Molecular genotyping and strain typing are essential tools for the analysis of infectious etiological agents of human diseases isolated during investigations of epidemiological outbreaks, laboratory contamination, and recurrent infection. A wide variety of genotyping and strain typing methods have been described using contemporary nucleic acid–based technologies. These methods are used for identifying virulence factors, drug resistance, markers of disease progression within an institution or a community, and in certain cases, patient prognosis. Clinical and Laboratory Standards Institute guideline MM24—Molecular Methods for Genotyping and Strain Typing of Infectious Organisms examines the biology behind molecular genotyping and strain typing and the process of characterizing and validating typing systems. The prevalent methods currently being used in laboratories that perform genotyping and strain typing include nucleic acid amplification tests, ribotyping, sequence-based typing (Sanger and next-generation sequencing), hybridization-based typing methods (microarrays, line-probe arrays), molecular fingerprinting (pulse-field gel electrophoresis, restriction fragment-length polymorphism analysis, multiple locus variable–number of tandem repeat analysis), and protein-based typing. Each of these areas is described in detail specific to the genotyping and strain typing of nucleic acid in clinical testing and monitoring, particularly in bacterial, fungal, and viral diseases. This guideline also includes an update on technologies used for molecular genotyping and strain typing, sample preparation, standards, calibrators, reference materials, analytical and clinical verification/validation, reporting and interpreting results, and clinical utility.

This guideline replaces the previous edition of the approved guideline, MM11-A, published in 2007. MM24 also builds on topics introduced in CLSI document MM10, published in 2006, which has since been withdrawn from CLSI's library. Several changes were made in this edition, including: 

• Adding a process flow chart showing the basic steps that are followed to perform genotypic and strain typing of infectious organisms – Each step in the process is mapped to the relevant section in this guideline. 

• Providing detailed descriptions on how genotyping and strain typing are used in different settings, in particular, genotyping and strain typing in the clinical setting vs epidemiological applications of genotyping and strain typing of infectious organisms 

• Updating information on the current technologies used for genotyping and strain typing – Discussion of technologies that are no longer used and/or have been replaced by newer methods has been eliminated. 

• Providing detailed descriptions of the quality system essentials that are relevant for laboratories that perform genotyping and/or strain typing of infectious organisms 

• Adding appendixes that provide example forms used in genotyping and strain typing, additional details on various technologies, and information on relevant software and Web-based applications

This guideline provides a framework for facilitating consistency in reporting genotypes and bacterial, viral, and fungal strain typing and will support laboratories that perform these studies and the professionals applying the results. Its purpose is to present not only the technologies used but also the criteria to be considered for design, verification, validation, and determination of clinical utility of such testing. These technologies are now being used in many different contexts, including: 

• Clinical care settings 

• Public health investigations, particularly of emerging infections 

• Food and pharmaceutical industries 

• Environmental analyses in the clinical setting 

• Regulatory agencies This guideline is intended for manufacturers or laboratories that develop assays, laboratories that perform assays, clinicians who use the results to diagnose or manage patients, and agencies that regulate their use. 

This guideline is not intended for use by research laboratories or to provide manufacturing guidelines. It is not intended to provide manufacturing guidelines. This guideline does not discuss the development of standard reference materials for QC use It is recommended that this guideline be used together with CLSI documents MM03, MM06, MM09, MM12, MM13, MM14, MM17, MM18, and MM22.