Microbial detection and identification methods: Bench top assays to omics approaches

Mariateresa Ferone*, Aoife Gowen, Séamus Fanning, Amalia G.M. Scannell

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Citations (Scopus)


Rapid detection of foodborne pathogens, spoilage microbes, and other biological contaminants in complex food matrices is essential to maintain food quality and ensure consumer safety. Traditional methods involve culturing microbes using a range of nonselective and selective enrichment methods, followed by biochemical confirmation among others. The time-to-detection is a key limitation when testing foods, particularly those with short shelf lives, such as fresh meat, fish, dairy products, and vegetables. Some recent detection methods developed include the use of spectroscopic techniques, such as matrix-assisted laser desorption ionization-time of flight along with hyperspectral imaging protocols.This review presents a comprehensive overview comparing insights into the principles, characteristics, and applications of newer and emerging techniques methods applied to the detection and identification of microbes in food matrices, to more traditional benchtop approaches. The content has been developed to provide specialist scientists a broad view of bacterial identification methods available in terms of their benefits and limitations, which may be useful in the development of future experimental design. The case is also made for incorporating some of these emerging methods into the mainstream, for example, underutilized potential of spectroscopic techniques and hyperspectral imaging.

Original languageEnglish
Pages (from-to)3106-3129
Number of pages24
JournalComprehensive Reviews in Food Science and Food Safety
Issue number6
Early online date07 Sept 2020
Publication statusPublished - Nov 2020
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by Science Foundation Ireland (SFI) under the investigators programme Proposal ID 15/IA/2984. HyperMicroMacro.

Publisher Copyright:
© 2020 Institute of Food Technologists®


  • food microbiology
  • food safety
  • hyperspectral imaging (HIS)
  • microbial identification
  • spectroscopic techniques

ASJC Scopus subject areas

  • Food Science


Dive into the research topics of 'Microbial detection and identification methods: Bench top assays to omics approaches'. Together they form a unique fingerprint.

Cite this