CLSI MM11 A : 1ED 2007

Abstract
Committee Membership
Foreword
1 Scope
2 Standard Precautions
3 Terminology
   3.1 Definitions
   3.2 Comments on Microbiological and Epidemiologic
        Definitions
   3.3 Abbreviations and Acronyms
4 The Biology Behind Molecular Strain Typing
   4.1 Sources of Genetic Variation
   4.2 Population Structure of Bacterial Species
   4.3 Impact of Selective Pressure on Diversity
   4.4 Applications of Molecular Strain Typing
5 Validation of Typing Methodologies
   5.1 Reproducibility
   5.2 Discriminatory Power
   5.3 Requirements for Characterizing a Molecular Typing
        System
   5.4 Assessment of Competency for Molecular Strain Typing
6 Methods for Molecular Strain Typing
   6.1 Controls
   6.2 Pulsed-Field Gel Electrophoresis (PFGE)
   6.3 Ribotyping
   6.4 Sequence-Based Strain Typing
   6.5 Repetitive Sequence-Based PCR (rep-PCR)
7 Analyzing Electrophoretic Typing Data
   7.1 Visual Analysis of Electrophoresis Gels
   7.2 Analyzing Electrophoresis Gels by Software
   7.3 Population Genetics and the Analysis of PFGE
        Patterns: a Cautionary Note
8 Analyzing Sequence Data
   8.1 Percent Identity
   8.2 Pattern Recognition
   8.3 BURST
   8.4 Sequence Analysis Methods for Evolutionary Genetics
9 Interpreting Variation in Molecular Typing
   9.1 Categories of Genotypic Relatedness in Molecular
        Strain Typing
   9.2 Step One: Identify the "Reference Isolate" or Type
        That Focuses the Question
   9.3 Step Two: Compare Each Isolate to the Reference
        Isolate
   9.4 Translating Genotypic Relatedness Into Epidemiologic
        and Clinical Relatedness
   9.5 Comparison to the "Tenover Criteria"
10 Reporting Molecular Typing Results
11 General Technical Issues
   11.1 Identifying Isolates
   11.2 Archiving Isolates-Freezing
12 Examples of Molecular Typing of Bacterial Species
   12.1 Streptococcus pyogenes
   12.2 Streptococcus pneumoniae
References
Summary of Delegate Comments and Committee Responses
The Quality Management System Approach
Related CLSI/NCCLS Publications

Examines the biology behind molecular strain typing and the process of characterizing and validating typing systems.

Bacterial strain typing is now performed in a wide range of venues, including hospital-based clinical microbiology laboratories; federal, state, and local reference laboratories; as well as industrial and commercial laboratories. Similarly, the results of bacterial strain typing are now used in many different contexts, including clinical care settings; public health investigations, particularly of emerging infections; the food and pharmaceutical industries; and environmental analyses.
The goal of this guideline is to provide a framework that will facilitate consistency in reporting bacterial strain typing and will assist both the laboratories performing these studies and the professionals applying the results. A general approach to the analysis of molecular typing data will be presented, as well as specific criteria for interpreting typing results obtained with the most commonly used methods. This guideline will focus on techniques that analyze bacterial chromosomal DNA, particularly pulsed-field gel electrophoresis (PFGE) and nucleotide sequencing; phenotypic techniques (e.g., serotyping, phage typing) and plasmid-based methods will not be addressed