<abstract xmlns="http://www.w3.org/1999/xhtml"><p>The research on similarity between bacteria in outbreak investigations enables the identification of bacterial strain responsible for infections, their source and modes of transmission. These investigations are also necessary for the analysis of spreading of bacteria, not only locally, e.g. in a hospital in a specific country, but also internationally and globally. Therefore, it is of great importance to have the most up to date knowledge regarding different methods used in bacterial typing. This review discusses and compares methods facilitating bacterial typing at a strain level. Phenotyping methods analysed in this article are: Biotyping, Antimicrobial Susceptibility Typing, Phage Typing and protein-based methods. Genotyping techniques reviewed in this article are based on digestion of genomic DNA, methods using amplification of DNA, and based on sequencing DNA. This would include Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS). Methods used in identification of bacterial strains are being constantly improved, and gaining more in depth knowledge and familiarising with their effectiveness enables better analysis and control of epidemiological situation e.g. in hospitals.1. Introduction. 2. Phenotyping methods. 2.1. Biotyping. 2.2. Phage typing. 2.3. Antimicrobial susceptibility typing. 2.4. Protein-based methods. 2.5. Mass spectrometry. 3. Genotyping methods. 3.1. Genotyping without DNA sequencing. 3.1.1. REA-PFGE. 3.1.2. RFLP and PCR-RFLP. 3.1.3. AFLP. 3.1.4. RAPD. 3.1.5. Microarrays. 3.1.6. MLVA. 3.2. Genotyping using DNA sequencing 3.2.1. Sequencing technologies. 3.2.2. MLST and SLST. 3.2.3. WGS – wgSNP, cgMLST, wgMLST. 3.2.4. Advantages and disadvantages of WGS. 4. Popularity of typing methods in biomedical research – PubMed database analysis. 5. Conclusions</p></abstract>

The research on similarity between bacteria in outbreak investigations enables the identification of bacterial strain responsible for infections, their source and modes of transmission. These investigations are also necessary for the analysis of spreading of bacteria, not only locally, e.g. in a hospital in a specific country, but also internationally and globally. Therefore, it is of great importance to have the most up to date knowledge regarding different methods used in bacterial typing. This review discusses and compares methods facilitating bacterial typing at a strain level. Phenotyping methods analysed in this article are: Biotyping, Antimicrobial Susceptibility Typing, Phage Typing and protein-based methods. Genotyping techniques reviewed in this article are based on digestion of genomic DNA, methods using amplification of DNA, and based on sequencing DNA. This would include Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS). Methods used in identification of bacterial strains are being constantly improved, and gaining more in depth knowledge and familiarising with their effectiveness enables better analysis and control of epidemiological situation e.g. in hospitals.1. Introduction. 2. Phenotyping methods. 2.1. Biotyping. 2.2. Phage typing. 2.3. Antimicrobial susceptibility typing. 2.4. Protein-based methods. 2.5. Mass spectrometry. 3. Genotyping methods. 3.1. Genotyping without DNA sequencing. 3.1.1. REA-PFGE. 3.1.2. RFLP and PCR-RFLP. 3.1.3. AFLP. 3.1.4. RAPD. 3.1.5. Microarrays. 3.1.6. MLVA. 3.2. Genotyping using DNA sequencing 3.2.1. Sequencing technologies. 3.2.2. MLST and SLST. 3.2.3. WGS – wgSNP, cgMLST, wgMLST. 3.2.4. Advantages and disadvantages of WGS. 4. Popularity of typing methods in biomedical research – PubMed database analysis. 5. Conclusions

The application of genotyping and phenotyping techniques for epidemiological analysis of microorganisms

Advancements of Microbiology

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<trans-abstract xml:lang="pl" xmlns="http://www.w3.org/1999/xhtml"><p>1. Wstęp. 2. Metody fenotypowe. 2.1. Biotypowanie. 2.2. Typowanie fagowe. 2.3. Analiza profili lekowrażliwości. 2.4. Metody analizy białek. 2.5. Spektroskopia mas. 3. Metody genotypowe. 3.1. Genotypowanie bez wykorzystania sekwencjonowania. 3.1.1. REA-PFGE. 3.1.2. RFLP i PCR-RFLP. 3.1.3. AFLP. 3.1.4. RAPD. 3.1.5. Mikromacierze (CHIP DNA). 3.1.6. MLVA. 3.2. Metody genotypowe wykorzystujące sekwencjonowanie. 3.2.1. Technologie sekwencjonowania. 3.2.2. MLST i SLST. 3.2.3. WGS – wgSNP, cgMLST, wgMLST. 3.2.4. Zalety i wady WGS. 4. Popularność metod typowania bakterii w badaniach biomedycznych na podstawie analizy bazy PubMed. 5. Podsumowanie
</p></trans-abstract>

1. Wstęp. 2. Metody fenotypowe. 2.1. Biotypowanie. 2.2. Typowanie fagowe. 2.3. Analiza profili lekowrażliwości. 2.4. Metody analizy białek. 2.5. Spektroskopia mas. 3. Metody genotypowe. 3.1. Genotypowanie bez wykorzystania sekwencjonowania. 3.1.1. REA-PFGE. 3.1.2. RFLP i PCR-RFLP. 3.1.3. AFLP. 3.1.4. RAPD. 3.1.5. Mikromacierze (CHIP DNA). 3.1.6. MLVA. 3.2. Metody genotypowe wykorzystujące sekwencjonowanie. 3.2.1. Technologie sekwencjonowania. 3.2.2. MLST i SLST. 3.2.3. WGS – wgSNP, cgMLST, wgMLST. 3.2.4. Zalety i wady WGS. 4. Popularność metod typowania bakterii w badaniach biomedycznych na podstawie analizy bazy PubMed. 5. Podsumowanie

METODY GENOTYPOWE I FENOTYPOWE WYKORZYSTYWANE W TYPOWANIU DROBNOUSTROJÓW DO CELÓW EPIDEMIOLOGICZNYCH

The research on similarity between bacteria in outbreak investigations enables the identification of bacterial strain responsible for infections, their source...

The application of genotyping and phenotyping techniques for epidemiological analysis of microorganisms

Published Online: Jan 01, 2022

Page range: 353 - 366

Received: Apr 01, 2017

Accepted: May 01, 2017

DOI: https://doi.org/10.21307/PM-2017.56.3.353

2017 @ Author., Published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.