Agarose Gel Electrophoresis-Based RAPD-PCR—An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies
Agarose gel electrophoresis is a well-known tool to detect DNA fragments amplified in polymerase chain reaction (PCR). Its usefulness has also been confirmed for epidemiological studies based on restriction fragments length polymorphism (RFLP), usually performed using pulsed-field gel electrophoresi...
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| Format: | Article |
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MDPI AG
2022-11-01
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| Online Access: | https://www.mdpi.com/2310-2861/8/12/760 |
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| author | Tomasz Bogiel Agnieszka Mikucka Piotr Kanarek |
| author_facet | Tomasz Bogiel Agnieszka Mikucka Piotr Kanarek |
| author_sort | Tomasz Bogiel |
| collection | DOAJ |
| description | Agarose gel electrophoresis is a well-known tool to detect DNA fragments amplified in polymerase chain reaction (PCR). Its usefulness has also been confirmed for epidemiological studies based on restriction fragments length polymorphism (RFLP), usually performed using pulsed-field gel electrophoresis (PFGE). Little is known on the effectiveness for alert-pathogen epidemiological studies of another less time-consuming and costly technique called randomly amplified polymorphic DNA-PCR (RAPD-PCR). Meanwhile, its usefulness is believed to be comparable to RFLP-PFGE. Therefore, the aim of the study was to establish and optimize the conditions of agarose gel electrophoresis following RAPD-PCR for 19 <i>Enterococcus faecium</i> strains derived from epidemic outbreaks at intensive care units. An application of different PCR primers, primer combinations, and, in particular, agarose gel concentrations and electrophoresis conditions revealed the usefulness of this relatively fast and inexpensive method based on RAPD-PCR for epidemiological studies without a compulsion to use the specialized equipment necessary for RFLP-PFGE. |
| first_indexed | 2024-03-09T16:32:27Z |
| format | Article |
| id | doaj.art-90edc0b12708471fb5b3c4186a6be0af |
| institution | Directory Open Access Journal |
| issn | 2310-2861 |
| language | English |
| last_indexed | 2024-03-09T16:32:27Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
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| series | Gels |
| spelling | doaj.art-90edc0b12708471fb5b3c4186a6be0af2023-11-24T15:00:30ZengMDPI AGGels2310-28612022-11-0181276010.3390/gels8120760Agarose Gel Electrophoresis-Based RAPD-PCR—An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological StudiesTomasz Bogiel0Agnieszka Mikucka1Piotr Kanarek2Microbiology Department, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, PolandMicrobiology Department, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, PolandDepartment of Microbiology and Food Technology, Faculty of Agriculture and Biotechnology, Bydgoszcz University of Science and Technology, 85-029 Bydgoszcz, PolandAgarose gel electrophoresis is a well-known tool to detect DNA fragments amplified in polymerase chain reaction (PCR). Its usefulness has also been confirmed for epidemiological studies based on restriction fragments length polymorphism (RFLP), usually performed using pulsed-field gel electrophoresis (PFGE). Little is known on the effectiveness for alert-pathogen epidemiological studies of another less time-consuming and costly technique called randomly amplified polymorphic DNA-PCR (RAPD-PCR). Meanwhile, its usefulness is believed to be comparable to RFLP-PFGE. Therefore, the aim of the study was to establish and optimize the conditions of agarose gel electrophoresis following RAPD-PCR for 19 <i>Enterococcus faecium</i> strains derived from epidemic outbreaks at intensive care units. An application of different PCR primers, primer combinations, and, in particular, agarose gel concentrations and electrophoresis conditions revealed the usefulness of this relatively fast and inexpensive method based on RAPD-PCR for epidemiological studies without a compulsion to use the specialized equipment necessary for RFLP-PFGE.https://www.mdpi.com/2310-2861/8/12/760agaroseagarose gelalert pathogens<i>Enterococcus faecium</i>gel electrophoresisGREfm |
| spellingShingle | Tomasz Bogiel Agnieszka Mikucka Piotr Kanarek Agarose Gel Electrophoresis-Based RAPD-PCR—An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies Gels agarose agarose gel alert pathogens <i>Enterococcus faecium</i> gel electrophoresis GREfm |
| title | Agarose Gel Electrophoresis-Based RAPD-PCR—An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies |
| title_full | Agarose Gel Electrophoresis-Based RAPD-PCR—An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies |
| title_fullStr | Agarose Gel Electrophoresis-Based RAPD-PCR—An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies |
| title_full_unstemmed | Agarose Gel Electrophoresis-Based RAPD-PCR—An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies |
| title_short | Agarose Gel Electrophoresis-Based RAPD-PCR—An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies |
| title_sort | agarose gel electrophoresis based rapd pcr an optimization of the conditions to rapidly detect similarity of the alert pathogens for the purpose of epidemiological studies |
| topic | agarose agarose gel alert pathogens <i>Enterococcus faecium</i> gel electrophoresis GREfm |
| url | https://www.mdpi.com/2310-2861/8/12/760 |
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