microbial interactions, the differences in clinical presentations, and responses to treatment observed with different genomic and epigenetic variations in the host, bacterial load issues, quorum sensing, and the keystone pathogen concept that describes how a pathogen can induce host changes that converts a microbial community to become dysbiotic Endodontic microbiology research still has many frontiers that have not been adequately studied These include the reasons why chronic infections can exacerbate to produce severe and spreading infections, the degree to which endodontic microflora travel to distant sites in acute and chronic infections, the exact relationship between residual bacteria and healing, and the effects of residual bacteria on the success of regenerative therapies The interaction of the microbial community in the deep carious lesion or the necrotic pulp with the host response can produce chronic asymptomatic disease or severe pain The degree to which the composition of the microflora, the expressed virulence factors, and the host’s innate susceptibility to disease interact to produce the resultant clinical manifestation needs further elucidation The ability to eliminate microbial irritants is paramount to adequate healing in endodontics There are still no clinical markers that can predict the longterm responses to vital pulp therapy or to endodontic treatment Scientific explorations that utilize cutting edge technologies, such as shotgun sequencing or metagenomics, transcriptomics, and proteomics have not been sufficiently incorporated in endodontic research The degree to which microbial elimination is required to mediate the regeneration of the dental pulp, or even just revitalization in the pulp space, is not clear Finally, we still not have rapid molecular methods of identifying antibiotic resistance, which would allow the efficient and effective selection of the right antibiotic These and many other questions will continue to inspire many studies and insights that would allow us to improve the success of our treatment modalities, save more teeth from extraction, and improve the patients’ quality of life Ashraf F Fouad xi Preface to the First Edition Endodontic infections are very prevalent, because they mostly represent complications of dental caries and its treatment, as well as traumatic injuries to teeth, which are all very prevalent occurrences Collectively, they represent the majority of dental infections that present with significantly acute local and systemic signs and symptoms This is the first textbook devoted to the study of endodontic infections, which hitherto has been limited to isolated single chapters in endodontic textbooks This textbook is intended to provide a collection of work showing the state of the knowledge in this field It is also intended to provide some research questions and hypotheses that, hopefully, will stimulate more efforts to understand the disease process and identify effective treatment methods The study of endodontic microbiology has been complicated by difficulty in epidemiological data in obtaining adequate endodontic diagnosis on large numbers of nonpatient populations In addition, sampling is a major challenge in endodontics Contamination from the tooth surface, caries, or saliva must first be avoided Access to the potentially very complex root canal anatomy and disruption of biofilm on the majority of canal walls in these areas is necessary It is almost impossible to differentiate specimens obtained from the apical and coronal portions of the root canals; thus, the effect of location of microflora within the canal is poorly understood, and can only be studied in teeth that are extracted Finally, sampling after completion of treatment to assess effectiveness of treatment and determine the long-term outcome risk is complicated by the fact that only the areas that could be reached could be sampled The difference in sensitivity between traditional culturing and modern molecular methods are especially important in endodontic microbiology, because the endodontic specimen has so little material, and sensitivity, therefore, has a major role in microbial identification The description of traditional bacterial pathogens and their virulence factors represents most of the available literature today The contributions of the not-yet-cultivated bacteria and the bacteria rendered temporarily uncultivable by traditional treatment methods have not been adequately studied Likewise, we are just beginning to understand some of the contributions of fungi and viruses to the pathogenesis of endodontic infections The debate on viable versus dead microorganisms that are detected by molecular techniques must be resolved by using more accurate technologies that assess microbial counts, their viability, and their pathogenicity Likewise, consistent and stringent methodologies, including sequencing of amplification products, are essential for assuring accurate results and enabling comparisons among studies Persistent endodontic pathosis may be due to persistent infection or new infection after treatment Sampling of apical lesions during periapical surgery is complicated by the lack of sterility of the surgical field Therefore, the microbiology of nonhealing endodontic cases is still in its infancy at this time It is clear that in order to determine effective treatment modalities, better sampling and identification techniques must be employed and more adequately designed outcome studies need to be performed Finally, the relationship between endodontic pathosis and systemic disease must be more comprehensively studied Endodontic infections were historically thought to contribute to numerous systemic diseases While the potential for systemic spread of an acute xiii xiv Preface to the First Edition endodontic infection is well-known and documented, earlier studies have failed to demonstrate that chronic endodontic infections contribute to systemic diseases However, these hypotheses must be reexamined now that we have more accurate research tools In addition, the creation of large patient databases for longitudinal analysis of treatment outcomes, and their relationships with systemic disease will be imperative in future studies that address this issue Ashraf F Fouad 438 Index necrotizing fascitis (Continued) diagnosis 241 head and neck infections 20, 232, 233, 234–49, 397–8 treatments 20, 241, 244–5, 246–9 needles head and neck infection aspiration 245–6 irrigating solutions 290, 297 negative samples, culture-based analysis 58–9 Neisseria 4, 27–37, 54–75, 292, 316 Neisseria gonorrheae Neisseria mucosa 316 Neisseria subflava 292 neomycin 274 neoplasia 391 neoplasms 395 see also cancers nephritis 159 nerve growth factors (NGFs) 254, 258–62 see also pain nerves see also neurons head and neck infections 234–49 pain 251–62 nested PCR (nPCR) 89, 101–10 definition 89 neuralgia 386, 392 neuritis 386 neurons 183, 206, 252–62 see also nerves; nociceptors HSV and 183 neuropathic pain diabetes 386 systemic syndromes that mimic endodontic pathosis 386, 392 neuropeptides 254–62, 386 neurotransmitters 254–62 neurovascular pain, systemic syndromes that mimic endodontic pathosis 386 neutralization reaction, sodium hypochlorite 291–2 neutropenia 395 neutrophils 64–72, 159, 191, 209, 257–60 newly-cultivated and characterized species 108–10 next-generation DNA sequencing technologies (NGS) 95–7, 101–4 see also molecular analysis NFkB ligand 258–60, 392 Ng et al study (2011) 344, 345 NGFs see nerve growth factors NGS see next-generation DNA sequencing technologies nickel-titanium instruments 143 NiTi files 112–18, 261–2 nitric oxide (NO) 213–14 NMDA receptor 254–62 nociceptors 252–62 see also neurons; pain definition 252–3 NOMA, definition 240 non-Hodgkin’s lymphoma 183, 184 non-mutans streptococci (non-MS), definition 34 non-pathogens see also pathogenesis definition 149–50 nonchemical-based antimicrobials see also antimicrobials overview 290, 296–7 ‘nonhealed’ outcome criteria, prognosis of treatment 112–19, 352 noninfectious conditions, pulp 11–12 nonpredictive preoperative variables, prognosis of treatment 18–21, 359–60, 362, 366–7 nonspecific interactions, yeasts 199–200 nonsteroidal anti-inflammatory drugs (NSAIDs) 261–2, 397 Norway 19 not-yet-cultured terminology, culture-based analysis 83–4, 97–8, 108–18 NSAIDs see nonsteroidal anti-inflammatory drugs nucleus caudalis 253–62 nursing bottle caries, definition 31 nutrition bacteria 27–45, 57–8, 71–5, 76–7, 82–3, 84–5, 130–1, 144, 151–2, 288 biofilms 27–45, 72–5, 84–5, 130–1, 144, 149, 151–2, 288 microorganisms 27–45, 57–8, 71–5, 76–7, 82–3, 84–5, 130–1, 144, 151–2, 180–1, 205–8, 288 yeasts 205–8 nystatin 216, 220, 273 see also antifungal agents effectiveness 220, 273 obesity 8, 275, 389, 402 obturation 43, 72–7, 143–4, 212, 320–1 see also sealants odontoblasts 253–62, 312–33 see also dentin odontogenic infections of the head and neck see head and neck infections odynophagia 241 ofloxacin 275 Oguntebi et al study (1982) 65–6 oligonucleotides 87–119 oligosaccharides 158–9 Olsenella 30–7, 54–75, 92, 108–18, 165 Olsenella profusa 30–7 Olsenella uli 54–75, 92, 108–18, 165 open apex, incompletely developed teeth 63, 311–33 oral candidosis definition 198 etiology 198, 208–9 immunocompromised hosts 198, 204–5, 208–9, 216 susceptibilities 198 oral hairy leukoplakia 183, 184 oral health 20, 198 strategies 20 oral hygiene 20, 198 oral infections, HSV and 183 Index oral inflammatory burden, definition 402 oral yeasts 30–7, 197–220 see also Candida…; fungi; yeasts definition 197–9 virulence factors 198–203 orbital space, head and neck infections 234, 238 Ord, Robert A 231–50 organic constituents, definition 290 orgnelles, fungi 197 Ørstavik, Dag 11–24, 343 Ørstavik study (1996) 343 orthodontic appliances 31–2 orthodontic considerations, incompletely developed teeth 327–30 orthograde retreatment, prognosis of treatment studies 342, 345, 351, 360–2, 364, 368, 371 osteoblasts 159–61, 328, 387–8 osteoclasts 133, 257–60 osteodentin 321–3 osteomyelitis 231 osteonecrosis 231, 396 osteoporosis 388, 396 outcome predictors, prognosis of treatment 15, 19–20, 143, 358–60, 361–2, 364–5 oxacillin 233, 272 oxicillin 280 oxygen 27–45, 64–5, 82–5, 151–2, 288, 298–300, 301–2 see also ozone biofilms 27–45, 84–5, 151–2, 288 oxyluciferin 96–7 Ozbeck et al study (2013) 186 ozone 301–2 see also antimicrobials background 301–2 concentrations 301–2 definition 301 effectiveness 301–2 mode of action 301 pAD1 plasmid 154–5 Paenibacillus 170 PAI see Periapical Index pain 12–16, 21, 65–77, 159, 190–1, 251–67, 280, 386–7 see also analgesics; proinflammatory reactions allodynia 251–2, 253, 254–62 background 12–16, 21, 65–77, 251–62, 386–7 biology 251, 252–4 central sensitization 251–2, 253, 254–5 chronic pain 14–15, 255–6 definitions 251–3 detection/processing/perception aspects 252–3, 254–6, 260–2 drugs 255, 260–2 dynamic alterations 251–2 hydrodynamic theory 253 hyperalgesia 252, 254–62 management/treatment 21, 251, 252, 260–2 mandibular teeth 261 mechanics of pain due to endodontic infections 12–16, 256–60 percussion tests 251–2, 317, 342 postendodontic therapy persistent pain 255–6, 262 posttreatment pain 255, 262, 391 processes 252–3 psychosocial symptoms 15, 256 public health issues 13–15 referred pain 256 spontaneous pain 252 statistics 15, 251, 255–6, 261–2 systemic syndromes that mimic endodontic pathosis 386–7 pancreas 388–91 see also diabetes Panton–Valentine leukocidin (PVL) 161–2 Parascardovia 29–37 Parascardovia denticolens 30–7 parasthesia 395 paresthesia 367 439 PARs see proteinase activated receptors partially vital pulps, incompletely developed teeth 323–7 Parvimonas 33–7, 54–75, 92, 104–18, 135, 164–5, 169, 180, 233, 277, 302, 399 Parvimonas micra 38–45, 54–75, 92, 108–18, 137–9, 164–5, 169, 180, 277, 302, 316, 399 see also Peptostreptococcus micros passive ultrasonic irrigation (PUI) 113 Pasteur, Louis patency-regained factors, prognosis of treatment 361 pathogen-associated molecular patterns (PAMPs) 256–60 pathogenesis see also virulence factors bacteria 1–9, 25–45, 92, 98–9, 101–19, 130–44, 149–50, 158–71, 231–2, 233–40, 256–60, 312, 314–16, 370–1, 385–403 definition 4–5, 6–7, 8–9, 133–4, 149–50 head and neck infections 20, 233–40, 397–8 herpes viruses 179–81, 188–91, 392–4 immune system concepts 8–9, 133–4, 149–50, 164, 231–2, 256–60, 270–1, 275, 287–8 immunocompromised hosts 20, 149, 150, 231–2, 280, 388–9, 391–4, 395 incompletely developed teeth 29–37, 314–16 systemic disease pathogenesis 20, 397–403 viruses 179–81, 188–91, 391–4 yeasts 30–7, 199–200, 201, 203–14 pathogenicity islands accessory genetic elements 153–7 definition 157 440 Index pathways of access to the pulp 63–5, 131 see also cracks/fractures; dental caries; trauma pattern recognition receptors (PRRs) 256–60 see also toll-like receptor… PDLs see periodontal ligaments PDLSCs see periodontal ligament stem cells Peciuliene et al study (2001) 212–13, 219 pedunculated microbial communities see also biofilms definition 150–2 pellicles 27–37 penicillin 61, 231, 233, 261–2, 269–70, 271–3, 277, 279 see also amoxicillin; B-lactam antibiotics advantages 271, 272 allergies 272, 274, 276–7, 282 background 61, 261–2, 269–70, 271–3, 277, 279 definition 271–3 Fleming 269 Florey and Chain’s mass produced penicillin 269–70 mode of action 271–3 penicillin G 272, 277 penicillin V 272, 280 penicillin-binding proteins (PBPs) 271–3 peptides 7, 27–45, 157, 159, 162, 165, 200, 254–62, 272–3, 386 peptidoglycan (PG) see also peptides; polysaccharides bacterial virulence factors 7, 129–30, 154, 158, 159, 165, 271–3 definition 7, 129, 159 Peptostreptococcus 37–45, 65–75, 92, 104–18, 135, 141–2, 166, 169, 233, 302, 399 background 37–45, 65–75, 135, 141–2, 166, 169, 233, 302, 399 head and neck infections 233, 399 Peptostreptococcus anaerobius 67–75, 92, 104–18, 166, 169, 399 Peptostreptococcus micros 38–45, 54–75, 92, 104–18, 142, 302, 316 see also Parvimonas micra Peptostreptococcus stomatis 108–18 perception aspects, pain 252–3, 254–6, 260–2 percussion tests see also diagnosis pain 13, 251–2, 317, 342 periadicular nociceptors 252–62 Periapical Index (PAI), definition 17–18, 342, 349 periapical tissues 11–24, 40–1, 69–72, 118, 130–44, 159, 162, 166–7, 169–71, 179–82, 184–91, 213–14, 231–49, 269–83, 318–21, 357–8, 370–1, 391–4, 395–6, 398–9, 400–3 see also apical… bacteria 6, 8–9, 13, 17–21, 40–1, 42–5, 52–3, 64–72, 92–3, 98–9, 103–19, 131–4, 135–44, 159, 162, 166–7, 169–71, 181, 213–14, 232–49, 255–6, 269–83, 318–21, 323–7, 359, 370–1, 391–4, 398–9, 400–3 biofilms 135–44 contaminated zone 133 EBV 184–91, 392–4 fibrous scars 130, 352, 357–8, 364, 366 HCMV 184–91 hormonal variation 395–6, 403 infected zone 133 lesion types 133 noninfectious conditions 11–12 viruses 179–82, 184–91, 391–4 yeasts 213–14 zone of irritation 133 zone of stimulation 133 pericoronitis 232–49 Peridex 323 perinatal infection, HCMV 182–3 periodic acid–Schiff staining (PAS) 209, 214 periodontal ligament stem cells (PDLSCs), definition 331–3 periodontal ligaments (PDLs) 131–4, 252–62, 314, 327–8, 331–3, 368–9 incompletely developed teeth 314, 327–8, 331–3 replantation 368–9 periodontal scaling 399 periodontal tissues 13, 15, 35–7, 44–5, 131–4, 159, 161, 179–80, 183–91, 202, 208–9, 232–49, 252–62, 280–1, 302, 312–14, 359–60, 362, 389–91 bacteria 13, 35–7, 44–5, 92, 131–4, 159, 161, 208–9, 232–49, 280–1, 302 diabetes 389–91 radicular dentin invasions 44–5 smoking 9, 356, 391, 402, 403 tooth development review 312–14 tooth loss 15, 44–5 viruses 179–80, 183–91, 391–4 yeasts 202, 208–9 periodontitis see also apical…; gingival…; root caries definition 35 etiology 6, 8–9, 11–13, 20, 25–6, 35–7, 63–72, 92, 129–30, 169, 179–80, 183–4, 187, 189–91, 208–9, 280, 370–1 recommendations 280, 281 permanent teeth, outcome of treatments on young permanent teeth 321–3 permeability factors, dentin 38–40, 43–5 persistent apical periodontitis 19–21, 69–72, 73–7, 110–19, 137–44, 352–3, 370–1 definition 353 etiology 19–21, 73–7, 137–8, 370–1 Index persistent infection after apical surgery 138–44, 362–8, 371 persistent pain, postendodontic therapy persistent pain 255–6, 262 persistent root canal infections 19–21, 69–72, 73–7, 129–44, 212–13, 220, 352–3, 364, 366, 368–9, 370–1 bacteria 19–21, 69–72, 73–7, 92, 129–44, 212–13, 220, 352–3, 364, 366, 368–9, 370–1 yeasts 212–13, 220 persister cells, biofilms 134, 142, 151–2, 288–9 Peters et al study (2002) 54 Peters et al study (2004) 343 Peters and Lau study (2003) 387 PG see peptidoglycan pH 27–37, 41–5, 82, 130–1, 151–2, 165, 166, 201–2, 217, 218, 291–2, 295 see also acids phagocytosis 64–72, 134, 144, 161, 167 pharyngeal space, head and neck infections 234, 236, 238, 241–5 phenothiazinium chromophore 298–9 phenotypic switching biofilms 1–2, 72–3, 151–2, 164, 288 yeasts 202 pheromone initiated conjugative plasmid transfers 155–6, 166–7 phospholipases 198, 201, 254 phosphorescence, photodynamic therapy 298–300 photoactivation stage, photodynamic therapy 297–300 photodynamic therapy 297–300, 326–7 background 297–300, 326–7 challenges 299 definition 297–8 effectiveness 299–300, 326–7 light sources 298–9 steps 297–9 photon-initiated photoacoustic streaming (PIPS) see also laser… definition 301 photosensitization stage, photodynamic therapy 297–300 phyla overview, bacteria 3–4, 28–37, 83, 91–3, 104–18, 130–1, 135, 141, 153 physical/chemical effects, irrigating solutions 290, 291–5 picotiter plates 95–7 Pinheiro, Ericka T 75, 129–48, 277 Pinheiro et al study (2003) 75, 277 PIPS see photon-initiated photoacoustic streaming planktonic cells 27–45, 143–4, 201, 202, 215, 302 plasma cells 73–5 plasmids 2–3, 5, 152–7 see also bacteria clumping responses 156 cytolysins 155–6, 166–7 cytotoxicity 155–7 definition 153–4 Enterococcus faecalis 153–6 enzymes 155–6 genetic aspects of bacterial virulence 5, 152–7 pheromone initiated conjugative plasmid transfers 155–6, 166–7 resistance 155–6 yeasts 154 Plasmodium falciparum 394 pluripotent stem cells see also stem cells definition 330–3 pneumonia 2, 182, 184, 187 polymerase chain reaction (PCR) 3–4, 30–2, 42–5, 52, 76, 86–93, 95–101, 104–19, 138, 210–11, 213–14, 275, 400 441 see also DNA; molecular analysis; multiplex PCR; nested PCR; quantitative PCR; reverse transcriptase PCR; RNA; species-specific PCR advantages 87–8, 97–101 background 3–4, 30–2, 76, 86–93, 95–101, 104–19 broad-range PCR 87, 90–3, 95, 98, 101–19 clones 90–3, 97, 101–4, 113–18 contamination 91 databases 90–1, 95, 96–7, 104–18 dead-cell bacterial DNA 98, 99–100, 113 definition 86–93 derivatives 31–5, 87–93 effectiveness 87–8 ERIC-PCR 90, 108 historical background 87 limitations 76, 97–101 microbial typing 90 NGS 95–7, 101–4 REP-PCR 90 too-high sensitivity issues 97–9 polysaccharides 54, 60–77, 129–44, 151, 158–9, 161, 256–60 see also lipo…; peptides Porphyromonas 4, 32–45, 54–75, 92, 107–18, 133, 135, 141–2, 161–2, 164, 169, 170, 180, 187, 256, 259–60, 395–6, 399, 400 cardiovascular disease 400 Porphyromonas cancgingivalis Porphyromonas catoniae 34–7 Porphyromonas endodontalis 66–75, 92, 99, 107–18, 133, 134, 138–9, 142, 164, 180, 316, 400 cardiovascular disease 400 Porphyromonas gingivalis 27–45, 62–75, 92, 99, 107–18, 134, 138–9, 161–2, 164, 169, 170, 180, 187, 259–60, 316, 395–6, 399, 400 Portugal, extractions 19 442 Index postirradiation caries, yeasts 204 posts, prognosis of treatment 351, 359, 366 posttreatment apical periodontitis 112–18, 135–44, 212–14, 255–6, 288, 341–72 see also prognosis of treatment extraradicular infections 137–44 yeasts 212–14 posttreatment healing 135–42, 143–4, 255, 312, 317–33, 341–84, 389–90, 395, 396–7, 398–9, 403 see also prognosis of treatment background 143–4, 312, 317–33, 341–72, 395, 396–7, 398–9, 403 incompletely developed teeth 312, 317–33 radiation therapy 396 posttreatment infections 112–18, 135–42, 212–14, 280–1, 288, 389, 391 bacteremia 280–3 smoking 356, 391, 403 studies 112–18, 143–4, 280, 389–90 posttreatment pain 255, 262, 391 posttreatment prognosis see prognosis of treatment potential for healing, prognosis of treatment 15–16, 356–7, 360–1, 364 poverty factors, incompletely developed teeth 314 Practice-based Research Network (PBRN) 255 prebiotic bacteria pregnancy, systemic disease 395–6, 403 premolars, prognosis of healing studies 136, 138–9, 351, 368–9 prenatal transmission, herpes viruses 182–3 prescription rules, antibiotics 270, 276–7, 279 pressure gradients, irrigating solutions 42–3, 290 prevention strategies 19–20, 26 Prevotella 4, 30–45, 53–77, 85, 92, 99, 107–18, 133, 135, 138–9, 142, 161, 164, 166, 169–70, 180, 187, 233, 256, 276, 279, 399 background 4, 30–45, 53–77, 85, 107–19, 133, 135, 138–9, 142, 161, 164, 166, 169–70, 233, 256, 276, 279, 399 head and neck infections 233, 399 Prevotella albens Prevotella baroniae 92, 107–18 Prevotella buccae 66–75, 277 Prevotella denticola 30–7 Prevotella intermedius 38–45, 54–75, 92, 99, 107–18, 133, 161, 164, 169, 180, 187, 277, 316, 400–1 Prevotella melaninogenica 30–7, 277, 316, 399 Prevotella multisaccharivorax 30–7, 107–18 Prevotella nigrescens 34–7, 54–75, 92, 99, 107–18, 164, 180, 187, 277, 292, 316 Prevotella oralis 67–75, 166, 169, 277 Prevotella pallens 66–75 Prevotella tannerae 92, 107–18 primary root canal infections bacteria 61–3, 69–72, 104–8, 130–44, 209, 211 yeasts 209–12, 220 primary spaces, head and neck infections 234–40, 397–8 primers, molecular analysis 86–119 probes, molecular analysis 86–119 probiotic bacteria processing aspects, pain 252–3, 254–5 prognosis of treatment 12–13, 15, 19–21, 61–3, 73–7, 112–19, 130–44, 255, 312, 341–84, 389–90, 395, 396–7 see also posttreatment… age factors 359, 362, 365 apical surgery 342, 346–9, 351–2, 355–6, 362–8, 371 background 12–13, 15, 19–21, 73–7, 255, 312, 341–72, 389–90, 395, 396–7 bacterial cultures before root filling 359 bias factors 342, 349–50, 353–4, 355–6 central sensitization 255 chlorhexidine 358 clinical outcome measures 342, 355 cohort studies 343–56, 358, 362–72 ‘complete healing’ outcome criteria 58–9, 73–4, 143, 350–2, 356–7, 360, 364 complications 359, 361, 367 conclusions 371–2 cracked/fractured roots 61–3, 371 critical importance 15–16, 341–2 crypt sizes 365 defective/missing restorations 358 definitions 341–2 dental materials 12–13, 143–4, 350, 359–60, 361–2, 364–5, 371 diabetes 389–90, 395 EDTA 361 EDTA/NaOCl-treated enamel/cementum 361 evidence levels in assessments 352–6 evidence-based medicine 354–6 extruded root fillings 130, 140, 358, 359, 362, 365 flareups 358, 359 ‘functional retention’ outcome criteria 19–20, 352, 357, 362–3, 364, 371 ‘healed’ outcome criteria 20, 58–9, 73–4, 143, 350–2, 356–7, 360, 362–3 ‘incomplete healing’ outcome criteria 363–4 Index incompletely developed teeth 312, 317–33 interproximal bone level factors 364 lesion sizes 74–5, 358, 362 magnification/illumination levels 368, 371 methodological rigor of studies 353–4, 355–6 multi-rooted teeth 358 ‘nonhealed’ outcome criteria 112–19, 352 nonpredictive preoperative variables 18–21, 359–60, 362, 366–7 outcome assessment measures/ criteria 15, 19–20, 112–19, 137–9, 143–4, 342–52, 354–6, 360–3, 364–5 outcome predictors 15, 19–20, 143, 358–60, 361–2, 364–5 patency-regained factors 361 posttreatment apical periodontitis after apical surgery 138–44, 362–8 posttreatment apical periodontitis after intentional replantation 342, 349, 356, 368–70 posttreatment apical periodontitis after orthograde retreatment 135–42, 342, 345, 351, 360–2, 364, 368, 371 potential for healing 15–16, 356–7, 360–1, 364 previous perforations 361 primary apical periodontitis after initial treatment 15–16, 19–20, 112–19, 129–31, 142–4, 343–4, 356–60, 371 radiograph uses 342, 349–57, 358–72 retreatments 342, 345, 351, 360–2, 364, 368, 371 reversal of the healing process 358, 359 root canal instruments 19–20, 142–4, 359–60, 362 root filling method 15–16, 19–20, 112–18, 359, 361–2, 364–5, 366 scar formation 352, 357–8 session numbers 359–60, 361–2 short root fillings 359, 362, 365 skill factors 12–13, 19, 20–1, 367–8, 371 statistics 19–20, 342–72 studies 19–20, 143–4, 280, 342–72, 389–90 study data reporting and analysis 354 study designs 352–3, 355–6 ‘success’ outcome criteria 20, 58–9, 73–4, 143–4, 350–2, 362–3, 368–9, 371 systemic disease 356–8 time-course of healing 15, 20–1, 74–5, 342–55, 356–8, 360–3, 364, 366 ‘uncertain healing’ outcome criteria 363–4 variables for predictions 18–21, 358–60, 361–2, 364–8 proinflammatory reactions 8–9, 11–16, 26, 37–45, 64–77, 129–44, 149, 158–71, 181, 187–91, 213–14, 241, 251–2, 256–62, 269, 295, 328–30, 386–7, 390–2, 396, 397–8, 400–3 see also edema; immune system; pain bacteria 8–9, 11–16, 26, 37–45, 64–77, 129–44, 149, 158–71, 241, 251–2, 256–62, 269, 295, 328–30, 390–2, 397–8, 400–3 viruses 181, 187–91, 392–4 yeasts 213–14 prokaryotes 116–18, 153, 161, 197, 297 see also bacteria own immune system 153 prolactin 254–62 proline-rich peptides (PRPs) 27–8, 200 prophylactic antibiotic therapy 20, 280–1 443 propidium monoazide (PMA) 100 Propionibacterium 29–45, 54–75, 92, 104–18, 134, 138–9, 140–2, 167–9, 180 definition 167–9 Propionibacterium acidifaciens 30–7, 92, 104–18 Propionibacterium acnes 33–7, 67–75, 92, 104–18, 137–9, 167–9 Propionibacterium propionicum 92, 108–18, 134, 137–9, 140–2, 167–9, 180, 370 propionic short-chain fatty acids 162 prostaglandins 188–91, 254–62 prosthetic joint replacements 283 proteases 167–71, 256–8 see also enzymes protein production interference abilities, antibiotics 273–5 proteinase activated receptors (PARs) 256–60 proteinases 151, 161–2, 198, 200–1, 256–60 see also enzymes Proteobacteria 3–4, 92–3, 104–18 proteomic analysis, genomic techniques 170 pseudohyphae 198–9, 205–6 see also fungi definition 198–9 Pseudomonas 6, 157, 215, 295, 302 Pseudomonas aeruginosa 157, 215, 295, 302 Pseudomonas fluorescens 302 Pseudoramibacter 30–7, 55–75, 92, 104–18 Pseudoramibacter alactolyticus 30–7, 55–75, 92, 108–18 psychoactive drugs 198 psychosocial symptoms, pain 15, 256 pterygomandibular masticator space 234, 237–9, 243 public health issues, endodontic infections 12, 13–16, 31–5 444 Index pulp 11–24, 26, 30, 42–5, 52–77, 81–119, 131–44, 158–9, 162–71, 187, 189–91, 212, 234–49, 251–62, 269–83, 287–302, 311–33, 386–403 see also endodontic infections; pain incompletely developed teeth 311–12, 314–16, 317, 318, 321–3, 327, 331 noninfectious conditions 11–12 pathways of access to the pulp 63–5, 131 sequelae of pulp infection 131–4 stones 402 tooth development review 312–14 pulp polyps 327 pulpal pathosis, herpes viruses 187, 189–91, 392 pulpitis 11–24, 26, 30, 35, 38–45, 63–5, 103–19, 131–4, 162–71, 251–62, 279–83, 287–302, 316–33 see also endodontic infections; irreversible…; reversible… bacteria 30, 35, 38–45, 63–5, 92, 103–19, 131–4, 162–71, 251–2, 279–83, 287–302 definition 11–12, 13–14, 287–8 diagnostic criteria 12–17 extractions 15 herpes viruses 189–91, 392 public health issues 12, 13–16, 31–5 recommendations 42–5, 261, 280, 281–3 pulpotomies, incompletely developed teeth 311, 317, 318, 321–3, 327, 331 pus, abscesses 61–3, 64–72, 134–5, 234–49, 277 ‘putative’ species, biofilms 170 Pyramidobacter piscolens 92, 104–18 pyrosequencing techniques 95–7, 101–4, 116–18, 170 QMiX 294 definition 294 qPCR see quantitative PCR quantitative PCR (qPCR) 31–5, 89–90, 102–7, 112–18 definition 89–90 quinolones 275–6, 279, 280, 319–21 see also ciprofloxacin; levofloxacin; moxifloxacin; ofloxacin critique 276 definition 275 quorum sensing 6–7, 28–37, 84–5, 157, 289 definition 6–7, 28–9, 84, 157, 289 radiation exposures, radiograph uses 17 radiation therapy 181, 204, 396 posttreatment healing 396 yeasts 204 radicular dentin 37–9, 42–5, 205–8 radiograph uses 12–14, 17–21, 40–5, 73–4, 129–30, 136–7, 138, 139, 242, 255, 314, 323, 324, 342, 349–57, 358–72, 387–9, 393, 394–5 apical periodontitis 12–14, 17–21, 40, 73–4, 129–30, 136–7, 138, 139, 255, 323, 324, 349–57, 358, 387–9, 393 background 12–13, 17–21, 40 bias factors 17, 342, 349–50, 353–4 dentinal tubule infections 40–1 diagnostic criteria 12–14, 17 endodontic therapy 255 epidemiology 17–21 head and neck infections 242, 387–9 incompletely developed teeth 314, 323, 324 jawbone radiolucencies that mimic endodontic pathosis 387–9, 394–5 lamina dura 17–21, 387–8 methodologies 17–21, 387–8 PAI 17–18, 342, 349 prognosis of treatment 342, 349–57, 358–72 radiation exposures 17 RAGE receptors 390–1 random amplified polymorphic DNA (RAPD) 90, 108 see also arbitrarily primed PCR definition 90 randomized clinical trials (RCTs) 261, 279–80, 282–3, 352–3, 355–6, 365, 389 antibiotics 279–80, 282–3 background 279–80, 352, 353–6 definition 279–80, 352, 353 diabetes 389 pain management 261 RANK-L 392, 396 RAPD see random amplified polymorphic DNA RCTs see randomized clinical trials rDNA 16S rDNA genes 86–7, 88 18S rDNA genes 86–7 recA 86–7 recommendations, antibiotics 261, 280, 281–3 reconstructive surgery, head and neck infections 240, 246–8 red blood cells, sickle cell disease 394–5 redographic lesions 190–1, 323 referred pain 256 regeneration barriers, apical surgery 367–8 regeneration innovations, incompletely developed teeth 132–3, 332, 333 regression rates, apical surgery 362–3, 364 renal failure, head and neck infections 231, 232, 241, 389, 395 REP-PCR see repetitive extragenic palindromic sequences PCR repetitive extragenic palindromic sequences PCR, (REP-PCR), definition 90 Index replantation, prognosis of treatment studies 342, 349, 356, 368–70 replication see also colonization… bacteria 6–7, 76–7, 82–5, 152–7, 170–1, 271–3, 275 genetic aspects of bacterial virulence 1–9, 152–7, 170–1, 271–3, 275 herpes viruses 179–80, 181–2, 188–90 resection levels, apical surgery 368 resistance see also methicillin-resistant Staphylococcus aureus; vancomycin-resistant enterococci antibiotics 1–2, 62–3, 72–7, 156–7, 161–2, 165, 167, 231–2, 233, 269–70, 272–3, 275–9, 288 antifungal agents 198, 201, 202, 219–20 background 1–2, 6–7, 20, 27–8, 62–3, 72–7, 130–1, 143–4, 276–83, 288, 327 bacteria 1–2, 6–7, 20, 27–45, 59–61, 62–3, 72–7, 130–1, 134, 135, 144, 150–2, 153, 155–7, 161–2, 166, 167, 202, 219–20, 231–2, 233, 269–70, 275–9, 288, 370–1 biofilms 6–7, 20, 27–45, 59–61, 72–7, 130–1, 134, 135, 143–4, 150–2, 153, 155–6, 170, 202, 219–20, 288, 326–7 cross-resistance 220 Enterococcus faecalis 40–1, 62 plasmids 155–6 studies 62–3, 276–9 tetracyclines 276–8 resorption dynamics, intentional replantation 369–70 resuscitation-promoting factors (Rpfs) retreatments, prognosis of posttreatment apical periodontitis after orthograde retreatment 342, 345, 351, 360–2, 364, 368, 371 retropharyngeal space, head and neck infections 234, 236, 238, 242–5 Retroplast 365, 366 reversal of the healing process, prognosis of treatment 358, 359 reverse transcriptase PCR (RT-PCR) 89, 100, 113–18 definition 89 reversible pulpitis 12–13, 63–5, 131–4, 287–8, 316–17, 323–7 see also diagnosis; pulpitis diagnosis 12–13 incompletely developed teeth 316–17, 323–7 ‘revitalization’ protocol, incompletely developed teeth 132–3, 323–30, 333 rheumatoid arthritis 183, 283, 395 herpes viruses 183 Rho GTPase regulators 161–2 Ribosomal Database Project (RDP) 91 ribosomes 2–9, 86–7, 273–5 see also RNA Ricucci, Domenico 311–39, 344, 345 Ricucci et al study (2011) 344 rifamycins 274–5, 277, 279 definition 274–5 RNA 2–3, 6, 29–37, 45, 82–119, 135, 142, 151, 159, 179–80, 183, 187, 273–5, 396–7 see also genomics; m…; polymerase chain reaction; r…; t… background 2–3, 6, 82–119, 142 Robertson’s meat broth 210 Rˆoc¸as et al study (2008) 106, 114 Rˆoc¸as et al study (2011) 105–6 Rˆoc¸as, Isabela N 81–128, 278 Rˆoc¸as and Siqueira study (2012) 114, 278 Rˆoc¸as and Siqueira study (2013) 278 445 Roche 454 sequencing system 2–3 Rodotorula mucilaginosa 209 root canal instruments 19–20, 31, 42–5, 55, 72–7, 112–18, 142–3, 152, 215–16, 219, 261–2, 276–8, 280–1, 318–21, 359–60, 362, 398–9 see also endodontic files; endodontic procedures prognosis of treatment 19–20, 142–4, 359–60, 362 types 42–5, 55, 112–13, 142–4 root canals see also biofilms; endodontic…; pulp…; treatments anatomy 57, 289 bacteria 7, 11–21, 26–8, 42–5, 52–77, 92, 112–19, 129–44, 150–2, 156–7, 159, 162–3, 164–71, 180–1, 209, 211, 212–14, 219, 256–62, 270–83, 287–302, 314–16, 359, 370–1, 398–9 cardiovascular disease 402–3 commensals 164 cracked/fractured roots 61–3, 131, 371 extruded root fillings 130, 140, 358, 359, 362, 365 failed therapy 15–16, 19–20, 59–63, 73–7, 112–19, 130, 135, 137–9, 143, 166, 212–13, 219, 358–60, 370–1 HIV/AIDS 209–10, 391–2 incompletely developed teeth 311–33 literature 209–13 microflora 70–5 persistent root canal infections 19–21, 69–72, 73–7, 129–44, 212–13, 220, 352, 364, 366, 368–9, 370–1 primary root canal infections 61–3, 69–72, 104–8, 130–44, 209–12, 220 prognosis of treatment studies 19–21, 143–4, 342–4, 350–6 secondary root canal infections 112–18, 142–3, 212, 220 446 Index root canals (Continued) temporary restorations 212 tooth development review 312–14, 321–3 yeasts 116, 199–200, 202, 204, 205, 208, 209–13, 214, 215, 219 root caries see also dental caries; gingival…; periodontitis microbiota 35–7 root-canal filling materials 11–13, 19–20, 42–5, 55, 59–61, 72–7, 92, 112–18, 130, 132–4, 138, 140, 142–4, 152, 162–3, 199–200, 318–21, 350, 358, 359–60, 361–2, 364–5, 366, 371 adherence of yeasts 199–200 extruded root fillings 130, 140, 358, 359, 362, 365 functions 43–4, 72–7 prognosis of treatment 12–13, 19–20, 112–18, 143–4, 350, 359–60, 361–2, 364–5, 366, 371 root-end fillings, prognosis of treatment 19–20, 44, 366–7, 369, 371 Rothia 29–37 Rothia dentocariosa 30–7 Rpfs see resuscitation-promoting factors rpoB 86–7 RpoH 151–2 RpoS 151–2 rRNA 2–3, 29–37, 45, 82–7, 88, 90–3, 95, 97, 101, 108, 115, 135, 142 see also genomics; RNA 16S rRNA genes 2–3, 29, 31, 35–6, 45, 82–5, 86–7, 88, 90–3, 95, 97, 101, 108, 115 18S rRNA genes 86–7 23S rRNA genes 86–7 RT-PCR see reverse transcriptase PCR rubber dam isolation procedures 55–7, 61, 73–7, 130, 280–1, 317–18 rubber/latex drains, head and neck infections 246–8 Rud et al study (1996) 346, 348 Rud et al study (1997) 346 Rud et al study (2001) 346 Sabeti, Mohamed 179–95 Sabouraud agar, yeasts 208–13, 219 Saccharomyces cerevisiae 207–8, 209, 212, 214, 219 Sakamoto et al (1998) 65–6 saline solution 219, 246, 261–2, 297 saliva 27–45, 60–1, 153, 182–3, 184, 201–2, 209, 241 herpes viruses 182–3, 184 salivary gland infections 232 salivary gland tissue 181, 182–3, 184, 232, 395 EBV 181, 183 HCMV 181, 182–3 HHV-6 181, 184 HHV-7 181, 184 salivary proteins 201 see also IgA sampling culture-based analysis 52, 55–7, 58–9, 76, 82–5 molecular analysis 81–119 Sanger DNA sequencing approach 91, 95, 96–7, 102–4, 116–18 saponification reaction, sodium hypochlorite 291–2 sarcoma 182, 387–8 scanning electron microscope (SEM) 44, 136–41, 207–10, 213–14 SCAP see stem cells from apical papilla scar formation, prognosis of treatment studies 352, 357–8 Scardovia 29–37 Scardovia inopinata 30–7 Scardovia wiggiae 30–7 Schneiderian membrane 386 sealants 19–20, 43, 72–7, 130, 143, 212–13, 219 see also dental materials; obturation root canal failed therapy 19–20, 130, 143, 212–13, 219 sebaceous cysts 232, 387–8 secondary root canal infections 112–18, 142–3, 212, 220 secondary spaces, head and neck infections 234–40, 397–8 secreted aspartyl proteinases (SAPs) 200–1 see also enzymes Sedgley, Christine 149–77 selective serotonin reuptake inhibitors (SSRIs) 396 selective toxicity principle, antibiotics 270 Selenomonas 30–7, 55–75, 85, 92, 104–18, 180 Selenomonas artemidis 33–7 Selenomonas dianae 33–7 Selenomonas flueggei 33–7 Selenomonas infelix 33–7 Selenomonas noxia 33–7 Selenomonas sputigena 30–7, 92, 104–18, 180 SEM see scanning electron microscope semen, herpes viruses 182 Sen, Bilge Hakan 197–230 sensitivity/specificity considerations, culture-based analysis 58–61, 65–77, 82–5 sensory nerve ganglia HSV and 181 VZV 181 septa see also fungi definition 197, 199 septic shock 159, 244–8 sequelae of pulp infection 131–4 serum albumin 27–8, 220 serum amyloid (SAA) 397 sessile microbial communities see also biofilms definition 150–2, 302 session numbers, prognosis of treatment 359–60, 361–2 Sharpey’s fibers 323 SHED stem cells 331–3 Index short root fillings, prognosis of treatment 359, 362, 365 short-chain fatty acids 129–30, 154, 158, 162, 164 see also metabolic by-products bacterial virulence factors 154, 158, 162, 164 definition 162 sickle cell disease 387, 394–5, 403 definition 394–5 SILVA 91 silver nanoparticles 296–7 single nucleotide polymorphisms (SNPs) 255–6, 396–7 singlet oxygen, definition 298 sinus tracts 69–75, 134–5, 137–9, 140–2, 168–9, 190–1, 323–7, 342, 350, 358–9, 362 see also abscesses definition 69 sinusitis 232, 386 Siqueira et al studies (2002) 210–14 Siqueira et al studies (2011) 118 Siqueira, Jos´e F 81–128, 278 Siren et al study (1997) 75, 21113 Sjăogren et al study (1990) 343, 345 Sjăogren et al study (1997) 74, 343 skill factors apical surgery 367–8, 371 prognosis of treatment 12–13, 19, 20–1, 367–8, 371 skin grafts, head and neck infections 240, 246–8 skin lesions 232 Slackia exigua 55–75, 108–18 smear layers, dentin 42–5 smoking 9, 356, 391, 402, 403 SNPs see single nucleotide polymorphisms sodium hypochlorite (NaOCl) 42–5, 76, 112–18, 214–16, 219, 262, 291–2, 294, 296, 301, 302, 317–18, 319–21, 323–7, 361 see also antimicrobials advantages 42–3, 112, 262, 324–7, 361 background 42–5, 76, 112–18, 214–16, 219, 262, 291–2, 294, 296, 301, 302, 317–18, 319–21, 323–7, 361 concentrations 42, 112, 214–15, 219, 291–2, 294, 296, 317–18, 323–7 definition 42, 214–15, 291–2 effectiveness 42–5, 112–18, 214–16, 219, 262, 291–2, 294, 301, 302, 317–18, 319–21, 323–7, 361 mode of action 42–3, 291 pain management 262 temperature factors 42–3, 291–2 soft tissue debridement 240, 246–8, 270, 280, 281 soil bacteria, teixobactin solid media overview, culturebased analysis 57–8 SOLiD NGS 95–7 Solobacterium 30–7, 92, 108–18 Solobacterium moreii 30–7, 92, 104–18 Sommer and Crowley study (1940) 53 Sousa et al study (2013) 277 South Korea 110–12 soy 210 speaking difficulties 241 species-specific PCR 88, 102–4 definition 88 specific immunity see adaptive immune system specificity considerations, antibiotics 270 spiramycin 208–9 Spirochetes 3–4, 54, 63, 65–75, 92–3, 104–18 see also Treponema spontaneous pain see also pain definition 252 SR1 SSRIs see selective serotonin reuptake inhibitors staphylococci 20, 202, 209, 272–3, 274–5 447 Staphylococcus aureus 4, 20, 54–75, 157, 159, 161–2, 215, 233, 234, 272, 295, 399, 400 see also methicillin-resistant Staphylococcus aureus background 4, 20, 54–75, 157, 159, 161–2, 233, 234, 272, 295, 399, 400 cross-linking step during cell wall synthesis 272 definition head and neck infections 233, 234, 399 Staphylococcus epidermis 33–7, 62–75, 137–9, 215, 400 statherin 27–8 statins 396 stem cells 312, 313–14, 326–7, 330–3 see also dental pulp stem cells; multipotent…; periodontal ligament…; pluripotent…; SHED…; totipotent… background 312, 313–14, 326–7, 330–3 definition 330–1 recent form-regeneration innovations 332, 333 sources 330, 331 stem cells from apical papilla (SCAP) 312, 327, 331–3 definition 331–3 sterilization, culture-based analysis 55–7 steroid treatments 198, 232, 395 stomach 86 strategies oral health 20 treatments 19–20 Streptococcus 5, 8, 20, 27–45, 53–77, 85, 92, 104–18, 135, 138–9, 141–2, 153, 156–7, 162, 165, 166, 169, 170, 200, 203, 212, 233, 234, 272–3, 292, 399 background 5, 8, 20, 27–45, 54–75, 85, 92, 104–18, 135, 138–9, 141–2, 153, 156–7, 162, 165, 166, 169, 170, 233, 234, 292, 399 448 Index Streptococcus (Continued) head and neck infections 233, 234, 399 non-MS 34 Streptococcus agalactiae 5, 170 Streptococcus anginosus 54–75, 92, 104–18, 162, 165, 166, 169 Streptococcus constellatus 33–7, 54–75, 92, 104–18, 277 Streptococcus cricetus Streptococcus cristatus 30–7 Streptococcus fermentum 30–7 Streptococcus ferus Streptococcus genomospecies 142 Streptococcus gordonii 30–7, 38–45, 142, 153, 156–7, 162, 165, 169, 170, 200 Streptococcus intermedius 30–7, 54–75, 92, 104–18 Streptococcus milleri 66–75, 233, 399 Streptococcus mitis 30–7, 40–5, 54–75, 165 Streptococcus mutans 8, 28–37, 38–45, 54–75, 153, 165, 169, 200, 203, 399, 400 dental caries 28–37, 42–5 Streptococcus oralis 7, 33–7, 54–75, 162, 165, 200, 399 Streptococcus parasanguinis 30–7 Streptococcus pneumoniae 153, 161, 401 Streptococcus pyogenes 161–2 Streptococcus rattus Streptococcus salivarius 30–7, 54–75, 165, 200, 399 Streptococcus sanguis 30–7, 40–5, 54–75, 165, 200, 299, 399 Streptococcus sobrinus 8, 30–7, 38–45 Streptococcus viridans, head and neck infections 233, 399 Streptomyces streptomycin 156–7, 274 strokes 400–3 structural overview, biofilms 26–8, 42, 59–61, 135–44, 151–2, 288, 295 sublingual space, head and neck infections 234, 235–6 submandibular space, head and neck infections 234, 235, 238, 241, 243 submental space, head and neck infections 231, 234, 235–7, 238 substance P (SP) 257–60 substantivity, definition 290 ‘success’ outcome criteria, prognosis of treatment 20, 58–9, 73–4, 143–4, 350–2, 362–3, 368–9, 371 sugars 25–6, 27–45, 64–5, 201–2 dental caries 25–6, 27–37, 64–5, 201–2 sulfa drugs, definition 275 sulfonamides 269 sulfur granules, definition 140–1 sulfurylase 96–7 Sunde et al study (2008) 186 Sundqvist et al study (1998) 75, 345 Sundqvist study (1976) 52–3 Sundqvist study (1992) 53–4, 68, 72 ‘super bugs’, antibiotics 231–2, 269–70, 276–83 Super-EBA 352, 362, 365 superoxide anions see also metabolic by-products bacterial virulence factors 158, 162, 298–300 definition 162 surface charge 200 surface free energy 200 surgery 143–4, 242–9, 255, 280, 342–72, 399 see also apical…; endodontic procedures; extractions; prognosis of treatment head and neck infections 242–9, 399 posttreatment infections 280 principles 245 swallowing difficulties 241 SYBR stain 88–93 synapses 252–62 Synergistetes 3–4, 91, 92–3, 104–18 systematic reviews 280, 321–33, 355–6, 362–72 systemic antibiotics’ overview 269–83, 398–9 see also antibiotics systemic disease 12, 19, 20, 61–3, 65–77, 356–8, 385–407 see also cancers; diabetes; herpes…; HIV/AIDS; viruses background 12, 19, 20, 356–8, 385–403 bacteremia 280–3, 398–9 cardiovascular disease 12, 20, 386–7, 391, 399–403 endodontic infections 19, 20, 356–8, 385–403 endodontic infections’ contribution to the pathogenesis of systemic disease 20, 397–403 genetic/epigenetic variations 356–8, 396–7, 399–403 herpes zoster (shingles) 387, 392–4, 403 hormonal variation 395–6, 403 jawbone radiolucencies that mimic endodontic pathosis 387–9, 394–5 pain syndromes that mimic endodontic pathosis 386–7 pregnancy 395–6, 403 prognosis of treatment 356–8 sickle cell disease 387, 394–5, 403 smoking 9, 356, 391, 402, 403 systemic examinations, head and neck infections 241 systemic medications 231, 396, 403 see also drugs T lymphocytes 68–75, 159–60, 161–2, 183–4, 187, 188–91, 391–2 see also CD…; lymphocytes EBV 183, 187, 189–91 Index functions 159–60, 161–2, 189, 392 HHV-6 183–4 T-RFLP see terminal restriction fragment length polymorphism tachycardia 241 Tanner, Anne C.R 25–49 Tannerella forsythia 27–47, 66–75, 92, 99, 104–18, 138–9, 141–2, 180, 187, 316, 399, 400–1 Taq 90–3 TaqMan 89–93 targeted antimicrobials 2–3, 288–9, 297 teixobactin TEM see transmission electron microscopy temperature factors 13, 42–3, 130–1, 151–2, 165–6, 199–200, 252, 253, 291–2, 316–17, 397–8 see also cold…; hot… adherence of yeasts 199–200 biofilms 151–2, 165–6 cytokines 397–8 sodium hypochlorite 42–3, 291–2 temporal masticator space 234, 237, 238–40 temporary restorations, root canals 212 terminal restriction fragment length polymorphism (T-RFLP) 93, 98, 101–4 see also molecular analysis definition 93 limitations 98 termination stage of bacterial protein synthesis 273–5 Terrahaemophilus 34–7 Terrahaemophilus aromaticivorans 34–7 test types 251–3, 316–17, 323, 342, 349–53 see also diagnosis tetL 278 tetM 278 tetQ 278 tetracyclines 156–7, 270, 273–5, 276–7, 279, 293–4, 319–21 see also doxycycline; glycylcyclines; minocycline background 156–7, 270, 273–5, 276, 279, 293–4, 319–21 critique 274, 276 definition 274 food product interference 270 historical background 274 resistance 276–8 side effects 274 tetS 278 tetW 278 Th1 cells 187, 188–91 Th2 cells 187, 188–91 thalamus 252–3 therapeutic index levels see also minimum inhibitory concentration antibiotics 270–1 thigmotropism (contact sensing), fungi 199, 205–6 thioglycolate media 57–8, 213 thiosulphate solution 55, 56–7, 60–1 thrombosis 231, 318, 325, 400–1 thrush 8, 198 tigecycline 274, 279 see also glycylcyclines time factors culture-based analysis 74–5, 83–5, 98 endodontic interventions 15, 20–1, 74–5, 333, 366 molecular analysis 98 prognosis of treatment 15, 20–1, 74–5, 342–55, 356–8, 360–3, 364, 366 treatments 15, 20–1, 74–5, 333, 342–55, 356–8, 360–3, 364, 366 time-dependent and depth effects of chemicals, dentin 290 TLRs see toll-like receptors TM7 3–4 TNF see tumor necrosis factor toll-like receptor (TLR2) 159, 165, 258–60 449 toll-like receptor (TLR3) 258–60 toll-like receptor (TLR4) 158–9, 256–60 toll-like receptors (TLRs) 158–9, 162, 164, 256–60 tongue 241, 242–4 too-high sensitivity issues, molecular analysis 97–9 tooth brushing effects 282–3, 399 tooth development review, endodontic infections 312–14, 321–3 tooth loss see also extractions periodontal tissues 15, 44–5 topical antimicrobials 2–3, 112–18, 161, 214–20, 246–7, 270, 287–309 see also antimicrobials; irrigating… agitation benefits 113–14, 290, 291–2 background 112–18, 287–302 biofilms 287–302, 326–7 challenges 289–90, 302 chemical-based antimicrobials 290–6 classification 290–302 conclusions 302 definitions 289–90 molecular analysis 112–18 nonchemical-based antimicrobials 290, 296–7 primary requirements 290 requirements 290 secondary requirements 290 therapeutic strategies against biofilms 288–90 types 112–18, 289–302 Toronto Study series 359 totipotent stem cells see also stem cells definition 330–3 toxic shock syndrome toxin-1 (TSST-1) 161–2 toxicities, antibiotics 129–30, 276–83 toxin–antitoxin systems (TA) 151–2 450 Index tracheotomies, head and neck infections 242–4 TraG 170 transduction method of horizontal gene transfers 152–7 transformation method of horizontal gene transfers 152–7 transforming growth factor-B (TGF-B) 318 transient receptor potential ionotropic channels (TRPs) 253–4, 258–62 transmission electron microscopy (TEM) 38, 141, 213 transmission methods, herpes viruses 182 transpeptidase enzyme 271–5 transplants 9, 240, 281–2, 328–30 transportation, culture-based analysis 52, 56, 57, 59–61, 82–5, 98 transposons 153–7 definition 156–7 trauma 11–12, 13, 19–20, 26, 38–40, 63–5, 131, 313–14, 317–18 endodontic infections 11–12, 13, 19–20, 26, 38–40, 131, 317–18 incompletely developed teeth 313–14, 317–18 treatments see also anti…; disinfectants; endodontic procedures; irrigating…; prognosis…; surgery abscesses 135–6, 241, 244–9, 270, 280, 281, 323–7 apexification 318–21, 323–30 apexogenesis 316, 317–18, 323–7 apical periodontitis 15–16, 19–21, 42–5, 61–3, 129–31, 135–42, 212–14, 255–6, 288, 341–72 bacteremia 280–3, 398–9 bacteria 1–2, 9, 26, 42–5, 61–3, 72–7, 112–18, 131–4, 142–4, 171, 231, 232, 233, 240, 269–83, 287–302, 398–9 biofilms 72–7, 130, 142–4, 171, 275, 279–83, 287–302, 326–7 cellulitis 241, 244–9, 283 clinical management with antibiotics 279–80 costs 19–20, 232, 280 culture-based analysis 72–7 dental caries 41–5 direct pulp capping 317–18, 321–3 ethics 342 evidence-based medicine 354–6 extraradicular endodontic infections 142–4 fecal transplants fungi 200, 203, 205, 207–8, 291, 292, 302 future prospects head and neck infections 231, 232, 233, 240, 242–9, 280 incompletely developed teeth 311–12, 316–33 indirect pulp capping 317–18, 321–3 MTA 317–23, 325–7, 330, 351, 361, 362, 365, 366, 369, 371 necrotizing fascitis 20, 241, 244–5, 246–9 NOMA 240 objectives 72–7, 287–8, 350–2 orthodontic considerations in incompletely developed teeth 327–30 outcome of treatments on young permanent teeth 321–3 pain 251, 252, 260–2 prebiotic bacteria prevention strategies 19–20, 26 probiotic bacteria pulpotomies 311, 317, 318, 321–3, 327, 331 RCTs 279–80, 282–3, 352, 353–6, 365 retreatments 342, 345, 351, 360–2, 364, 368, 371 session numbers 359–60, 361–2 strategies 19–20 time factors 15, 20–1, 74–5, 333, 342–55, 356–8, 360–3, 364, 366 yeasts 200, 203, 205, 207–20, 291, 292 Treponema 53–77, 92, 104–18, 135, 141–2, 170, 180, 187, 316, 400–1 see also Spirochetes Treponema amylovorum 104–18 Treponema denticola 66–75, 92, 104–18, 135, 142, 170, 180, 187, 316, 400–1 Treponema lecithinolyticum 104–18 Treponema maltophilum 92, 104–18 Treponema medium 104–18 Treponema parvum 104–18 Treponema pectinovorum 104–18 Treponema putidum 104–18 Treponema socranskii 92, 104–18 Treponema vincentii 104–18 Trichomonas vaginalis trigeminal ganglia 252–62 triggers, herpes viruses 181, 189–91 triplet state, definition 298 trismus 241, 242–4 TrkA receptor 254 tRNA 273–5 TRPs see transient receptor potential ionotropic channels TRPV1 agonists 253–4, 259–60 trypsin 256–60 see also enzymes trypticase broth 57–8, 210 TSBV agar 213 tuberculosis 150 tuf 86–7 tumor necrosis factor (TNF) 133–4, 164, 165, 167–9, 187, 188–91, 213–14, 256–60, 390–2, 394–5, 397 turbomycin A and B 5–6 Turkey, yeasts 202 Tween 80 60 twenty-first century perspectives, microbiology 1–9 Index UK, prophylactic antibiotic therapy 281–2 ulcerative colitis 9, 395 ulcers herpes zoster 183 HSV and 183 ultrasonic tips 366–8 ultrasound uses 42–3, 113–18, 242, 245–6, 290, 326–7, 366–7 head and neck infections 242, 245–6 irrigating solutions 113–18, 290, 326–7 ultraviolet light (UV) 91, 155, 157, 301–2 ‘uncertain healing’ outcome criteria, prognosis of treatment 363–4 uncultivable bacteria 3–4, 29–30, 76, 82–5, 97–8, 108, 118, 141–2 see also molecular analysis urticaria 214 US 110–12, 202, 232, 251, 255, 276, 280–1, 320, 389 allergy statistics 276 diabetes 389 Food and Drug Administration (FDA) 320 prophylactic antibiotic therapy 280–1 treatment costs 232 yeasts 202 UV light 91, 155, 157, 301–2 vaccines, historical backgroun vagina 86, 182 van… 278 vancomycin 231–2, 272–3, 277 see also glycopeptides vancomycin-resistant enterococci (VRE) 231–2, 273 vapor lock effect, definition 290 variables for predictions, prognosis of treatment 18–21, 358–60, 361–2, 364–8 varicella-zoster virus (VZV) 181, 183, 387, 392–4, 403 see also herpes…; viruses background 181, 183, 387, 392–4, 403 definition 181, 183 infection 183, 392–4 latent-state cell locations 181 vascular endothelial growth factor (VEGF) 158–9, 164 VBNC see viable but not cultivable bacteria VEGF see vascular endothelial growth factor Veillonella 27–37, 54–75, 92, 104–18, 180, 292 Veillonella atypica 30–7 Veillonella dispar 30–7, 292 Veillonella parvula 30–7, 92, 104–18, 180 veins, head and neck infections 234–49 Verdugo et al study (2013) 186 vertical gene transfers, genetic aspects of bacterial virulence 152–7 vertically compacted root fillings, prognosis of treatment 359 viability-PCR, definition 100 viable but not cultivable bacteria (VBNC) 83–5 Vibrio fischeri 6–7 VimA 164 virulence factors see also pathogenesis background 1–9, 20, 25–45, 86–7, 92, 101–19, 131–4, 149–71, 231–49, 256–60, 333, 370–1 bacteria 1–9, 20, 25–45, 86–7, 92, 101–19, 131–4, 149–71, 231–3, 256–60, 298–300, 333, 370–1 Candida albicans 8, 20, 30–7, 198–203 definition 4–5, 6–7, 8–9, 133–4, 149–50, 158, 170–1 endodontic infections 1–9, 20, 25–45, 92, 101–19, 131–4, 158–71, 256–60, 333, 370–1 fungi 4, 8, 20, 30–7, 197–203 genetic aspects of bacterial virulence 1–9, 86–7, 101–19, 451 135, 141–2, 152–7, 170–1, 275, 288, 400–1 herpes viruses 187 immune system concepts 8–9, 133–4, 149–50, 164, 231–2, 256–60, 270–1, 275, 287–8 types 4–5, 6–7, 8–9, 92, 133–4, 149–50, 158, 170–1 yeasts 4, 8, 20, 30–7, 198–203 viruses 2, 116, 131, 153, 179–95, 214–15, 276, 387, 391–4 see also bacteriophages; herpes…; individual types antivirals 214–15 apical periodontitis 179–82, 184–91, 391–4 background 2, 116, 131, 153, 179–91, 214–15, 276, 387, 391–4 bacteria 153, 180–1, 187, 189–91, 391–4 cancers 182–3, 184 conclusions 191 definition 2, 179–82 genomics 2–3 immune system 179–91 immunosuppression effects 179–80, 182, 184, 187, 188–91 Mimivirus molecular analysis 116 pathogenesis 179–81, 188–91, 391–4 periapical tissues 179–82, 184–91, 391–4 periodontal tissues 179–80, 183–91, 391–4 proinflammatory reactions 181, 187–91, 392–4 sizes Vista Dental Products 292, 293 vitamin K 276 vitamins 57–8, 276 vitronection 200 VMG I transport medium 56 VMG III transport medium 52 VMGA III transport medium 52, 56, 57, 60 von Arx et al study (2012) 347 von Arx et al study (2014) 348 452 Index VRE see vancomycin-resistant enterococci VZV see varicella-zoster virus Wade, William 1–10 Waltimo et al study (1997) 212–13 Waltimo et al study (2001) 343 Wasfy et al study (1992) 54 Weiger et al study (2000) 343 Wesson and Gale study (2003) 346 Wharton’s duct 235 white spot lesions (WSLs) 29–37 see also dental caries definition 29–31 wide-spectrum bactericidal agents 271, 272, 274, 275–6, 293–4 see also antibiotics Williams et al study (1982) 65–6 Wilson and Hall study (1968) 210, 212 Woese studies on genes 86–7 WSLs see white spot lesions Yazdi et al study (2008) 185 yeasts 4, 8, 20, 30–7, 54, 61, 63, 65–75, 116, 118, 131, 137–9, 197–220, 291, 292, 302 see also antifungal agents; Candida…; fungi; individual types; oral… adherence 30–7, 199–200, 203–5, 207–8, 216 antibiotics 198, 202, 208–9 bacteria 200, 201–2, 207–8, 219, 220, 302 biofilms 30–7, 201–2, 208, 215–16, 302 cancers 204–5, 214 cementum 203–4, 217–18 children 203, 204–5 collagen 200–1, 203–4, 207–8 colonization 199–200, 201–2, 203–14, 219, 220 conclusions 220 culture-based analysis 209–12 definition 197, 198–9 dental caries 30–7, 203–5 dental plaque 30–7, 201, 203–5 dental tissues affected 199–200, 202, 203–14 dentin 30–7, 201–2, 205–8, 215, 220 enamel 203–5 enzymes 199, 200–1, 203, 216 evasion 201 extraradicular endodontic infections 213–14 HIV/AIDS 198, 202, 203, 208–10, 391–2 immunocompromised hosts 198, 202, 204–5, 208–9, 214, 220, 391–2 molecular analysis 116, 118, 209–12 nutrition 205–8 pathogenesis 30–7, 199–200, 201, 203–14 periapical tissues 213–14 periodontal tissues 202, 208–9 persistent root canal infections 212–13, 220 phenotypic switching 202 plasmids 154 postirradiation caries 204 primary root canal infections 209–12, 220 proinflammatory reactions 213–14 root canals 199–200, 202, 204, 205, 208, 209–13, 214, 215, 219 secondary root canal infections 212, 220 thigmotropism (contact sensing) 199, 205–6 treatments 200, 203, 205, 207–20, 291, 292 virulence factors 4, 8, 20, 30–7, 198–203 Yildrim et al study (2006) 185 zinc ions 296–7 zinc oxide 43 zone of irritation/stimulation, periapical tissues 133 Index compiled by Terry Halliday ... in microbiology and to highlight selected Endodontic Microbiology, Second Edition Edited by Ashraf F Fouad © 2017 John Wiley & Sons, Inc Published 2017 by John Wiley & Sons, Inc Endodontic Microbiology. .. 9781118975503 (epub) Subjects: | MESH: Dental Pulp Diseases microbiology | Dental Pulp Diseases–drug therapy | Periapical Diseases microbiology | Periapical Diseases–drug therapy | Anti-Infective... improvement in the Endodontic Microbiology, Second Edition Edited by Ashraf F Fouad © 2017 John Wiley & Sons, Inc Published 2017 by John Wiley & Sons, Inc 11 12 Endodontic Microbiology concept of diagnosis