ASTM E2048-99
(Guide)Standard Guide for Detection of Nucleic Acids of the Mycobacterium Tuberculosis Complex and Other Pathogenic Mycobacteria by the Polymerase Chain Reaction Technique
Standard Guide for Detection of Nucleic Acids of the Mycobacterium Tuberculosis Complex and Other Pathogenic Mycobacteria by the Polymerase Chain Reaction Technique
SCOPE
1.1 This guide covers basic considerations, criteria, principles and recommendations that should be helpful when developing, utilizing, or assessing PCR-specific protocols for the amplification and detection or identification of mycobacterial nucleic acids. This guide is not a specific protocol for the detection of specific mycobacteria. It is intended to provide information that will assist the user in obtaining high quality and reliable data. The guide is closely related to and should be used concurrently with the general PCR Guide E 1873.
1.2 This guide has been developed for use in any molecular biology or biotechnology laboratory. It may be useful for the detection of mycobacteria in clinical, diagnostic laboratories.
1.3 This guide does not cover details of the various methods such as gel electrophoresis that can be utilized to help identify PCR-amplified mycobacterial nucleic acid sequences, and it does not cover details of instrument calibration.
1.4 This guide does not cover specific variations of the basic PCR or RT-PCR technology (for example, quantitative PCR, multiplex PCR and in situ PCR), and it does not cover details of instrument calibration.
1.5 Warning-Laboratory work involving certain clinical specimens and microorganisms can be hazardous to personnel. Precaution: Biosafety Level 2 facilities are recommended for potentially hazardous work, and Biosafety Level 3 facilities are required for propagating and manipulating Mycobacteria tuberculosis cultures (). Safety guidelines should be adhered to according to NCCLS M29-T2, I17-P and other recommendations ().
General Information
Relations
Standards Content (Sample)
NOTICE: This standard has either been superseded and replaced by a new version or withdrawn.
Contact ASTM International (www.astm.org) for the latest information
Designation: E 2048 – 99
Standard Guide for
Detection of Nucleic Acids of the Mycobacterium
Tuberculosis Complex and Other Pathogenic Mycobacteria
by the Polymerase Chain Reaction Technique
This standard is issued under the fixed designation E 2048; the number immediately following the designation indicates the year of
original adoption or, in the case of revision, the year of last revision. A number in parentheses indicates the year of last reapproval. A
superscript epsilon (e) indicates an editorial change since the last revision or reapproval.
INTRODUCTION
This guide covers detection of nucleic acids (deoxyribonucleic acid (DNA) or ribonucleic acid
(RNA)) of mycobacteria and specific identification of the Mycobacterium tuberculosis complex
(MTBC,whichincludes M. tuberculosis, M. bovis, M. microtiand M. africunum), M. avium, M. leprae
and M. intracellulare nucleic acids by the polymerase chain reaction (PCR) technique.
PCR is a widely known molecular biology procedure that involves the amplification of a piece of
DNAby as much as a million-fold over the course of several hours. It is also possible to use PCR to
detect RNAby first copying RNAwith the enzyme reverse transcriptase to produce a complementary
DNA molecule, which is then amplified by PCR; the combined process is known as RT-PCR. The
amplified DNA fragments can then be detected, identified and quantitated by classical procedures of
biochemistry/molecular biology. As few as only several molecules of DNA in a biological test
specimen can be rapidly and accurately identified. PCR is used as a tool in molecular biology
laboratories for basic and applied research, in clinical laboratories to aid in the diagnosis of genetic,
neoplastic and infectious diseases, and in biotechnology laboratories for the preparation of biotech-
nology products and to test for contaminants.
Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB) in humans, and TB
isoneoftheleadingcausesofhumandeathintheworld(1,2) .Aboutonethirdofthepresentworld’s
population is infected with MTB (1). The definitive test for tuberculosis, isolation and specific
identification of MTB in culture, requires several weeks. Microscopic examination of acid-fast smears
is rapid, but non-specific and relatively insensitive. The value of using PCR or other DNA/RNA
amplification procedures for TB diagnosis is rapidity; clinical specimens can be evaluated within a
day. Thus, patient care and treatment can be initiated more rapidly when a specific diagnosis has been
determined.
This guide was developed byASTM in collaboration with DIN (German Institute for Standardiza-
tion) Subcommittee E3/E9 on Molecular Biological Detection of Mycobacteria, Department for
Medical Standards (NAMed). It is recommended that this mycobacteria-specific PCR guide be used
in conjunction withASTM’s general PCR Guide E 1873.The combination of the two guides provides
recommendations, basic considerations, criteria, and principles that should be employed when
developing, utilizing or assessing PCR-specific protocols for the detection of the DNA or RNA of
specific mycobacteria.
This guide assumes a basic knowledge of microbiology and molecular biology. It assumes the
availability of, and the ability to search the literature for, mycobacteria target-specific PCR protocols.
1. Scope
1.1 This guide covers basic considerations, criteria, prin-
ciples and recommendations that should be helpful when
developing, utilizing, or assessing PCR-specific protocols for
ThisguideisunderthejurisdictionofASTMCommitteeE48onBiotechnology
and is the direct responsibility of Subcommittee E48.02 on Characterization and
the amplification and detection or identification of mycobacte-
Identification of Biological Systems.
rial nucleic acids. This guide is not a specific protocol for the
Current edition approved October 10, 1999. Published January 2000.
detection of specific mycobacteria. It is intended to provide
The boldface numbers in parentheses refer to the list of references at the end of
this standard. information that will assist the user in obtaining high quality
Copyright © ASTM International, 100 Barr Harbor Drive, PO Box C700, West Conshohocken, PA 19428-2959, United States.
E2048–99
and reliable data. The guide is closely related to and should be 4. Significance and Use
used concurrently with the general PCR Guide E 1873.
4.1 This guide is intended for use in any laboratory utilizing
1.2 This guide has been developed for use in any molecular
PCR or RT-PCR to amplify and detect nucleic acid sequences
biology or biotechnology laboratory. It may be useful for the
of mycobacteria from a biological preparation and to identify
detection of mycobacteria in clinical, diagnostic laboratories.
the species of origin.
1.3 This guide does not cover details of the various methods
4.2 The criteria used for the identification and evaluation of
such as gel electrophoresis that can be utilized to help identify
the amplification reactions should be administered by an
PCR-amplified mycobacterial nucleic acid sequences, and it
individual trained in the use of molecular biological and
does not cover details of instrument calibration.
microbiological techniques associated with PCR and MTB.
1.4 Thisguidedoesnotcoverspecificvariationsofthebasic
PCR or RT-PCR technology (for example, quantitative PCR,
5. Background Information about TB, MTB, Other
multiplex PCR and in situ PCR), and it does not cover details
Mycobacteria, and Detection of Mycobacteria by PCR
of instrument calibration.
5.1 The mycobacteria are acid-fast, non-motile, rod-shaped,
1.5 Warning—Laboratory work involving certain clinical
aerobic bacteria that do not form spores. They contain several
specimens and microorganisms can be hazardous to personnel.
species pathogenic to humans. The primary human pathogens
Precaution: Biosafety Level 2 facilities are recommended for
are members of the Mycobacterium tuberculosis complex (M.
potentiallyhazardouswork,andBiosafetyLevel3facilitiesare
tuberculosis, M. bovis, M. africanum and M. microti) and M.
required for propagating and manipulating Mycobacteria tu-
leprae. Other mycobacteria, such as the M. avium complex (M.
berculosis cultures (3). Safety guidelines should be adhered to
avium and M. intracellulare) and M. kansasii, cause disease in
according to NCCLS M29-T2, I17-P and other recommenda-
immunocompromised individuals.
tions (3).
5.2 Tuberculosis has been a major public health problem in
2. Referenced Documents
the world for many centuries, particularly in overcrowded city
areas. In the 18th and 19th centuries, TB was responsible for a
2.1 ASTM Standards:
E 1873 Guide for Detection of Nucleic Acid Sequences by quarter of all adult human deaths in European cities (4).
Severalpublichealthmeasuresthatfinallyledtoaconsiderable
the Polymerase Chain Reaction Technique
2.2 NCCLS Standards: improvement include the pasteurization of milk, and the
antibiotics streptomycin (introduced in 1944) and
M29-T2 Protection of Laboratory Workers from Infectious
Disease Transmitted by Blood, Body Fluids, and Tissue- p-aminosalicylic acid (introduced in 1946) (4). However, the
emergenceofdrug-resistantMTBstrainsisbecomingaserious
Second Edition; Tentative Guideline
C24-A2 Statistical Quality Control for Quantitative Mea- problem. For this and other reasons,TB is presently on the rise
again and is one of the leading infectious causes of death of
surements: Principles and Definitions; Approved
Guideline-Second Edition adult humans in the world.
MM3-A Molecular Diagnostic Methods for Infectious Dis- 5.2.1 The isolation of a species from the MTBC is required
eases; Approved Guideline forthedefinitivediagnosisoftuberculosis.Routineculturesare
time-consuming and can take up to eight weeks. Microscopic
3. Terminology
examination of acid-fast smears is the most rapid method for
3.1 Basic PCR definitions apply according to the general
the detection of mycobacteria, but it is insensitive and non-
PCR Guide E 1873 (Section 3).
specific.Immunologicalandserologicaltechniquesarelimited,
3.2 Definitions of Terms Specific to This Standard:
in general, due to poor sensitivity or specificity, or both (5, 6).
3.2.1 internal control, n—in PCR, a control used to assess
Species-specific nucleic acid probes have significantly im-
the amplifiability of the reaction, that is, to determine whether
proved the opportunity for rapid confirmation of culture results
or not PCR inhibitors may be present in the reaction; for
for several mycobacterial species (7).
example, an internal control can be a synthetic DNA segment
5.3 The M. avium complex (MAC) consist of 28 serovars
that can be added to the sample prior to amplification, that is of
(subspecies) of two distinct species, M. avium and M. intrac-
similar length and base composition to the target gene se-
ellulare (8). The criteria used to distinguish M. avium from M.
quence, and that contains primer binding regions identical to
intracellularearenowwellestablished(9-11).MACorganisms
those of the target sequence.
are ubiquitous in nature and have been isolated from water,
3.2.2 restriction enzymes, n—naturally occurring proteins
soil, plants, and other environmental sources (12). These
(also called restriction endonucleases) that are purified from
organisms are of low pathogenicity and frequently colonize
bacteria and that recognize specific nucleic acid sequence
healthy individuals without causing disease. Person-to-person
patterns (sites) and cleave the nucleic acid at or near that
transmission is thought to be unlikely, but many investigators
sequence (site).
believe that pulmonary disease may result from inhalation of
infectious environmental aerosols. MAC infections have be-
come increasingly more common in the United States, and M.
For referenced ASTM standards, visit the ASTM website, www.astm.org, or
contact ASTM Customer Service at service@astm.org. For Annual Book of ASTM
avium is the most common non-tuberculous mycobacterial
Standards volume information, refer to the standard’s Document Summary page on
speciesassociatedwithhumandisease.Thegreatestincreasein
the ASTM website.
MAC infections during the past decade has been in AIDS
Available from the National Committee for Clinical Laboratory Standards, 771
E. Lancaster Ave., Villanova, PA 19085. patients for whom MAC has become the third most common
E2048–99
opportunistic disease (13). In one report, 98 % of MAC react with other mycobacteria. Clinical specimens that yielded
infections in 45AIDS patients were due to M. avium, whereas M. tuberculosis, or other non-MAC mycobacteria, when cul-
40 % of MAC infections in patients withoutAIDS were due to tured gave negative results when tested by MAC-specific PCR
M. intracellulare (14). assays. Sensitivity for MAC is generally greater than 90 %.
5.3.1 The isolation of MAC by culture is required for
6. Principle of the PCR Method
definitive diagnosis of MAC infection. However, routine cul-
6.1 See Guide E 1873 (Section 5) for a description of the
tures are time consuming and can take up to eight weeks for
PCR method.
final diagnosis. Additionally, culture does not distinguish
6.2 In addition to 6.1, the amplification of target sequences
between M. avium and M. intracellulare infection. Several of
takes place in vitro. Procedures for detection of specific
the therapeutic agents used currently in the treatment of MAC
amplified products that allow a differentiation to be made
disease have different in vitro activity against M. avium and M.
between species of the MTBC and ubiquitous mycobacterial
intracellulare (15). As additional therapeutic agents become
species should be used preferentially.
available, the ability to distinguish between M. avium and M.
intracellulare may become more important.
7. Target Material
5.4 Mycobacterium leprae, the causative agent of leprosy,
7.1 For general information see Guide E 1873 (Sections 6
remains a serious health problem worldwide (16). Diagnosis of
and 9).
M. leprae infections is a problem due to the fact that this
7.2 In addition to 7.1, for the detection of nucleic acid
organism cannot be cultured by conventional methods. Classi-
sequences of the MTBC, immediate transport of the test
cal methods of diagnosis, such as microscopic examination of
material to the laboratory is recommended. It is possible that
skin biopsies and antibody testing lack sensitivity and speci-
transport periods of >48 h can interfere with the nucleic acid
ficity (17). However, PCR can be used for rapid and sensitive
detection.
diagnosis of M. leprae infections.
7.3 Typical biological specimens for the detection of myco-
5.5 PCR has proven to be a useful procedure for the
bacteria or their nucleic acid sequences include:
detection of mycobacteria and the specific identification of the
7.3.1 Specimens Used in Biotechnology or Basic Molecular
species present. Mycobacterial DNA in a clinical sample is
Biology Research Laboratories—Cultures of mycobacteria,
typically extracted and amplified, and the PCR product is then
purified preparations of mycobacteria or mycobacterial nucleic
identified. Depending on the PCR amplification target em-
acid.
ployed, the analytic sensitivity of amplification assays ranges
7.3.2 Specimens Used in Clinical, Diagnostic Laboratories
from about 1 to 100 mycobacteria (17). Primers used in the
in the Case of Suspected MTB Infection—Respiratory sample
PCR amplification from mycobacterial genomes can be either
material (for example, sputum, bronchoalveolar lavages), gas-
species-specific or genus-specific. PCR-based tests specific for
tric juice, stomach aspirate, urine, sperm and prostatic secre-
mycobacteria have been shown to improve the rapid diagnosis
tion, puncture exudate, cerebrospinal fluid, bone marrow and
of tuberculosis and other mycobacteria-caused diseases by
biopsy material (tissues).
allowing the direct detection of mycobacteria in clinical
7.4 Methods currently used for extraction of the target
specimens.
sequence from mycobacteria are:
5.5.1 Clinical studies have demonstrated that PCR-based
7.4.1 Alkaline Lysis—In the presence of sodium hydroxide
assays accurately detect MTB in respiratory specimens (18-
and detergent with increased temperature and subsequent
22). The specificity of these tests ranges from 95 to 100 %.
neutralization of the reaction mixture.
Furthermore, these MTB-specific tests do not cross-react with
7.4.2 Guanidium Isothiocyanate—Extraction.
other mycobacteria. Clinical specimens that yielded non-
7.4.3 Enzymatic Extraction—Of nucleic acid using protein-
tuberculosis mycobacteria when cultured gave negative results
ase K plus lysozyme or detergent treatment, or both.
when tested by MTB-specific PCR assays. The MTB PCR
7.4.4 Mechanical-Phys
...
Questions, Comments and Discussion
Ask us and Technical Secretary will try to provide an answer. You can facilitate discussion about the standard in here.