Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing

Abstract

Rapid and accurate classification and discrimination of bacteria is an important task and has been highlighted recently for rapid diagnostics using real-time results. Coupled with a recent report by Jim O'Neill [https://amr-review.org] that if left unaddressed antimicrobial resistance (AMR) in bacteria could kill 10 million people per year by 2050, which would surpass current cancer mortality, this further highlights the need for unequivocal identification of microorganisms. Whilst traditional microbiological testing has offered insights into the characterisation and identification of a wide range of bacteria, these approaches have proven to be laborious and time-consuming and are not really fit for purpose, considering the modern day speed and volume of international travel and the opportunities it creates for the spread of pathogens globally. To overcome these disadvantages, modern analytical methods, such as mass spectrometry (MS) and vibrational spectroscopy, that analyse the whole organism, have emerged as essential alternative approaches. Currently within clinical microbiology laboratories, matrix assisted laser desorption ionisation (MALDI)-MS is the method of choice for bacterial identification. This is largely down to its robust analysis as it largely measures the ribosomes which are always present irrespective of how the bacteria are cultured. However, MALDI-MS requires large amounts of biomass and infrared spectroscopy and Raman spectroscopy are attractive alternatives as these physicochemical bioanalytical techniques have the advantages of being rapid, reliable and cost-effective for analysing various types of bacterial samples, even at the single cell level. In this review, we discuss the fundamental applications, advantages and disadvantages of modern analytical techniques used for bacterial characterisation, classification and identification.