16S rRNA Gene sequencing: A practical approach to confirming the identity of food borne bacteria

  • E.E. Chukwu
  • F.O. Nwaokorie
  • A.O. Coker
  • M.J. Avila-Campos
  • F.T. Ogunsola
Keywords: Foodborne pathogens, Microbial detection, Phylogenetic relationship, Phenotypic identification, 16S rRNA gene sequencing

Abstract

One of the main challenges for clinical practice and public health surveillance is rapid and accurate identification of food borne pathogens. In Nigeria, the use of sophisticated molecular tools for foodborne pathogens detection has not been extensively adopted. Bacterial strains isolated from food products sold in Lagos, Nigeria, were subjected to phenotypic techniques and 16S rRNA gene sequencing for specie level identification. Bacterial identification was performed using colonial morphology, Gram staining, conventional biochemical tests, and 16S rRNA gene sequencing. The pairwise sequence similarities between all the bacterial species with official names were analysed. Out of the 30 bacterial strains isolated and sequenced, 29 (96.7%) strains had nucleotide identity to known bacterial species in the GenBank. One (3.3%) sequence contained a large number of undetermined nucleotides and was not associated with specific strain identification. This technique was efficient showing 96.6% of the isolates being identified to the genus level and 93.1% being identified to the species level. The strains that were not identified due to low similarity levels were assigned phylogenetic positions, suggesting that they may belong to new taxa. This study demonstrates that 16S rDNA sequence analysis is more accurate and objective for identification of foodborne pathogens and also offers the possibility of rapidly recognizing yet undescribed taxa.

Keywords: Foodborne pathogens; Microbial detection; Phylogenetic relationship; Phenotypic identification; 16S rRNA gene sequencing

Published
2019-12-18
Section
Articles

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eISSN: 0794-4896