Open AccessBacterial strain typing in the genomic era
Author(s) -
Li Wenjun,
Raoult Didier,
Fournier PierreEdouard
Publication year - 2009
Publication title -
fems microbiology reviews
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.91
H-Index - 212
eISSN - 1574-6976
pISSN - 0168-6445
DOI - 10.1111/j.1574-6976.2009.00182.x
Subject(s) - genotyping , typing , biology , genomic dna , multilocus sequence typing , genetics , microbiology and biotechnology , genotype , population , strain (injury) , dna , gene , anatomy , demography , sociology
Bacterial strain typing, or identifying bacteria at the strain level, is particularly important for diagnosis, treatment, and epidemiological surveillance of bacterial infections. This is especially the case for bacteria exhibiting high levels of antibiotic resistance or virulence, and those involved in nosocomial or pandemic infections. Strain typing also has applications in studying bacterial population dynamics. Over the last two decades, molecular methods have progressively replaced phenotypic assays to type bacterial strains. In this article, we review the current bacterial genotyping methods and classify them into three main categories: (1) DNA banding pattern‐based methods, which classify bacteria according to the size of fragments generated by amplification and/or enzymatic digestion of genomic DNA, (2) DNA sequencing‐based methods, which study the polymorphism of DNA sequences, and (3) DNA hybridization‐based methods using nucleotidic probes. We described and compared the applications of genotyping methods to the study of bacterial strain diversity. We also discussed the selection of appropriate genotyping methods and the challenges of bacterial strain typing, described the current trends of genotyping methods, and investigated the progresses allowed by the availability of genomic sequences.