microbial control and identification · microbial control and identification strategies methods...

MICROBIAL CONTROLAND

IDENTIFICATION

www.pda.org/bookstore

Microbial Controland Identification

Strategies

Methods

Applications

Dona Reber and Mary GriffinEditors

PDABethesda, MD, USA

DHI Publishing, LLCRiver Grove, IL, USA

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To order this book, please visit: go.pda.org/MCID

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ISBN: 978-1-942911-27-2Copyright © 2018 Dona Reber and Mary GriffinAll rights reserved.

All rights reserved. This book is protected by copyright. No part of it maybe reproduced, stored in a retrieval system or transmitted in any means,electronic, mechanical, photocopying, recording, or otherwise, withoutwritten permission from the publisher. Printed in the United States ofAmerica.

Where a product trademark, registration mark, or other protectedmark is made in the text, ownership of the mark remains with the lawfulowner of the mark. No claim, intentional or otherwise, is made byreference to any such marks in the book. Websites cited are current at thetime of publication. The authors have made every effort to provideaccurate citations. If there are any omissions, please contact the publisher.

While every effort has been made by the publisher and the authors toensure the accuracy of the information expressed in this book, theorganization accepts no responsibility for errors or omissions. The viewsexpressed in this book are those of the authors and may not represent thoseof either Davis Healthcare International or the PDA, its officers, or directors.

This book is printed on sustainable resource paper approved by the Forest StewardshipCouncil. The printer, Gasch Printing, is a member of the Green Press Initiative and all paperused is from SFI (Sustainable Forest Initiative) certified mills.

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We dedicate this book to Cynthia Sarnoski, Ph.D., our long-timementor and advisor who offered invaluable encouragement and

support throughout the writing and editing of this book.

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CONTENTS

Foreword xiiiPreface xvAbout the Editors xvii

SECTION 1 – STRATEGIES

1 REGULATORYAND COMPENDIALGUIDANCE ON MICROBIAL IDENTIFICATION 3Tony CundellIntroduction 3Regulatory Guidelines 5Compendial Guidelines 7Detecting and Identifying Fungal Isolates from

Manufacturing Facilities 10Human Microbiome 14Panel-based Molecular Diganostics 16Strain Typing 17Whole Genomic Analysis for the Detection

and Identification of Microbial Pathogens 18Conclusions 18References 18About the Author 22

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2 MICROORGANISM IDENTIFICATIONANDITS ROLE IN CONTAMINATION CONTROL 23Jeanne MoldenhauerIntroduction 23Background 24Identification Methods 25How Does the Organism Identification Aid in Finding

a Root Cause for Contamination? 28Conclusion 39References 39About the Author 41

3 MEANINGFUL CONTAMINATIONCONTROLTRENDING INBIOLOGICAL MANUFACTURING 43Ren-Yo Forng and Jeanne MateffyPurpose 43Trending 45Process Monitoring 58Conclusion 65Case Study 66References 68About the Authors 70

4 ASSESSMENT OF MICROBIAL IMPACTFROMA LOW BIOBURDEN PERSPECTIVE 73Hilary Chan and Lynn JohnsonIntroduction 73Microbial Impact and Significance for Patient Safety

and Product Quality 78Microbial Impact Assessment Considerations 81Microbial Impact Assessment Tools 91Lifecycle Management and Quality by Design 106Summary 108References 109About the Authors 115

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5 QUALITY RISK MANAGEMENT INTHECONTEXT OFVIRAL CONTAMINATION 117Consortium on Adventitious Agent Contamination inBiomanufacturing (CAACB)Introduction 117Use of QRMTools 124Initiation of Risk Management Process 146Risk Assessment 149Risk Control 153Result of Risk Management Process 156Risk Review 161References 161About the CAACB 163

6 TRENDING OF MICROBIOLOGICALISOLATES INTHE BIOPHARMACEUTICALENVIRONMENT 165Dona ReberRegulations and Guidelines 166Uses for EM Trending 168EM Sample Types of Monitoring Trended 172Trending Frequency 172Microbial Identification Strategy 174Steps in Isolate Trending 176Conclusion 191References 191About the Author 194

7 BURKHOLDERIA CEPACIA COMPLEX:CHARACTERISTICS, PRODUCT RISK,ANDTESTINGASSESSMENTS 197Tim SandleIntroduction 197Organism Characteristics 199Origins in Pharmaceutical and Healthcare 200Potential Risk to Patients 203FDA Alert and the Testing Debate 204Testing Scope 212

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Tests for BCC 212Assessment of Test Data 216Summary 219References 220About the Author 228

SECTION 2 – METHODOLOGIES

8 OVERVIEW OF CONVENTIONALANDEMERGING MICROBIAL IDENTIFICATIONMETHODS 231Frank E. Matos and Jennifer R. ReyesIntroduction 231Microbial Identification: What Method to Use 232Isolation of Microorganisms in Pure Culture 234Methods for Characterization and Preliminary Screening 235Phenotypic Methods for Microbial Identification 241Fatty Acid Analysis Using the Midi Sherlock® 246MALDI-TOF 248Genotypic Methods for Bacterial Identification 249Ribotyping 254Identification of Fungi 258Molecular Methods for Fungal Identification 265Use of Contract Laboratories for Microbial Identification 268Conclusion 269References 269About the Authors 273

9 QUALIFICATIONAND IMPLEMENTATIONOF MALDI-TOFTECHNOLOGY FOR USEINA QUALITY CONTROL LABORATORY 275Jennifer R. Reyes, Frank E. Matos and Gary KruppaIntroduction: Microbial Identification Using MALDI-TOF

Mass Spectrometry 276In-House Evaluation 285Qualification Activities 287Improvements 293Routine Use Activities 295References 298About the Authors 301

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10 TESTING FOR MYCOPLASMAIN BIOTHERAPEUTICS 303Houman Dehghani and Martina KoppIntroduction 303General Biology of Mycoplasma 304Regulatory Guidelines 306Traditional Testing Methods for Mycoplasmas 307Emerging Rapid Testing Methods for Detection

of Mycoplasma 309Conclusion 315References 315About the Authors 317

11 VIRUS DETECTIONANDTESTING METHODS 319Cassandra L. Braxton and Maria M. BednarIntroduction 319Key Elements 320Adventitious Virus Detection 323New Rapid Molecular Methods 328AdvancedVirus Detection Using NGS 330Challenges of NGS in a Biopharmaceutical Setting 346NGS Regulatory Guidance 349Conclusion 351References 352About the Authors 360

12 DATA INTEGRITY IN THE LABORATORY 361Jeanne MoldenhauerIntroduction 362What are Data? 363Requirements for Data Integrity 363Data Pedigree 364Regulatory Expectations for Data Integrity 365Difficulties in Having Complete Data 366Evaluating Data Integrity in the Laboratory 367Triggers for Checking Data Integrity in the Laboratory 369The Effect of Personnel Behavior on Data Integrity 375Conclusion 376References 376About the Author 377

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SECTION 3 – APPLICATIONS

13 DISINFECTANT PERFORMANCEAGAINSTFUNGI,VIRUSESAND BACTERIA 381James Polarine, Jr., David Shields, and Jennifer LoughmanIntroduction 381Disinfectant and Sporicide Activity against Fungal Spores 382Disinfectant and Sporicide Activity against Viruses 391Disinfectant and Sporicide Activity against Bacteria 393Conclusion 400References 401About the Authors 403

14 ENVIRONMENTAL ISOLATES INPHARMACEUTICAL MANUFACTURING 405Angel L. Salamán-ByronIntroduction 405Regulatory and Compendia Guidance 406Evaluation and Selection of EIs 409Application EIs in Pharmaceutical Test Methods 421Conclusion 426References 427About the Author 438

15 MANAGING STOCK CULTURES 439Vanessa Vasadi-FigueroaIntroduction 439Applications and Use 440Top Six Lineup 441Culture Libraries 442Handling 443Storage Methods 444Cryopreservation 446Lyophilization 448Culture Recovery 449Market Availabilities 452Documentation and Inventory Management 454Conclusion 454References 455About the Author 456

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16 COMPETENCY-BASEDTRAININGAPPROACHFOR MICROBIAL IDENTIFICATIONS 457Edward S. Balkovic and Gary C. du MoulinScope of Microbiology Based Training 461Expectations for Establishing the Training Program 462Expectations for Those Participating in the Training Program 466Training Material Development 469Training Phase – Process 474Training Phase – Task Specific Considerations 478Assessment Phase 484Summary 486References 487About the Authors 491

17 MOLD CONTAMINATION IN THEPHARMACEUTICAL INDUSTRY 493Brian G. Hubka and Jeanne MoldenhauerWhat is Mold? 493Why do I Care About Mold? 494Criteria for Mold Growth 499Mold Detection and Identification 501Setting Limits for Mold Contamination 509Mold Remediation Methods 511Mold Prevention Methods 514References 517About the Authors 520

18 KEY FEATURES OFA BIOSAFETY PROGRAMFORTHE BIOPHARMACEUTICAL INDUSTRY 523Jessica AvizinisRelevance of Biosafety to Drug Development,

Manufacturing and Testing Operations 524The Importance of Biosafety: Impacts of Exposure 527Key Features of a Biosafety Program 530Future Biopharmaceutical Biosafety – Special Challenges 560Conclusion 561References 562About the Author 567

Index 569

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FOREWORD

Many years have gone by since I first dabbled in microbiology,specifically as it relates to the manufacture of medical products andthe impact microbiology has upon the pharmaceutical industryworldwide. I would have greatly appreciated being better versedback in those days with Strategies, Methods, Applications, all topicsthat remain to be within our focus and scientific realm of interest.

The book’s stable of authors are subject matter experts, worldrenowned and highly respected microbiologists in their respectivefield of science. That said, you will appreciate reading their depthand breadth of experience regarding current microbiologicalchallenges. For example, Cundell, Moldenhauer, Mateffy andSandle provide their perspectives on strategies that you will findworthy of your consideration.

The microbiological control and identification as well asmicrobiological assessment are areas that we all, and quite rightlyso, continue to focus our energies and resources. Part and parcelwith microbial identification includes trending of the microbial dataand corrective measures that may need to be implemented topreclude and/or reduce the presence of microbial and bacterialendotoxin contamination. We all appreciate an inability to escape

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from having a scientific discussion without including some form ofrisk assessment and risk management, which is no less importantwith regards to viral inactivation. I dare say you will find thechapter worthy of your read.

The rapid microbiological methods (e.g., MicroSEQ®, MALDI-TOF) are more common place in todays’ laboratories and a far cryfrom someone who used to prepare a sea of the biochemicals,micro-bial test reagents, poured a river of agar plates and yes,indeed I washed my share of test tubes. The chapter includeslaboratory equipment qualification considerations that historicallymay have not been performed by the laboratory staff. The readerwill find it rewarding as they come to better understand and betterappreciate how the equipment qualification can impact themicrobiological results.

There is a subject that has captured much of our time and to anotable extent has stretched precious resources. JeanneMoldenhauerprovides welcomed guidance and perspectives on this subject, DataIntegrity, which youwill findworthy of consideration to address andimplement the necessary measures to preclude the accidental orunintentional deletion or omission of microbiological data.

I continue to assess how well a company understands themicrobiological impacts upon the manufacturing processes.Irrespective of whether the commodity is sterile or non-sterile, acomprehensive microbiological assessment is value added to anymanufacturing operation. Equally important, which all have heardme say throughout the years, did the comprehensive assessmentsinclude a Microbiologist at the discussion table during theevaluation and implementation process. The individual topicswithin the text are of welcomed value to any organization. Thatsaid, when considering the Strategy, Methods and Applications,collectively, I would point out that is not unlike how I might possiblyassess a medical products manufacturer.

Thomas J. AristaJune 14, 2018

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PREFACE

It has been six years since we edited our initial volume on MicrobialIdentifications: The Keys to a Successful Program for the PDA and DHIPublishing, LLC. Microbial identification continues to evolve withnew technologies and expectations, yet remains so fundamental tomicrobial control of quality biopharmaceutical products.

We decided it was the perfect time to once again bring togethera group of expert microbiologists and biopharmaceutical industryleaders to discuss microbial identifications in a new light, that ofhow microbial identification knowledge is a cornerstone in theconcept of microbial and contamination control programs. Thechapters show how microbial control programs for our facilities,equipment and personnel result in a positive impact on ourproducts and ultimately our patients.

Some of these authors were included in our initial volume andwe welcome them back for their continued support and excellentand informative chapters: Drs. AnthonyM. Cundell, JeanneMolden-hauer, Martina Kopp and Houman Dehghani. The remainingauthors are new for us, but not to our industry by anymeans – all are

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well known for their expertise, and we are very pleased that theyhave joined us here. Please open the book and you will most likelyrecognize some of these authors, others are newcomers to writingchapters, and we are delighted they all rose to the challenge.

This book has three sections: Strategies, Methods andApplications. Strategies cover regulations and regulatoryexpectations as well as strategies for trending, risk assessments, andrisk management. Methods include current best practicemicroorganism identification methods, both conventional andemerging rapid methods for bacteria, viruses, mycoplasma andfungi. Applications include microbiology laboratory training foridentifications, use of environmental and control microorganisms,disinfectant effectiveness and best practices, and an up and comingchapter subject, biosafety for laboratories, manufacturing facilitiesand personnel.

It is recognized that each author has taken time from his or hervery busy schedules and free time because of a passion formicrobiology and microbial control, and with it the desire to shareknowledge with others in our industry. This is very muchappreciated by us. We also share this passion and dedication asevidenced by our many years of working and presenting onmicrobiological issues.

This text will provide valuable information for the new micro-biologist as well as a reference for well-seasoned professionals. Wesincerely hope you enjoy the book.

Dona Reber and Mary GriffinJune 2018

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ABOUT THE EDITORS

Dona Reber has more than 25 years of academic and industrialmicrobiology experience, including developing and implementingcontamination control strategies for aseptic/non aseptic manu-facturing, microbiology testing/development, and managing/networking microbiology laboratories. She is Senior Manager ofMicrobiology and Aseptic Support, Global Quality Operations forPfizer, responsible for assessing aseptic processing facilities,investigations, troubleshooting, and developing policy documentsfor microbiology.

Dona holds B.S. and M.S. degrees in related sciences, is (SM)NCRM certified, has been a PDA member for 20+ years, and alongtime chair of the Pharmaceutical Micro Expert DiscussionGroup. She has numerous publications on microbial identificationssystems, environmental monitoring and microbiology riskassessments. She has co-authored three PDA Technical Reports:TR#13, Fundamentals of an Environmental Monitoring Program;TR#67, Exclusion of Objectionable Microorganisms from NonSterile Pharmaceutical, Medical Devices and Cosmetics; and TR#70,

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Fundamentals of Cleaning and Disinfection. She is on a PDA TaskForce for Low Bioburden Environmental Monitoring. She hasparticipated in instructing new FDA inspectors, and is an instructorfor the PDA on TR#13, Fundamentals of an EM Program. Shepresented at the most recent PDA Micro Conference onenvironmental monitoring for low bioburden processes.

Mary Griffin, Principal, MG Quality Microbiology Consulting,LLC, is a subject matter expert in microbiology with more than 35years of academic (University of Michigan; University ofMassachusetts) and global biopharmaceutical experience.

She initiated and directed the Quality Control Microbial Scienceand Technology department at Pfizer (previously Wyeth, Andover,MA) during a period of significant growth. She adapted herextensive knowledge of microorganisms and classical identificationtechniques to successfully implement both identification and rapidautomated detection systems to keep the facility on the cutting edgeof novel technologies.

She continues to support the industry as a consultant throughthe application of her microbiological identification and rapidtechnologies expertise for microbial control. She holds a M.S. degreein Microbiology and is certified as a Specialist Microbiologist SM(NRCM). She is an active member of the Parenteral DrugAssociation (New England Chapter) and is published in thepharmaceutical industry.

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