Microbiology with Diseases by Body System (2018) PDF

one of the more studied organisms in the world is Escherichia coli, commonly known as E. coli (featured in a colorized scanning electron micrograph on the cover). many different strains of E. coli are present...

one of the more studied organisms in the world is Escherichia coli, commonly known as E. coli (featured in a colorized scanning electron micrograph on the cover). many different strains of E. coli are present micro with diseases by body system biology in the environment, in various foods, and in both animal and human Bauman intestines. some strains have special characteristics that allow them to cause disease. among these characteristics are fimbriae, bristle-like with diseases by body system micRobiology proteins (colored yellow in the cover photo) that extend from the cell’s surface and can attach to human cells, causing diarrhea or urinary fifth edition tract infections. this Fifth edition includes a disease in depth feature on bacterial urinary tract infections that investigates how E. coli causes these infections, their signs and symptoms, and how to treat them. learn about these and other diseases, as well as how microorganisms impact health, with Microbiology with Diseases by Body System. bring microbiology to life with stunning animations, engaging micro matters case studies, and multiple practice quizzes available in. Please visit us at www.pearsonhighered.com for more information. To order any of our products, contact our customer service department at (800) 824-7799, or (201) 767-5021 outside of the U.S., or visit your campus bookstore. www.pearsonhighered.com fifth edition ISBN-13: 978-0-13-447720-6 ISBN-10: 0-13-447720-0 9 0 0 0 0 9 780134 477206 RobeRt bauman BAUM7206_05_cvrmech.indd 1 14/11/16 5:41 PM  TABLE OF CONTENTS 1 A Brief History of Microbiology 1 14 Infection, Infectious Disease, and Epidemiology 410 2 The Chemistry of Microbiology 27 15 Innate Immunity 443 3 Cell Structure and Function 57 16 Adaptive Immunity 468 4 Microscopy, Staining, and Classification 96 17 Immunization and Immune Testing 499 5 Microbial Metabolism 124 18 Immune Disorders 521 6 Microbial Nutrition and Growth 160 19 Microbial Diseases of the Skin and Wounds 551 7 Microbial Genetics 192 20 Microbial Diseases of the Nervous System and Eyes 595 8 Recombinant DNA Technology 237 21 Microbial Cardiovascular and Systemic Diseases 629 9 Controlling Microbial Growth in the Environment 260 22 Microbial Diseases of the Respiratory System 671 10 Controlling Microbial Growth in the Body: Antimicrobial 23 Microbial Diseases of the Digestive System 709 Drugs 286 24 Microbial Diseases of the Urinary and Reproductive 11 Characterizing and Classifying Prokaryotes 321 Systems 747 12 Characterizing and Classifying Eukaryotes 350 25 Applied and Industrial Microbiology 777 13 Characterizing and Classifying Viruses, Viroids, 26 Microbial Ecology and Microbiomes 801 and Prions 381 VIDEO TUTORS 1 The Scientific Method 14 Some Virulence Factors 2 The Structure of Nucleotides 15 Inflammation 3 Bacterial Cell Walls 16 Clonal Deletion, Processing of Antigen 4 The Light Microscope 17 ELISA 5 Glycolysis, Electron Transport Chains 18 Hemolytic Disease of the Newborn 6 Bacterial Growth Media 19 Disease in Depths: Necrotizing Fasciitis, Rocky Mountain 7 Initiation of Translation, Elongation in Translation Spotted Fever, Papillomas 8 Action of Restriction Enzymes 20 Disease in Depth: Listeriosis 9 Principles of Autoclaving 21 Disease in Depth: Ebola 10 Actions of Some Drugs That Inhibit Prokaryotic Protein 22 Disease in Depth: Influenza Synthesis 23 Disease in Depths: Giardiasis 11 Arrangements of Prokaryotic Cells 24 Disease in Depth: Bacterial Urinary Tract Infections, 12 Principles of Sexual Reproduction in Fungi Candidiasis 13 The Lytic Cycle of Viral Replication Please turn to the end of the listed chapters to access relevant video tutors using a QR code reader on your mobile device. A02_BAUM7206_05_SE_FEP.indd 1 11/25/16 3:10 PM  This page intentionally left blank A01_BAUM7206_05_SE_WALK.indd 2 12/13/16 4:34 PM  Invest in your future: Microbiology Matters The Fifth Edition of Microbiology with Diseases by Body System encourages a deep understanding of why microbiology matters – to health and disease. Paired with innovative media including Micro Matters and Dr. Bauman Video Tutors, the Fifth Edition better showcases why micro matters in today’s world. 26 Microbial Ecology and Microbiomes A New Treatment? Penelope was diagnosed with cystic fibrosis (CF) when she was five years old. As with many CF patients, the diagnosis followed an earlier diagnosis of “failure to thrive” (insufficient weight gain for age). She has had many health issues throughout the 20 years since her diagnosis. Five years ago, Penelope was diagnosed with cystic fibrosis–related diabetes (CFRD). Penelope was recently admitted to the hospital with a lower respiratory tract infection of Pseudomonas aeruginosa (her third such infection in the past eight months). She is treated with a combination of three antibiotics, and after about 10 days, her symptoms begin to improve. Dr. Kasper also orders chest physiotherapy (vibrations used to clear the airway) and treatment with mucolytic drugs that help her cough up more mucus. On the day that she is being discharged from the hospital, Penelope expresses to Dr. Kasper her frus- tration over being sick so often. Dr. Kasper expresses his sympathy to Penelope and further adds that there is another serious factor to consider. The chronic nature of Penelope’s infections is damaging her lung tissue; if future infections cannot be controlled with antibiotics, there is a possibility that Penelope will require a lung transplant. However, there is another possibility—Dr. Kasper tells Penelope about a clinical trial looking at a new way to treat lung infections in CF patients. If Penelope is inter- ested, Dr. Kasper can set up an appointment for them to meet with the study coordinators. 1. What do you think? 2. Should Penelope consider enrolling in the clinical study investigating a new treatment approach? Turn to the end of the chapter (p. 815) to find out. Explore More: Test your readiness and apply your knowl- edge with dynamic learning tools at MasteringMicrobiology. M26_BAUM7206_05_SE_C26.indd 801 A new chapter on the Human Microbiome introduces the 11/19/16 2:17 AM rapidly changing and expanding knowledge about the impact microbes have on health and disease. A01_BAUM7206_05_SE_WALK.indd 3 12/13/16 4:34 PM  Understanding microbiology in a clinical context Many students taking microbiology need to not only master important principles but also apply these to 8 255 The ethics and Safety of recombinant DNA Technology clinical cases and real-world applications. The Fifth Edition of Microbiology with Diseases by Body System Recombinant DNA Technology incorporates all new chapter opening cases and features killed if pesticides were used. With fewer harmful insects to designed to contextualize chapter transmit fungi, Bt corn crops contain less cancer-causing fungal toxin, a potential benefit to human health. those entities have access to all the genetic information that concepts and results? Should businesses be allowed to have patents on and make profits from living organisms they have genetically encourage students to problem solve and master material standards relevant to clinical on laboratories involved careers. As the debate continues, governments impose additional in recombinant DNA tech- altered? Should governments be allowed to require genetic screening and then force genetic manipulations on individuals nology. These are intended to prevent the accidental release of to correct perceived genetic abnormalities that some claim are altered organisms or exposure of laboratory workers to poten- the bases of criminality, manic depression, risk-taking behavior, tial dangers. Additionally, genetic researchers often design and alcoholism? Should HMOs, physicians, or the government organisms to lack a vital gene so that they could not survive for demand genetic screening and then refuse to provide services long outside a laboratory. related to the birth or care of supposedly “defective” children? Security concerns arise because terrorists could apply the We as a society will have to confront these and other ethi- procedures used to create beneficial crops and animals to engi- cal considerations as the genomic revolution continues to affect neer biological weapons that are more infective or more resis- people’s lives in many unpredictable ways. Cause for Concern? tant to treatment than their natural counterparts are. Though international treaties prohibit the development of biological TELL ME WHY weapons, Bacillus anthracis (an-thrō′sis) spores were used in bio- terrorist attacks in the United States in 2001. Thankfully, the Why don’t scientists who work with recombinant DNA know all Since she was strain a young utilized waschild, Caroline and not genetically hertofamily altered realize its deadli- the long-term effects of their work? est potential. have traveled to Brazil every year to visit her grandpar- Emergent recombinant DNA technologies raise numer- ents. She loves being able to spend time with family, but ous other ethical issues. Should people be routinely screened she also forloves beingthat diseases ableare to go hiking in the untreatable mountains, or fatal? Who should pay swimming for in the ocean, these and wandering procedures: through individuals, the little prospective employers, employers, insurance companies, health town near her grandparents’ home. It’s always a fun, butmaintenance orga- nizations busy trip, (HMOs), and Caroline or government usually returns home agencies? tired. What rights do individuals have to genetic privacy? If entities other than indi- After beingpay viduals home the acosts couple of daysinfrom involved her screening, genetic latest should trip, Caroline starts having a headache. It isn’t too bad at first, but it continues over the next couple of days and gets quite severe. She also has a fever and a sharp pain behind her eyes, and she feels achy all over—her muscles and joints really hurt. Caroline stays home from Cause for Concern? work and focuses on getting plenty of rest and drinking 1. A sample of Caroline’s blood was sent to the Centers for Disease Control Caroline’s grandmother water. She takes Tylenol (acetaminophen) to helpsuspected with that she and Prevention (CDC) for confir- has dengue fever, an infection transmitted via mation of dengue. The CDC uses the headache and body aches. real-time polymerase chain reac- a mosquito bite. Dr. Watson does an initial Caroline’s grandmother calls to see how she’s set- tion (PCR) to confirm the presence physical exam, gets a medical history (including of dengue virus in a blood sample. tling in after her trip. Caroline tells her recent travel), andgrandmother draws blood for lab analysis. Explain how real-time PCR can be how she’s been feeling, andIn her grandmother addition, Dr. Watsoninsists thatsome bleeding notices used to identify the presence of a spe- she go to the doctor immediately. along Caroline’s gum line. Based on Caroline’s cific pathogen in a blood sample. symptoms and her recent travel to Brazil, Dr. Watson also suspects 2. The CDC also determines the particular strain of dengue in 1. Why is Caroline’s grandmother so concerned? each sample using genetic analysis. Caroline may have dengue. he admits her to the hospital, where she 2. Do can yoube think that Caroline’s constantly monitored. symptoms warrant 3. Similarities in DNA sequences indicate relatedness of differ- an immediate tripofto The results the doctor? Caroline’s blood work confirm the dengue diagno- ent viruses. What method could the CDC use to determine sis. There is no cure for dengue—rest, fluid replacement, pain reliev- the DNA sequence of the dengue virus isolated from Caro- Turn toand ers, thetime endfor of the theimmune chapter (p. 255) system to find the to conquer out.infection are all line’s blood sample? Provide a rationale for your choice. that can be done. Caroline remains in the hospital, and within a week, she has recovered enough to return home. Dr. Watson tells Caroline Check your answers to Micro in the Clinic Follow-up questions in the to thank her grandmother for pushing her to go to the doctor—the MasteringMicrobiology Study Area. relatively early diagnosis allowed for Caroline’s quick and complete recovery from dengue. Explore More: Test your readiness and apply your knowl- edge with dynamic learning tools at MasteringMicrobiology. M08_BAUM7206_05_SE_C08.indd 255 11/19/16 12:10 AM NEW! Solve the Problem solve the problem Smallpox: To Be or Not To Be? boxes explore current M08_BAUM7206_05_SE_C08.indd 237 Smallpox is likely the Medical doctors began vaccinating 11/19/16 12:10 people AM microbiologically-relevant worst infectious dis- ease of all time, killing with special two-pronged needles, and eventu- ally smallpox was eradicated worldwide. The last challenges in the world. an estimated 300 mil- lion people in the 19th case was documented on October 26, 1977. Eradication represents one of the great tri- Paired active-learning century alone. It is a ter- umphs of modern medicine, but smallpox virus rifying killer, with a death rate itself still exists. Stocks are kept frozen in secure instructor activities and as high as 33% and the survivors carrying life- laboratories at the Centers for Disease Con- long scars. trol and Preven- MasteringMicrobiology British medical doctor tion (CDC) in assessments are available to Edward Jenner is credited with inventing smallpox Atlanta, Georgia, and in the State encourage critical thinking. vaccination—the world’s first immunization. On May 14, Research Center of Virology and Smallpox Viruses 1796, Jenner collected secre- Biotechnology in tions from a cowpox sore on Koltsovo, Russia. the hand of a milkmaid and rubbed them into Imagine you are assigned to be part of a team What facts do you need to make an informed decision? scratches he made on the skin of an eight-year- tasked to determine what to do with the world’s old boy. Then, about a month later, he injected remaining stores of smallpox virus. If the decision were to be made today, the boy with secretions from a lesion on a small- how would you vote? Should governments and laboratories pox patient. The child did not get smallpox; he keep them? was immune. Jenner termed his technique vac- Or should they be destroyed? In other cination, which comes from the Latin term for words, should we intentionally make a Go to the study area to solve the problem. cow, vacca. species extinct forever? Science is the study of nature that proceeds by posing ques- tions about observations. Why are there seasons? What is the The Early Years of Microbiology function of the nodules at the base of this plant? Why does this The early years of microbiology brought the first observations bread taste sour? What does plaque from between teeth look of microbial life and the initial efforts to organize them into like when magnified? What causes the spread of diseases? logical classifications. Many early written records show that people have always asked questions like these. For example, the Greek physician Hippocrates (ca. 460–ca. 377 b.c.) wondered whether there is a What Does Life Really Look Like? A01_BAUM7206_05_SE_WALK.indd 4 link between environment and disease, and the Greek histo- 12/13/16 4:34 PM  Bring microbiology to life with stunning artwork and proven pedagogy and media! Up-to-date and clear artwork clarifies complex processes while Dr. Bauman Video Tutors deliver author-developed mini-lectures on key concepts New and Updated! Disease in Depth two-page spreads visually summarize important diseases and encourage critical thinking with Video Tutors and Investigate It questions. A01_BAUM7206_05_SE_WALK.indd 5 12/13/16 4:34 PM  Continuous Learning Before, During, and After Class MasteringMicrobiology improves results by engaging students before, during, and after class. BEFORE CLASS MicroBooster and Dr. Bauman Video Tutors, animations, reading questions, and art- based activities prepare students for in-depth class discussion. dumperina Micro Matters videos and Connecting Concepts coaching activities prompt greater understanding and application of core concepts. A01_BAUM7206_05_SE_WALK.indd 6 12/13/16 4:34 PM  with MasteringMicrobiology DURING CLASS NEW! Learning Catalytics is a ”bring your own device” (laptop, smartphone, or tablet) engagement, assessment, and classroom intelligence system. Students use their device to respond to open- ended questions and then discuss answers in groups based on their responses. Visit learningcatalytics.com to learn more. AFTER CLASS A wide variety of interactive coaching activities as well as high-level assessments can be assigned after class to continue student learning and concept mastery. A01_BAUM7206_05_SE_WALK.indd 7 12/13/16 4:34 PM  Visualize Microbiology with MasteringMicrobiology NEW! Interactive Microbiology is a dynamic suite of interactive tutorials and animations that teach key concepts in microbiology, including Operons; Biofilms and Quorum Sensing; Aerobic Respiration in Bacteria; Complement, and more. Students actively engage with each topic via a case study and learn by manipulating variables, predicting outcomes, and answering formative and summative assessment questions. MicroLab Tutors, Lab Technique Videos and Lab Practical Assessments ensure students connect lecture concepts with lab techniques and protocol and are better prepared for lab work. A01_BAUM7206_05_SE_WALK.indd 8 12/13/16 4:34 PM  Access the complete textbook on and offline with eText 2.0 NEW! The Fifth Edition is available in Pearson’s fully-accessible eText 2.0 platform.* NEW! Interactive eText 2.0 gives students access to the text whenever they can access the internet. eText features include: - Available on smartphones and tablets - Seamlessly integrated videos and other rich media - Accessible (screen-reader ready) - Configurable reading settings, including resizable type and night reading mode Powerful interactive and customization functions include instructor and student note-taking, highlighting, bookmarking, search, and links to glossary terms. *eText 2.0 will be available beginning Fall 2017 A01_BAUM7206_05_SE_WALK.indd 9 12/13/16 4:34 PM  Additional Support for Students and Instructors MODERN APPROACH NEW! Microbiology: A Laboratory Manual Eleventh Edition LAB and up-to-date course, this versatile, comprehensive, and clearly written manual can be logy text. The Eleventh Edition incorporates current safety protocols from M, and AOAC, and provides suggestions for alternate organisms for easy ty Level 1 and 2. A new lab exercise has been added on the Propagation James G. Cappuccino and Chad T. Welsh revised experiments include alternate media options. Ample introductory and laboratory safety instructions are provided for each experiment along ble lab reports with review and critical thinking questions. with e homework, assessment and answer-specific feedback. Flexible and comprehensive, Microbiology: A Laboratory t is proven These tutorials coach students to correctly following perform each lab procedure and interpret/ hin your analyze different lab results. logy library, Lab Technique Videos give students an Manual, is known for its thorough coverage, parate online opportunity to see techniques performed correctly and quiz themselves on proper lab r each of the 72 procedures both before and after lab time. New de 10 multiple- Lab Technique videos demonstrate The Scientific ment, along with straightforward procedures, and minimal equipment Method and How to Write a Lab Report. answers. MicroLab Practical Activities assess vities students’ ability to interpret and analyze eos and important lab tests, procedures, and results opriate, with before their Lab Practical. requirements. The Eleventh Edition incorporates Micro 5th Edition FOURTH EDITION MICROBIOLOGY CRO biology UPDATED safety protocols from governing bodies such as WITH DISEASES BY BODY SYSTEM OGY the EPA, ASM, and AOAC and offers alternate organisms N INTRODUCTION WITH DISEASES BY TAXONOMY ROBERT W. BAUMAN ROBERT W. BAUMAN ELEVENTH EDITION for Biosafety Level 1 and 2 labs. NEW labs on Food Safety, MICROBIOLOGY ntroduction Microbiology with Diseases Microbiology with Diseases crobiology®, by Taxonomy With by Body System With Gerard J. MasteringMicrobiology®, MasteringMicrobiology®, Funke, and Fifth Edition, by Robert Bauman Fourth Edition, © 2016 © 2017 by Robert Bauman © 2015 ample introductory material, and engaging clinical -4 978-0-133-94885-1 978-0-133-94885-1 0-133-94885-4 0-133-94885-4 hered.com for more A Laboratory Manual CAPPUCCINO WELSH ducts, contact our customer applications make this lab manual appropriate for all 9, (201) 767-5021 outside okstore. modern microbiology labs! Laboratory Experiments in Microbiology Techniques in Microbiology: A Student Handbook Eleventh Edition John M. Lammert Ted R. Johnson and Christine L. Case * Contact your Pearson representative for package options and ISBNs The Instructor Resources Area in MasteringMicrobiology includes the following downloadable tools: all of the figures, photos, and tables from the text in JPEG and PowerPoint® formats, in labeled and unlabeled versions, and with customizable labels and leader lines Step-edit Powerpoint slides that present multi-step process figures step-by-step Clicker Questions and Quiz Show Game questions that encourage class interaction Video Tutors, Interactive Microbiology, MicroFlix ™, MicroBooster and Microbiology Animations MicroLab Tutors and Lab Technique Videos to help prepare students for lab and make the connection between lecture and lab Customizable PowerPoint® lecture outlines with tables, figures, and links to animations and videos A comprehensive Instructor’s Manual including active learning Solve the Problem worksheets, chapter summaries to aid in class preparation as well as the answers to the end-of-chapter review and application questions. Test Bank with hundreds of customizable multiple choice, true/false and short answer/essay questions correlated to the book’s Learning Outcomes and Bloom’s Taxonomy. Questions are available in Microsoft® Word and TestGen® formats. A01_BAUM7206_05_SE_WALK.indd 10 12/13/16 4:34 PM  This page intentionally left blank A01_BAUM7206_05_SE_WALK.indd 2 12/13/16 4:34 PM  MICRO WITH DISEASES BY BODY SYSTEM BIOLOGY FIFTH EDITION ROBERT W. BAUMAN, Ph.D. Amarillo College Contributions By: Todd P. Primm, Ph.D. Sam Houston State University Amy M. Siegesmund, Ph.D. Pacific Lutheran University Clinical Consultants: Cecily D. Cosby, Ph.D., FNP-C, PA-C Jean E. Montgomery, MSN, RN A02_BAUM7206_05_SE_FM.indd 1 12/1/16 8:24 PM  Courseware Portfolio Manager: Kelsey Churchman Design Manager: Mark Stuart Ong, Side By Side Studios Content Producer: William Wenzler Interior Designer: John Walker Managing Producer: Nancy Tabor Cover Designer: John Walker Courseware Director, Content Development: Barbara Yien Illustrators: Lachina Courseware Sr. Analyst: Alice Houston Rights & Permissions Project Manager: Kathleen Zander, Cenveo Courseware Editorial Assistant: Kate Abderholden Rights & Permissions Management: Ben Ferrini Rich Media Content Producer: Lucinda Bingham Photo Researcher: Maureen Spuhler Full-Service Vendor: SPi Global Manufacturing Buyer: Stacey Weinberger, LSC Communications Copyeditor: Sally Peyrefitte Executive Marketing Manager: Neena Bali Art Coordinator: Morgan Ewald, Lachina Cover Photo Credit: Kim Kwangshin / Getty Images Copyright © 2018, 2015, 2012 Pearson Education, Inc. All Rights Reserved. Printed in the United States of America. This publication is protected by copyright, and permission should be obtained from the publisher prior to any prohibited reproduction, storage in a retrieval system, or transmission in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise. For information regarding permissions, request forms and the appropriate contacts within the Pearson Education Global Rights & Permissions department, please visit www.pearsoned.com/permissions/. Acknowledgements of third party content appear on page C-1, which constitutes an extension of this copyright page. PEARSON, ALWAYS LEARNING MasteringMicrobiology® and MicroFlix™ are exclusive trademarks in the U.S. and/or other countries owned by Pearson Education, Inc. or its affiliates. Unless otherwise indicated herein, any third-party trademarks that may appear in this work are the property of their respective owners and any references to third-party trademarks, logos or other trade dress are for demonstrative or descriptive purposes only. Such references are not intended to imply any sponsorship, endorsement, authorization, or promotion of Pearson’s products by the owners of such marks, or any relationship between the owner and Pearson Education, Inc. or its affiliates, authors, licensees or distributors. Library of Congress Cataloging-in-Publication Data on File 1 16 ISBN 10: 0-134-47720-0 (Student edition) ISBN 13: 978-0-134-47720-6 (Student edition) ISBN 10: 0-134-61899-8 (Instructor’s Review Copy) ISBN 13: 978-0-134-61899-9 (Instructor’s Review Copy) www.pearsonhighered.com A02_BAUM7206_05_SE_FM.indd 2 12/1/16 8:24 PM  To Michelle: My best friend, my closest confidant, my cheerleader, my partner, my love. Thirty-four years! I love you more now than then. —Robert A02_BAUM7206_05_SE_FM.indd 3 12/1/16 8:24 PM  About the Author ROBERT W. BAUMAN is a professor of biology and past chairman of the Department of Biological Sciences at Amarillo College in Amarillo, Texas. He has taught microbiology, human anatomy and physiology, and botany for over 30 years. In 2004, the students of Amarillo College selected Dr. Bauman as the recipient of the John F. Mead Faculty Excellence Award, and he has been nominated yearly, but winning has been limited to one time. He received an M.A. degree in botany from the University of Texas at Austin and a Ph.D. in biology from Stanford University. His research interests have included the morphology and ecology of freshwater algae, the cell biology of marine algae (particularly the deposition of cell walls and intercellular communication), environmentally triggered chromogenesis in butterflies, and terrestrial oil pollution remediation by naturally occurring bacteria. He is a member of the American Society of Microbiology (ASM) where he has held national offices; Texas Community College Teachers Association (TCCTA), where he serves in a statewide position of leadership; American Association for the Advancement of Science (AAAS); Human Anatomy and Physiology Society (HAPS); and the Lepidopterists’ Society. When he is not writing books, he enjoys spending time with his family: gardening, hiking, camping, rock climbing, backpacking, cycling, skiing, and reading by a crackling fire in the winter and in a gently swaying hammock in the summer. TODD P. PRIMM (contributor) is a professor at Sam Houston State University, where he teaches pre-nursing and general microbiology. He also serves as director of the Professional and Academic Center for Excellence, which focuses on improving teaching and learning on campus. In 2010, he was Distinguished Alumnus of the Graduate School of Biomedical Sciences of Baylor College of Medicine, where he earned a Ph.D. in biochemistry. He received a B.S. from Texas A&M University. He is very active in the American Society for Microbiology and received the Texas Branch 2015 Faculty Teaching Award. He was chair of the organizing committee for the 2013 ASM Conference for Undergraduate Educators, participated in the 2012 Research Residency of the ASM/NSF Biology Scholars Program, and currently serves on the editorial board for the Journal of Microbiology & Biology Education. He is also an affiliate staff member with the international organization Cru. He loves teaching and mentoring students and spending time with his wonderful wife of 25 years and their five children. About the Clinical Consultants CECILY D. COSBY is nationally certified as both JEAN E. MONTGOMERY is a registered nurse a family nurse practitioner and physician assistant. She is formerly teaching in the associate degree nursing program at a professor of nursing, currently teaching at Samuel Merritt Austin Community College in Texas. She received her MSN University in Oakland, California, and has been in clinical from the University of Texas Health Science Center at San practice since 1980. She received her Ph.D. and M.S. from Antonio, Texas. the University of California, San Francisco; her BSN from California State University, Long Beach; and her P.A. certificate from the Stanford Primary Care program. She is the Director of Samuel Merritt University’s Doctor of Nursing Practice Program. iv A02_BAUM7206_05_SE_FM.indd 4 12/1/16 8:24 PM  Preface The reemergence of whooping cough, mumps, and measles and the emergence of Zika virus infec- tions, spotted fever rickettsioses, Middle East respiratory syndrome, and other diseases; cases of strep throat, MRSA, and tuberculosis; the progress of research into microbial genetics; the chal- lenge of increasingly drug-resistant pathogens; the continual discovery of microorganisms previ- ously unknown—these are just a few examples of why exploring microbiology has never been more exciting, or more important. Welcome! I have taught microbiology to undergraduates for over 30 years and witnessed firsthand how students struggle with the same topics and concepts year after year. To address these challenging topics, I have created new Video Tutors: four in addition to those already incorporated into the first 18 chapters of the text and ten that cover the Disease in Depth features. The Video Tutors and Disease in Depth features walk students through key concepts in microbiology, bringing the art of the textbook to life and important concepts into view. In creating this textbook, my aim was to help students see complex topics of microbiology—especially metabolism, genetics, and immu- nology—in a way that they can understand, while at the same time presenting a thorough and accurate overview of microbiology. I also wished to highlight the many positive effects of micro- organisms on our lives, along with the medically important microorganisms that cause disease. New to This Edition In approaching the fifth edition, my goal was to build upon the strengths and success of the previ- ous editions by updating it with the latest scientific and educational research and data available and by incorporating many terrific suggestions received from colleagues and students alike. The feedback from instructors who adopted previous editions has been immensely gratifying and is much appreciated. Seven new Solve the Problem! features use problem-based learning, encourag- ing students to put knowledge into practice. The Disease at a Glance features have been widely praised by instructors and students, so I, along with art editor Kelly Murphy, developed six new Disease in Depth features, most as two-page spreads, that use compelling art and photos to pro- vide a detailed, visually unsurpassed overview of a specific disease. Each Disease in Depth fea- ture includes an Investigate It! question with a QR code directing students to a Video Tutor that explores the topic. These activities are assignable in MasteringMicrobiology®. Another goal for this edition was to provide additional instruction on important foundational concepts and pro- cesses. To that end, I developed and narrated three new core concept Video Tutors, accessible via QR codes in the textbook and assignable in MasteringMicrobiology®. The result is, once again, a collaborative effort of educators, students, editors, and top scientific illustrators: a textbook that, I hope, continues to improve upon conventional explanations and illustrations in substantive and effective ways. In this new edition: NEW Solve the Problem features carry education to a new level with problem-based learning exer- cises that excite, inspire, and stimulate students to apply critical thinking skills to current micro- biological quandaries. Each of the seven Solve the Problem features challenges students to work together to devise and articulate possible resolutions. Solve the Problem exercises can stand alone or be expanded with ambitious extensions and resources available in MasteringMicrobiology®. NEW Disease in Depth features highlight important diseases: Rocky Mountain spotted fever, candidiasis, malaria, papillomas, Ebola hemorrhagic fever, and influenza, extending the visual v A02_BAUM7206_05_SE_FM.indd 5 12/1/16 8:24 PM  vi Preface impact of the art program. Each of these new Disease in Depth features contains infographics, provides in-depth coverage of the selected disease, and includes a QR code and Investigate It! question that directs students to a Video Tutor exploring the topic and prompting further inquiry and critical thinking. New assignable Disease in Depth coaching activities in MasteringMicrobiol- ogy® encourage students to apply and test their understanding of key concepts. NEW Video Tutors developed and narrated by the author walk students through key concepts. New to this edition are Video Tutors on glycolysis, protein translation, and antigen process- ing. These Video Tutors bring the textbook art to life and help students visualize and under- stand tough topics and important processes. Thirty-two video tutorials are accessible via QR codes in the textbook and are accompanied by multiple-choice questions, assignable in MasteringMicrobiology®. New Micro Matters features tie together subjects from different chapters to encourage students to apply and synthesize new knowledge as they explore medical cases and answer pertinent questions. Each of the five Micro Matters video tutorials is accessible via QR code and paired with assessments in MasteringMicrobiology®. The genetics and immunology chapters (Chapters 7, 8, 15, and 16) have been reviewed and revised by genetics specialists. These now reflect the most current understanding of this rapidly evolv- ing field, including new discussion of next-generation DNA sequencing. Over 300 NEW and revised micrographs, photos, and figures enhance student understanding of the text and boxed features. NEW and EXPANDED MasteringMicrobiology® includes: NEW Interactive Microbiology, a dynamic suite of interactive tutorials and animations that teach key concepts in the con- text of a clinical setting. Students actively engage with each topic and learn from manipulat- ing variables, predicting outcomes, and answering formative and summative assessments. Topics include Operons; Complement; Biofilms and Quorum Sensing; Antibiotic Resistance, Mechanisms; Antibiotic Resistance, Selection; and more. NEW Micro Matters case tutorials and assessments connect chapter concepts and coach stu- dents through applying and synthesizing new knowledge. NEW MicroBoosters pair video tutorials and assessments covering key concepts that stu- dents often need to review, including Basic Chemistry, Cell Biology, Biology and more! The Microbiology Lab resources include MicroLab Tutors, which use lab technique videos, 3-D molecular animations, and step-by-step tutorials to help students make connections between lecture and lab. Lab Technique Videos and pre-lab quizzes ensure students come prepared for lab time. Lab Practical and post-lab quizzes reinforce what students have learned. MasteringMicrobiology ® also provides access to Dynamic Study Modules to help students acquire, retain, and recall information faster and more efficiently than ever before, with textbook- specific explanations and art. Dynamic Study Modules are available for use as a self-study tool or as assignments. Instructors also now have the option to give Adaptive Follow-Up assignments that provide student-specific additional coaching and practice. These question sets continuously adapt to each student’s needs, making efficient use of homework time. Additionally, Mastering- Microbiology® includes Learning Catalytics—a “bring your own device” student engagement, assessment, and classroom intelligence system. With Learning Catalytics, instructors can assess students in real time using open-ended tasks to probe student understanding using Pearson’s library of questions or designing their own. The following section provides a detailed outline of this edition’s chapter-by-chapter revisions. A02_BAUM7206_05_SE_FM.indd 6 12/1/16 8:24 PM  Chapter-by-Chapter Revisions 1 A Brief History of Microbiology 4 Microscopy, Staining, and Classification New chapter opener case study and photo New chapter opener case study and photo Two other new photos (1.3, 1.6b) One other new photo (4.18) Two figures revised for better pedagogy, clarity, and Revised one figure for enhanced pedagogy (4.11) accuracy [1.5 (2)] Revised Learning Outcome regarding simple stains, which Updated map showing countries having transmission of variant now include Gomori methenamine silver stain and hematoxylin Creutzfeldt-Jakob disease (vJCD) and eosin stains Introduced discussion of the success of gene therapy in treating Removed the Highlight box on microscopy of living biofilms and several inherited immune deficiencies incorporated relevant information, including the figure, into the text Deleted the Highlight box covering emerging and reemerging Added one new critical thinking question to Emerging Disease diseases, placed the discussion of this topic within the chapter Case Study: Necrotizing Fasciitis box text, and expanded coverage to include Middle East Respiratory Revised coverage of history of taxonomy Syndrome (MERS), Zika fever, Ebola, and chikungunya Expanded discussion of resolution, immersion oil, mordants, Spelling of Semmelweis corrected in Figure 1.19 definition of microbial species, and role of George Fox in the New Clinical Case Study: Can Spicy Foods Cause Ulcers? with discovery of the archaea and three domains of life questions Revised section on microbial taxonomy to more fully address New Solve the Problem: Smallpox: To Be or Not to Be? (problem- genomic techniques in taxonomy based learning exercise concerning complete smallpox virus At request of reviewers and instructors, reduced complexity destruction) and chapter length by removing detailed figures for dark-field, Expanded list of current problems in microbiology to include phase, and scanning electron microscopy Ebola control, biofilms, rapid testing for infections, and Added fill-in Concept Mapping exercise on Gram stain and cell antimicrobial-drug resistance by persistent cells wall structure Added fill-in Concept Mapping exercise on types of microbes and some of their major characteristics 5 Microbial Metabolism New chapter opener case study and photo 2 The Chemistry of Microbiology Revised twelve figures for greater clarity and better pedagogy New chapter opener case study and photo (5.9, 5.11, 5.12, 5.13, 5.14, 5.16, 5.17, 5.18, 5.19, 5.21, 5.25, 5.28) Five figures revised for better pedagogy (2.6, 2.21, 2.22, ether bond Removed the Highlight box on trimethylamine oxide (fishy smell) and amino group in Table 2.3) from the chapter New Learning Outcomes concerning terms regarding elements, Removed the Highlight box on glowing bacteria valence electrons and chemical bonding, organic compounds, Clarified and expanded discussion of the importance of redox contrasting ionic and covalent bonds, lipids reactions, the uses of ATP in cell, enzymatic activation through Clarified that most organisms code for 21 amino acids, though allosteric sites, competitive and noncompetitive inhibition of 20 are more common enzyme activity, and lipid catabolism and anbolism Added fill-in Concept Mapping exercise on nucleotide structure Expanded discussion of diverse metabolic pathways and function Changed the term Embden­Meyerhof pathway to Embden­Meyerhof­ Parnas pathway to reflect the contribution of Jakub Karol Parnas 3 Cell Structure and Function in elucidating the glycolytic pathway New Tell Me Why critical thinking question over analogous New chapter opener case study and photo structures of electron carriers and nucleotides Five other new/upgraded photos (3.5a, 3.5b, 3.8a, 3.24, 3.28a) Added Learning Outcome concerning metabolic diversity in bacteria Revised and enhanced artwork in nine figures for enhanced pedagogy (3.13, 3.15, 3.18, 3.20, 3.22, 3.23, 3.29, 3.30, 3.33b) New Solve the Problem: The Microbes Ate My Homework (problem-based learning investigation concerning use of genetic Removed the Highlight box on biofilms and incorporated modification of microbes to reduce the amount of waste paper in pertinent information into this chapter and into Chapter 6, landfills) including a new figure on quorum sensing Added fill-in Concept Mapping exercise on aerobic respiration Enhanced discussions of flagella and cilia structure and function, definition of endotoxin, comparison of and contrast between the outer and cytoplasmic membranes of Gram-negative cells, 6 Microbial Nutrition and Growth movement across cell membranes, and chemistry and function New chapter opener case study and photo of lipids in archaeal cytoplasmic membranes Two other new photos (6.13, 6.24b) Clarified that endotoxin refers to lipopolysaccharide (LPS), which Six figures revised for greater clarity and better pedagogy (6.4, 6.6, contains the toxic molecule lipid A 6.8, 6.17, 6.21, 6.24) Added Clinical Case Study: The Big Game about strep throat Removed the Highlight box on sulfur-metabolizing microbes in Added fill-in Concept Mapping exercise on bacteria cell wall Yellowstone’s springs structure One new figure on quorum sensing (6.7) vii A02_BAUM7206_05_SE_FM.indd 7 12/1/16 8:24 PM  viii Chapter-by-Chapter Revisions Expanded discussions of singlet oxygen and superoxide radicals Removed the Highlight box on healthy processing of sushi as oxidizing agents, the nature of extracellular matrix in biofilms, Material from the Highlight box on the overuse of antimicrobial and quorum sensing soaps into new Solve the Problem learning exercise Clarified the method of counting microbes using a cell counter Revised definition of heavy-metal ions Added fill-in Concept Mapping exercise on culture media Updated coverage of techniques for deactivating prions; thimerosal in vaccines; and activity of AOAC International in 7 Microbial Genetics developing disinfection standards Added critical thinking question concerning salmonellosis New chapter opener case study and photo pandemic from smoked salmon Upgraded 20 figures for greater clarity, accuracy, ease of reading, New Solve the Problem: How Clean is Too Clean? (problem- and better pedagogy (7.1, 7.5b, 7.6, 7.7, 7.8, 7.9, 7.10, 7.11, 7.13, 7.14, 7.20, based learning investigation concerning the potential overuse of 7.21, 7.22, 7.26, 7.27, 7.28, 7.32, 7.34, 7.35, 7.36) household and industrial disinfectants) Removed the Highlight box on RNA interference Added fill-in Concept Mapping exercise on use of moist heat in Updated and expanded text covering DNA replication, the smallest microbial control cellular genome at 112,091 bp (Candidatus Nasuia deltocephalinicola), alternative splicing in eukaryotes, the recent discovery that  Controlling Microbial Growth in the Body: chloroplast chromosomes are linear rather than circular, and the 10 Antimicrobial Drugs use of methylation in mismatch repair Increased discussion of use of RNA as enzymes (ribozymes) New chapter opener case study and photo Expanded table comparing and contrasting DNA replication, Seven figures revised for greater clarity, accuracy, ease of reading, transcription, and translation and better pedagogy (10.2; 10.3; 10.4; 10.6; 10.7; 10.15; map of Added discussion of codon and tRNA for 21st amino acid, worldwide community-associated MRSA) selenocysteine Three other new photos (box showing antimicrobial drug capsules, Enhanced and clarified discussion of lac and trp operons and of Figure 10.10, clinical case study on opportunistic thrush) the action of cAMP and CAP as activators Removed the Highlight box on reasons microbes make Expanded and reorganized discussion of DNA repair systems antimicrobials Clarified events in conjugation, particularly with Hfr cells Updated and revised tables of antimicrobials to include all new Expanded and clarified coverage of nucleotides and antimicrobials mentioned in disease chapters, including the pyrophosphate (diphosphate) antibacterial capreomycin and the anthelmintic bithionol; updated Revised the chapter to better explain differences between archaeal, sources of drugs, modes of action, clinical considerations, and bacterial, and eukaryotic genetics methods of resistance Added fill-in Concept Mapping exercise on point mutations New Clinical Case Studies: Antibiotic Overkill, concerning opportunistic candidiasis, and Battling the Enemy, concerning semisynthetic antimicrobials and diffusion susceptibility testing 8 Recombinant DNA Technology Enhanced and clarified discussion of the action and importance New chapter opener case study and photo of aminoacyl-tRNA synthetases; topical antibiotic mupirocin; Added six Learning Outcomes concerning uses of synthetic the mechanism of resistance against quinolone antibacterial nucleic acids, PCR, fluorescent in situ hybridization (FISH), drugs; adverse effects of aminoglycosides; therapeutic index functional genomics, Sanger sequencing, and next-generation andtherapeutic range; and adverse effects of gramicidin sequencing Removed mention of amantadine as a treatment for influenza A One other new figure (8.10) New section on drugs that interfere with the charging of tRNA Modified Figure 8.7 for better pedagogy molecules, including one new Learning Outcome on action of Deleted figures for Southern blots and Sanger automated mupirocin DNA sequencing, as these techniques are more historical than Added fill-in Concept Mapping exercise on resistance to current antimicrobial drugs Removed the Highlight box on edible vaccines and added its material to the text 11 Characterizing and Classifying Prokaryotes Enhanced or added discussion of real-time PCR (RT-PCR); Sanger New chapter opener case study and photo sequencing methods; next-generation DNA sequencing (NGS), Two new Learning Outcomes addressing epsilonproteobacteria including pyrosequencing and fluorescent methods; functional and zetaproteobacteria genomics; microbiomes; biomedical animal models; and successful Ten new photos [11.1 (2), 11.2a, 11.5, 11.11a, 11.17, 11.19, 11.21, 11.23, gene therapies 11.27b] Added Beneficial Microbes box: Our Other Organ on the Seven figures revised for better pedagogy (11.1, 11.4, 11.6, 11.10, sequencing and identification of human microbiomes 11.21, 11.26, 11.27) Added fill-in Concept Mapping exercise on recomb