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ASTM E1285-06

(Guide)

Standard Guide for Identification of Bacteriophage Lambda (λ) or Its DNA (Withdrawn 2014)

Standard Guide for Identification of Bacteriophage Lambda (λ) or Its DNA (Withdrawn 2014)

ABSTRACT
This guide covers laboratory characterization procedures for identifying bacteriophage lambda or its DNA and assumes that the reader has basic knowledge in virology and molecular biology. Bacteriohage lambda is a temperate bacteriophage with an icosahedral hear and a single, non-contractile tail ending in a single tail fiber. The lambda genome consists of a single molecule of linear double-stranded DNA and has cohesive ends. The naturally preferred hosts is Escherichia coli K12. Hundreds of lambda variants derived from wild type lambda can be used in biotechnology and differ in genome size and genotype. These are used primarily as DNA vectors for cloning DNA fragments. Judging uncontaminated, pure lambda should be done through restriction enzyme analysis DNA characterization and the presence and identification of lambda DNA is accomplished by polymerase chain reaction. The primers used for detection of bacteriophage lambda should be chosen based on the reason for detection.
SCOPE
1.1 This guide covers the procedures for identifying bacteriophage lambda used in biotechnology.
1.2 There are hundreds of lambda variants that can be used for biotechnology. These lambda variants are derived from wild type lambda and differ in genome size and genotype.
1.3 If the bacteriophage lambda is to be used to construct a recombinant molecule, then the same criteria as prescribed in Section 5 should be used to characterize the newly made DNA.
WITHDRAWN RATIONALE
This guide covers the procedures for identifying bacteriophage lambda used in biotechnology.
Formerly under the jurisdiction of Committee E55 on Manufacture of Pharmaceutical Products, this guide was withdrawn in August 2014. This standard was withdrawn without replacement due to its limited use by the industry.

General Information

Status
Withdrawn
Publication Date
31-Oct-2001
Withdrawal Date
04-Aug-2014
ICS
07.100.10 - Medical microbiology
Technical Committee
E55 - Manufacture of Pharmaceutical and Biopharmaceutical Products
Drafting Committee
E55.04 - General Biopharmaceutical Standards
Current Stage
Ref Project

Relations

Replaces
ASTM E1285-01 - Standard Guide for Identification of Bacteriophage Lambda (λ) or Its DNA
Effective Date
01-Nov-2001
Referred By
ASTM E2363-23 - Standard Terminology Relating to Manufacturing of Pharmaceutical and Biopharmaceutical Products in the Pharmaceutical and Biopharmaceutical Industry
Effective Date
01-Nov-2001

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ASTM E1285-06 - Standard Guide for Identification of Bacteriophage Lambda (λ) or Its DNA (Withdrawn 2014)ASTM E1285-06 - Standard Guide for Identification of Bacteriophage Lambda (λ) or Its DNA (Withdrawn 2014)
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ASTM E1285-06 - Standard Guide for Identification of Bacteriophage Lambda (λ) or Its DNA (Withdrawn 2014)
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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:E1285 −06
StandardGuide for
1
Identification of Bacteriophage Lambda (λ) or Its DNA
This standard is issued under the fixed designation E1285; 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 (´) indicates an editorial change since the last revision or reapproval.
INTRODUCTION
This guide is intended to determine the identification of bacteriophage lambda or its DNA. The
objective is to describe laboratory characterization procedures that are sufficient to verify that a
biological preparation believed to contain lambda or lambda DNA for use in any step of a
biotechnology process actually does contain this bacteriophage or its DNA.
This guide assumes a basic knowledge of virology and molecular biology.
1. Scope 3.1.4 multiplicity of infection—the ratio of infecting phage
to host bacteria.
1.1 This guide covers the procedures for identifying bacte-
3.1.5 temperate bacteriophage—a bacteriophage that can
riophage lambda used in biotechnology.
grow lytically, killing the host, or can exist stably in the host.
1.2 There are hundreds of lambda variants that can be used
3.1.6 vector—a fragment of DNA usually containing an
for biotechnology. These lambda variants are derived from
origin of replication that is engineered to accept a foreign piece
wild type lambda and differ in genome size and genotype.
of DNA.
1.3 If the bacteriophage lambda is to be used to construct a
3.1.7 wild type—the naturally occurring, original isolate.
recombinant molecule, then the same criteria as prescribed in
Section 5 should be used to characterize the newly made DNA.
4. General Information
4.1 Bacteriophagelambdaisatemperatebacteriophagewith
2. Referenced Documents
an icosahedral head about 50 nm in diameter.There is a single,
2
2.1 ASTM Standards:
non-contractile tail about 150 nm long, ending in a single tail
E1873 Guide for Detection of Nucleic Acid Sequences by
3
fiber.
the Polymerase Chain Reaction Technique
4.2 The genome of lambda consists of a single molecule of
3. Terminology linear double-stranded DNAwith a length of about 49 kilobase
pairs for wild type lambda. The ends of the genome are
3.1 Definitions:
cohesive; DNA molecule is terminated by single-stranded
3.1.1 bacteriophage—a virus that infects bacteria.
regions of complementary base sequence allowing circulariza-
3.1.2 induction—the relief of repression of transcription of
tion of a molecule. The sequence of the entire phage genome
lysogenic phage genes encoding the functions for lytic growth, 3
has been determined.
so that the phage will grow lytically.
4.3 The naturally preferred host is Escherichia coli K12.
3.1.3 lysogen—a bacterial strain that has a phage stably
The wild type phage makes turbid plaques. Many variants,
maintained. In the case of lambda, the phage is integrated into
however, have mutations in the cI gene encoding repressor.
the host genome. The integrated phage is called a prophage.
3
These variants produce clear plaques.
4.4 Bacteriophage lambda are used primarily as DNA vec-
tors for cloning DNA fragments. These vectors have been
1
This guide is under the jurisdiction of ASTM Committee E55 on Manufacture
engineered to accept easily the foreign DNA. The DNA
of Pharmaceutical Products and is the direct responsibility of Subcommittee E55.04
on General Biopharmaceutical Standards.
sequences of many vectors have been altered from the wild
Current edition approved Nov. 1, 2006. Published November 2006. Originally in
type, that is, whole (nonessential) regions have been deleted.
1989. Last previous edition approved in 2001 as E1285 – 01. DOI: 10.1520/E1285-
Wild type lambda DNA, when cut with restriction enzymes, is
06.
2
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
3
Standards volume information, refer to the standard’s Document Summary page on Hendrix, R., Roberts, J., Stahl, F., and Weisberg, R., Lambda II, Cold Spring
the ASTM website. Harbor Laboratory, Cold Spring Harbor, NY, 1983.
Copyright © ASTM International, 100 Barr Harbor Drive, PO Box C700, West Conshohocken, PA 19428-2959. United States
1

---------------------- Page: 1 ----------------------
E1285−06
used also as molecular weight markers in polyacrylamide or phage are desired, for purposes other than for DNAextraction,
3
agarose gel electrophoresis. Mice transgenic for bacterio- concentration should not be more than 50-fold, and resuspen-
phage lambda have been constructed to enable mutation sion, after precipitation, should be gentle.
4,5
detection in the mouse genome.
6. Characterization
5. Bacteriophage Growth and Purification
6.1 Bacteriop
...

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SIGNIFICANCE AND USE
5.1 This guide should be used by producers and potential producers of non-culture tests to determine the accuracy, selectivity, specificity, and precision of the tests, as defined in Practice E691. Results of such studies should identify the limitations and indicate the utility or applicability of the non-culture test, or both, for use on different types of samples. Guide E1488 recommends other statistical tools for evaluating the suitability and applicability of proposed new test methods.  
5.2 Non-culture test users and potential users should employ this guide to evaluate results of the non-culture test as compared to their present methods. Practices D5245 and D5465 should be reviewed in regards to the microbiological methods employed. If culture methods have not been used for monitoring the systems, then guidelines are included for obtaining microbiological expertise.  
5.3 Utilization of a non-culture test can reduce the time required to determine the microbiological status of the system and detect microbe that are not detected by culture testing. Consequently, non-culture tests can contribute to the improvement in the overall operating efficiency of microbial contamination condition monitoring and diagnostic efforts, and microbicide performance evaluations.  
5.4 Detecting microbial contamination levels that exceed predetermined upper control limits indicates the need for an addition of an antimicrobial agent or other corrective maintenance action. By accurately determining this in a shorter time period than is possible than by culture methods, treatment with antimicrobial agents may circumvent more serious problems than if the treatment were postponed until culture results were available. If the antimicrobial treatment program relied on an inaccurate non-culture test, then unnecessary loss of product and problems associated with inappropriate selection or improper dosing with antimicrobial agents would exist.  
5.5 Since many methods based on entirely diff...
SCOPE
1.1 The purpose of this guide is to assist users and producers of non-culture microbiological tests in determining the applicability of the test for processing different types of samples and evaluating the accuracy of the results. Culture test procedures such as the Heterotrophic (Standard) Plate Count, the Most Probable Number (MPN) method and the Spread Plate Count are widely cited and accepted for the enumeration of microorganisms. However, these methods have their limitations, such as performance time. Moreover, any given culture test method typically recovers only a portion of the total viable microbes present in a sample. It is these limitations that have recently led to the marketing of a variety of non-culture procedures, test kits and instruments.  
1.2 Culture test methods estimate microbial population densities based on the ability of mircoorganisms in a sample to proliferate in or on a specified growth medium, under specified growth conditions. Non-culture test methods attempt to provide the same or complimentary information through the measurement of a different parameter. This guide is designed to assist investigators in assessing the accuracy and precision of non-culture methods intended for the determination of microbial population densities or activities.  
1.3 It is recognized that the Heterotrophic Plate Count (HPC) does not recover all microorganisms present in a product or a system (1, 2).2 When this problem occurs during the characterization of a microbiological population, alternative standard enumeration procedures may be necessary, as in the case of sulfate-reducing bacteria. At other times, chemical methods that measure the rates of appearance of metabolic derivatives, the utilization of contaminated product components or genetic profile of the microbial population might be indicated. In evaluating non-culture tests, it is possible that the use of these alternative standard procedures might be...

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ASTM
ASTM E3251-20(Test Method)
Standard Test Method for Microbial Ingress Testing on Single-Use Systems

SIGNIFICANCE AND USE
4.1 Single-use systems (SUSs) used for biopharmaceutical manufacturing must maintain sterility and product quality of the fluid inside. Such articles or systems should therefore be validated as providing an effective barrier against microbial ingress. The microbial barrier properties of a SUS may be demonstrated using deterministic physical tests that have been correlated to microbial integrity. Two test methods (aerosol exposure and immersion exposure) are described that can be used to demonstrate microbial integrity of a SUS or determine the MALL, the maximum defect size that does not allow microbial ingress, into a SUS.  
4.2 It is important to note that the results of microbial ingress tests are heavily dependent on the conditions under which the test is performed and are not suitable for routine checking of a SUS due to the test’s destructive nature.  
4.2.1 Any size defect may be forced to fail under sufficiently aggressive conditions (including a large enough sample size, high differential pressure, or high hydrostatic pressure, for example) that would not ordinarily reflect normal use conditions. Thus, it is necessary to clearly define the relevant conditions for a test through a risk assessment of both the actual SUS claims and its final use (Practice E3244). Once that is established, the size of defect that can be detected under those conditions can be determined, if required, using defined defects.  
4.2.2 “Relevant conditions” refers to worse-case actual use conditions but does not mean that a SUS must be tested under theoretically absolute (extreme) “worst-case” conditions.  
4.2.3 Testing may be performed on individual components or entire systems. Considerations for defining “relevant conditions” and testing design should be based on a risk assessment for the SUS intended use and should include:
4.2.3.1 A channel created by a defect or breach through the film thickness or through a seam or connection which must be filled with liquid to allow mic...
SCOPE
1.1 The microbial test method outlined in this document applies to microbial ingress risk assessment of a single-use system (SUS) or its individual components that require integrity testing either by the assembly supplier or the end user of the assembly based on a potential risk of a breach to the product or manufacturing process.  
1.2 The aim of microbial ingress testing of sterile SUSs used in biopharmaceutical manufacturing is two-fold:  
1.2.1 Firstly, it is used to evaluate the ability of a SUS fluid path to remain sterile after a SUS has been challenged by microbial exposure. Microbial exposure is achieved either by directly placing a SUS into a container of microbial challenge solution, or by delivering an aerosolized microbial challenge onto a SUS that is placed inside a test chamber designed to generate and deliver the aerosol. The choice of the test challenge organism should be justified based on a risk assessment of the SUS and conditions of use.  
1.2.2 Additionally, microbial ingress testing can be used to determine the maximum allowable leakage limit (MALL) that does not allow microbial ingress under specific test conditions. The defect size that can be detected by specific physical integrity testing methods can be correlated to this MALL in order to claim microbial integrity. Test articles bearing calibrated defects over a range of dimensions, including up to a defect size expected to consistently allow microbial ingress as a positive control (defect-based positive control), may be tested to determine the MALL.  
1.3 Both purposes for microbial ingress testing as described in 1.2.1 and 1.2.2 can either be conducted by liquid immersion or aerosol exposure. For the purpose described in 1.2.2, the type of exposure should be determined according to the SUS’s use-case conditions and a risk assessment.  
1.4 The method used to create a breach, hole or defect in single-use film or in a SUS test article, as ...

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