Clinical Microbiology Procedures Handbook Volumes 1-3

2701 Pages·2010·155.211 MB·English

by  Garcia, Lynne Shore, Isenberg, Henry D

THIRD EDITION
Clinical
Microbiology
Procedures
Handbook
E D l TO R l N C H I E F, Third Edition and 2007 Update
Lvnne S. Garcia

4
LSG & Associates, Santa Monica, California
E D I TO R I N C H I E F, Original and Second Editions
Henry D. Isenberg
(Deceased)
ASM
PRESS
Washington, DC
Address editorial correspondence to ASM Press, 1752 N St., N.W., Washington, DC
20036-2904, USA
Send orders to ASM Press, P.O. Box 605, Hemdon, VA 20172, USA
Phone: [phone]
Fax: [phone]
E-mail: [email protected]
Online: http://estore.asm.org
Copyright 0 2010 ASM Press
American Society for Microbiology
1752 N St., N.W.
Washington, DC 20036-2904
Library of Congress Cataloging-in-PublicationD ata
Clinical microbiology procedures handbook.-3rd ed. / editor in chief, third edition and
2007 update, Lynne S. Garcia.
p. ; cm.
“Editor in chief, original and second editions Henry D. Isenberg.”
Includes bibliographical references and index.
ISBN- 13: 978-1-55581 -527-1
ISBN- 10: 1-55581 -527-8
1. Diagnostic microbiology-Laboratory manuals. I. Garcia, Lynne Shore.
11. Isenberg, Henry D.
[DNLM: 1. Microbiological Techniques-methods-Laboratory Manuals.
WQ 25 C6415 20101
QR67.C555 2010
6 16.9’041 4 ~ 2 2
2010014355
10 9 8 7 6 5 4 3 2 1
All rights reserved
Printed in the United States of America
Dedication
We dedicate the third edition of the Clinical Microbiology Procedures
Handbook to Henry D. Isenberg. Henry was a pioneer in clinical
microbiology who spearheaded the field of microbial diagnosis for more
than a half century. He was a gifted mentor, scholar, and scientist who
inspired several generations of clinical microbiologists. We are very
fortunate to have worked with such an outstanding microbiologist and
colleague.
Disclaimer
Microbiological analysis of clinical specimens is a constantly changing discipline;
new methods and technologies emerge. The contributors to the third edition of
CMPH believe that the procedures and guidelines suggested here are from reliable
sources and in line with the practices accepted at the time of publishing. Readers
are reminded that the naming of any specific product is not intended as an endorse-
ment of that specific product by ASM Press or any other agency, nor is it a sug-
gestion to exclude other equally acceptable products. CMPH is for laboratory use
only by qualified, experienced individuals or by personnel under the direct super-
vision of qualified, experienced individuals. Every effort has been made to ensure
that the contents of this update are comprehensive, accurate, reliable, and repro-
ducible.
xxix
How To Use This Handbook
General Format
The third edition of this handbook has been divided into three volumes containing
the front matter, 16 sections (composed of “procedures”), and an index. Volume 1
contains the front matter of the handbook plus sections 1 through 4. Volume 2
contains sections 5 through 9. Volume 3 contains sections 9 through 16 and the
index.
Included at the front of each volume is a short table of contents listing the items
contained in the front and back matter and the 16 sections of the handbook. In
addition to the table of contents for the entire handbook, each section is immediately
preceded by a detailed table of contents for that section, giving the section editors’
names, the procedure titles included in that section, and the authors’ names for each
procedure.
Sections
The content of the handbook has been organized into 16 sections as follows:
Section 1: Procedure Coding, Reimbursement, and Billing Compliance
Section 2: Specimen Collection, Transport, and Acceptability
Section 3: Aerobic Bacteriology
Section 4: Anaerobic Bacteriology
Section 5: Antimicrobial Susceptibility Testing
Section 6: Aerobic Actinomycetes
Section 7: Mycobacteriology and Antimycobacterial Susceptibility Testing
Section 8: Mycology and Antifungal Susceptibility Testing
Section 9: Parasitology
Section 10: Viruses and Chlamydiae
Section 11 : Immunology
Section 12: Molecular Diagnostics
Section 13: Epidemiologic and Infection Control Microbiology
Section 14: Quality Assurance, Quality Control, Laboratory Records, and Water
Quality
Section 15: Biohazards and Safety
Section 16: Bioterrorism
Procedures
Each section listed above consists of procedures. The procedures have been num-
bered and are referred to by number in cross-references in the text. The procedure
number consists of the section number plus the number of the procedure (plus the
number of a subprocedure if applicable). For example, “procedure 5.6” is the sixth
procedure in section 5; “procedure 7.4.2” is the second subprocedure of the fourth
procedure in section 7.
xvii
xviii How To Use This Handbook
Page Numbers
The page number within a procedure is the procedure number followed by the
number of the page within the procedure. Thus, from the examples given above,
“page 5.6.10” is the 10th page within procedure 5.6, and “page 7.4.2.3” is the 3rd
page within procedure 7.4.2. In all cases, the last number is the page number within
a procedure.
The index is numbered beginning with an “I” followed by the number of the
page within the index. For example, “page 1.3” is the third page in the index.
Preface
T
he third edition of the Clinical Microbiology Procedures Handbook
i
(CMPH) is based on the value and user requirements following the first and
second editions of CMPH, the companion volume Essential Procedures for
Clinical Microbiology, and the 2007 update of the second edition.
Almost all of the sixteen sections of the second edition of CMPH have been
revised and updated; sections that did not require extensive revision will be updated
during the next cycle of changes.
The purpose of the third edition of CMPH remains constant. That is to provide
everyone engaged in the microbiological analysis of clinical specimens with pro-
cedures that will enable them to correctly perform the appropriate tasks. CMPH
remains a cookbook that provides step-by-step descriptions of the numerous pro-
cedures used by workers at the bench.
As with the second edition of CMPH and the 2007 update of the second edition,
there is increased emphasis on molecular approaches, bioterrorism, infection control
in medical facilities, and the host’s immunological responses to microbial chal-
lenges. Also, continued emphasis is placed on the need to respond to governmental
regulations and fiscal constraints. Highly experienced workers with many years of
bench experience have written these procedures, and the format adheres to CLSI
document GP02-5A (5th ed., 2006).
All procedures have been reviewed extensively by section editors, the editor in
chief, and the ASM Press editors. We continue to encourage the users of these
documents to bring new methods of universal relevance to our attention so they
can be incorporated into the next update and shared with the clinical microbiology
community.
Readers are reminded that naming any specific product in CMPH is not intended
as an endorsement of that specific product or a suggestion to exclude other equally
acceptable products. CMPH is for laboratory use only by qualified, experienced
individuals or by personnel under the direct supervision of qualified, experienced
individuals. Every effort has been made to ensure that the contents of this update
are comprehensive, accurate, reliable, and reproducible.
Not all existing microbiological protocols are included; however, the editors and
authors are familiar with all commonly used protocols. As newer protocols become
more widely accepted and used, they will be incorporated into future CMPH re-
visions.
The third edition of CMPH is available in print, on CD, and as a downloadable
PDF.
Lynne S. Garcia
xxiii
J
Contents
VOLUME 1
Editorial Board ix
Contributors xi
How To Use This Handbook xvii
Abbreviations xix
Preface wciii
Acknowledgments xxv
Reader Response Form wcvii
Disclaimer mix
Procedure Coding, Reimbursement, and Billing Compliance 1. O. 1
Specimen Collection, Transport, and Acceptability 2.0.1
Aerobic Bacteriology 3.0.1
Anaerobic Bacteriology 4.0.1
VOLUME 2
Antimicrobial Susceptibility Testing 5.0. I
Aerobic Actinomycetes 6.0.1
Mycobacteriology and Antimycobacterial Susceptibility Testing 7.0.1
Mycology and Antifungal Susceptibility Testing 8.0.1
Parasitology 9.0.1
VOLUME 3
10 Viruses and Chlamydiae 10.0.1
11 Immunology 11. O. 1
12 Molecular Diagnostics 12.0.1
13 Epidemiologic and Infection Control Microbiology 13.0.1
14 Quality Assurance, Quality Control, Laboratory Records, and
Water Quality 14.0.1
15 Biohazards and Safety 15.0.1
16 Bioterrorism 16.0.1
INDEX 1.1
vii
1 Procedure Coding,
SECTION
Reimbursement, and Billing
Compliance
Alice S. Weissfeld
SECTION EDITOR:
Vickie S. Baselski
ASSOCIATE SECTION EDITOR:
1.1. Introduction
Alice S. Weissfeld and Vickie S. Baselski ........................................... .l.1 .1
1.2. Procedure Coding, Reimbursement, and Billing Compliance
Alice S. Weissfeld and Vickie S. Baselski ........................................... .1.2.1
1.0.1
1.1 Introduction
When the first edition of this handbook biology laboratories is provided for back- President. Statutes form the basis for sub-
was published, regulatory billing compli- ground. This may be reviewed in detail in sequent regulations that are rules estab-
ance for laboratory tests was not a major the Institute of Medicine’s report Medi- lished by a federal agency in response to
laboratory issue. Most hospital laborato- care Laboratory Payment Policy, Now its interpretation of a statute that it is its
ries generally performed services for their and in the Future (2). The history of re- duty to enforce. A number of federal agen-
own inpatients (and, occasionally, affili- imbursement and compliance begins with cies are directly or indirectly involved
ated outpatients), and tests were billed ac- Title XVIII, commonly known as the So- with laboratory reimbursement and com-
cording to a formula established by the cial Security Act. This act outlines the pliance. The CDC is responsible for the
business office. In the setting of prospec- principles of the Medicare program, spec- scientific and quality aspects of laboratory
tive payment (e.g., diagnosis-related ifying broad benefit categories, including testing under the Clinical Laboratory Im-
groups), payment credit was allocated physician and hospital services. In accor- provement Act (1967) and Clinical Labo-
based on a different formula. Today, how- dance with section 1862 (a)(l)(A), the ratory Improvement Amendment (CLIA)
ever, microbiologists must be aware not Medicare program provides payment only (1988). The CDC is advised in this process
only of the scientific basis of infectious- for diagnostic laboratory tests “that are by the Clinical Laboratory Improvement
disease diagnostics but also of the costing, reasonable and necessary for the diagnosis Advisory Committee. The Food and Drug
coding, billing, and reimbursement for in- or treatment of illness or injury.” It does Administration (FDA) is responsible for
dividual tests for patients seen in a broad not, however, authorize payment for new product clearance and, since 2003, for
spectrum of health care settings with cov- screening diagnostic services. Over the en- test complexity categorization under
erage by an enormous number of health suing 35 years since Title XVIII became CLIA. Medicare regulators have histori-
care plans. Jargon previously unknown in law, the interpretive determination of cally interpreted tests that are subject to
the clinical laboratory, such as reflex test- whether a test meets the criteria of being FDA approval or clearance but that have
ing, upcoding, downcoding, local cover- reasonable and necessary to justify pay- not obtained, such as “not reasonable or
age decision (LCD), and national cover- ment by Medicare has become known as necessary” for payment purposes. The
age decision (NCD), is now so extensive “medical necessity.” Most other third- FDA is assisted by its Microbiology Medi-
that a glossary of common terminology is party payers have established similar pay- cal Device Advisory Committee. The
included in this section (Appendix 1.1-1). ment guidelines with which the laboratory Centers for Medicare & Medicaid Ser-
The goal is to be reimbursed adequately must be familiar. It is notable that both vices (CMS), previously known as the
for all appropriate work performed in a Medicare and other payers may make spe- Health Care Financing Administration
manner that is in compliance with all reg- cific exceptions to allow payment for (HCFA), administers the Medicare Pro-
ulations. screening services (eg, coverage of Pap gram. CMS interprets statutes and regu-
The issues discussed in this section are smears or prostate-specific antigen test- lations and issues these interpretations
complex. In keeping with the mission of ing). In the event that a coverage policy dis- through a variety of official documents
this handbook, a model compliance pro- allows payment for a service on the basis of (e.g., The Medicare Program Integrity
cedure has been written. As with any pro- medical necessity, it is possible to transfer Manual [ 11, program memoranda and
cedure, we expect some customization to financial liability to the patient providing transmittals, and change requests) to de-
occur. The model procedure deals primar- an advanced beneficiary notice (ABN) has fine coverage criteria, establish national
ily with some of the more important reg- been properly executed which informs the limitation amounts, and establish national
ulatory principles. It should not, in any sit- patient of their financial responsibility. In coverage decisions (NCDs). CMS also
uation, take the place of guidance 2009, a laboratory-specific ABN, CMS-R- contracts with independent insurers
established by your own compliance com- 131-L, was discontinued and replaced known generically as contractors and spe-
mittee or of legal advice from your own with a generic ABN, CMS-R-131. Infor- cifically as carriers (for part B outpatient
institution’s legal counsel. It simply rep- mation may be accessed at http://www. services), as fiscal intermediaries (FIs; for
resents a starting point for review of sa- cms.hhs.gov/BNUO2~ABN.asp. part A inpatient services or part B services
lient issues. The Social Security Act is known as a through part A providers), and, more re-
A brief historical overview of the eco- statute, i.e., a piece of legislation voted cently, as Medicare administrative con-
nomic challenges faced by clinical micro- into law by Congress and signed by the tractors (MACs; for part A and part B ser-
1.1.1