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Curr Microbiol. 2017 Apr;74(4):476-483. doi: 10.1007/s00284-017-1210-5. Epub 2017 Feb 22.

Development of a Rapid Identification Method for the Differentiation of Enterococcus Species Using a Species-Specific Multiplex PCR Based on Comparative Genomics.

Park J1, Jin GD2, Pak JI2,3, Won J2,4, Kim EB5,6.

Author information

1
Department of Animal Life System, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea.
2
Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea.
3
Division of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea.
4
Institute of Animal Resources, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea.
5
Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea. itanimal@kangwon.ac.kr.
6
Division of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea. itanimal@kangwon.ac.kr.

Abstract

Enterococci are lactic acid bacteria that are commonly found in food and in animal gut. Since 16 S ribosomal RNA (rRNA) sequences, genetic markers for bacterial identification, are similar among several Enterococcus species, it is very difficult to determine the correct species based on only 16 S rRNA sequences. Therefore, we developed a rapid method for the identification of different Enterococcus species using comparative genomics. We compared 38 genomes of 13 Enterococcus species retrieved from the National Center of Biotechnology Information database and identified 25,623 orthologs. Among the orthologs, four genes were specific to four Enterococcus species (Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, and Enterococcus durans). We designed species-specific primer sets targeting the genes and developed a multiplex PCR using primer sets that could distinguish the four Enterococcus species among the nine strains of Enterococcus species that were available locally. The multiplex PCR method also distinguished the four species isolated from various environments, such as feces of chicken and cow, meat of chicken, cow, and pigs, and fermented soybeans (Cheonggukjang and Doenjang). These results indicated that our novel multiplex PCR using species-specific primers could identify the four Enterococcus species in a rapid and easy way. This method will be useful to distinguish Enterococcus species in food, feed, and clinical settings.

PMID:
28229213
DOI:
10.1007/s00284-017-1210-5
[Indexed for MEDLINE]

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