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Mycobacteria Practice Guidelines for Clinical Microbiology Laboratories

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Mycobacteria Practice Guidelines for Clinical Microbiology Laboratories PRACTICAL GUIDANCE FOR CLINICAL MICROBIOLOGY crossm Practice Guidelines for Clinical Microbiology Laboratories: Mycobacteria Betty A. Forbes,a Geraldine S. Hall,b† Melissa B. Miller,c Susan M. Novak,d Marie-Claire Rowlinson,e Max Salfinger,f Akos Somoskövi,g* David M. Warshauer,h Michael L. Wilsoni aVirginia Commonwealth University Medical Center, Richmond, Virginia, USA Downloaded from bCleveland Clinic, Cleveland, Ohio, USA cUniversity of North Carolina School of Medicine, Chapel Hill, North Carolina, USA dSouthern California Permanente Medical Group, North Hollywood, California, USA eFlorida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, USA fNational Jewish Health, Denver, Colorado, USA gSkaraborg Hospital, Skövde, Sweden h Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, USA http://cmr.asm.org/ iDenver Health, Denver, Colorado, USA SUMMARY ........................................................................................3 INTRODUCTION ..................................................................................3 Taxonomy of Mycobacteria ...................................................................3 Mycobacterium tuberculosis Complex .........................................................4 Mycobacterium tuberculosis..................................................................4 Mycobacterium bovis .........................................................................5 on April 2, 2018 by NIH Library Mycobacterium bovis BCG...................................................................5 Latent tuberculosis infection................................................................6 Mycobacterium leprae and Mycobacterium ulcerans .........................................6 Mycobacterium leprae........................................................................6 Mycobacterium ulcerans .....................................................................7 Nontuberculous Mycobacteria ................................................................7 Slowly growing nontuberculous mycobacteria frequently involved in human disease .....................................................................................9 (i) Mycobacterium avium complex ......................................................10 (ii) Mycobacterium kansasii ..............................................................11 (iii) Mycobacterium xenopi ...............................................................11 (iv) Mycobacterium malmoense..........................................................11 (v) Mycobacterium haemophilum........................................................11 (vi) Mycobacterium genavense...........................................................12 (vii) Mycobacterium marinum ...........................................................12 (viii) Mycobacterium szulgai .............................................................12 Published 31 January 2018 (ix) Mycobacterium scrofulaceum........................................................12 Citation Forbes BA, Hall GS, Miller MB, Novak Rapidly growing nontuberculous mycobacteria frequently involved in human SM, Rowlinson M-C, Salfinger M, Somoskövi A, disease....................................................................................12 Warshauer DM, Wilson ML. 2018. Practice (i) Mycobacterium abscessus and its subspecies .......................................13 guidelines for clinical microbiology (ii) Mycobacterium chelonae complex ..................................................14 laboratories: mycobacteria. Clin Microbiol Rev (iii) Mycobacterium fortuitum complex .................................................14 31:e00038-17. https://doi.org/10.1128/CMR REGULATORY REQUIREMENTS AND GUIDELINES FOR TESTING MYCOBACTERIA .....14 .00038-17. Introduction ..................................................................................14 Copyright © 2018 American Society for Clinical Laboratory Improvement Amendments ...........................................15 Microbiology. All Rights Reserved. College of American Pathologists Requirements ..........................................16 Address correspondence to Max Salfinger, International Organization for Standardization 15189 Standard ..........................16 salfi[email protected]. Statements Related to Mycobacterial Diseases from Various Professional Societies and Agencies.....................................................................................16 * Present address: Akos Somoskövi, Global Official American Thoracic Society/Infectious Diseases Society of America/Centers for Good Fund, Intellectual Ventures Laboratory, Disease Control and Prevention Clinical Practice Guidelines: Diagnosis of Tuberculosis Bellevue, Washington, USA. in Adults and Children....................................................................16 † Deceased. (continued) This review is dedicated to Gerri S. Hall, who passed away in January 2016. She was a passionate leader in the field of clinical microbiology. April 2018 Volume 31 Issue 2 e00038-17 Clinical Microbiology Reviews cmr.asm.org 1 Forbes et al. Clinical Microbiology Reviews An Official ATS/IDSA Statement: Diagnosis, Treatment, and Prevention of Nontuberculous Mycobacterial Diseases...................................................................16 US Cystic Fibrosis Foundation and European Cystic Fibrosis Society Consensus Recommendations for the Management of Non-Tuberculous Mycobacteria in Individuals with Cystic Fibrosis...........................................................16 World Health Organization ................................................................16 Healthy People 2020 ........................................................................16 Centers for Disease Control and Prevention ................................................17 Metrics.......................................................................................17 Import permit...............................................................................17 International Air Transport Association and U.S. Department of Transportation Packaging and Shipping Requirements ..................................................17 State Requirements ..........................................................................18 IDEAL ALGORITHM/ALTERNATIVE ALGORITHMS FOR TESTING SPECIMENS FOR MYCOBACTERIAL DISEASES .............................................................18 Tests for Detecting or Ruling Out Mycobacterium tuberculosis Complex Infection ......18 Downloaded from Tests for Detecting or Ruling Out NTM/Low Suspicion for TB Disease ..................21 Algorithm Summary/Frequently Asked Questions .........................................21 Can NAAT replace AFB smear? ...........................................................21 Do an AFB smear and culture need to be in the algorithm when a NAAT is performed? ..............................................................................21 When should a reflex MDR-TB screen be performed on a NAAT-positive specimen? ....21 When should identification be performed on a specimen positive for AFB? .........22 How does the algorithm change for nonrespiratory specimens? ......................22 What should be done when discrepant test results are obtained? ....................22 BIOSAFETY ......................................................................................22 http://cmr.asm.org/ Risk Assessment ..............................................................................22 Specimen Processing .........................................................................23 Decontamination and Disposal of Laboratory Waste ......................................23 WORK-UP OF SPECIMENS .....................................................................24 Acceptable Specimens and Rejection Criteria ..............................................24 Processing of Specimens for Mycobacterial Stains and Culture ..........................25 Sterile specimens ...........................................................................25 Nonsterile or contaminated specimens...................................................26 Media ..........................................................................................27 NUCLEIC ACID AMPLIFICATION TESTS.......................................................28 on April 2, 2018 by NIH Library Diagnostic .....................................................................................28 Detection of Antimicrobial Resistance ......................................................30 Infection Control .............................................................................31 SMEAR MICROSCOPY AND GROWTH DETECTION OF ACID-FAST BACILLI .............32 Diagnostic AFB Smear and Growth Detection .............................................32 AFB Smear and Growth Detection for Patient Management .............................32 AFB Smear Preparation, Fixation, Staining, and Examination .............................33 Interpretation and Reporting of Acid-Fast Smear Results .................................34 Growth Detection ............................................................................34 IDENTIFICATION ................................................................................35 Molecular Identification of Cultured Organisms ...........................................35 MALDI-TOF MS ...............................................................................36 HPLC ..........................................................................................37
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