Detection of Species-Specific Lipids by Routine MALDI TOF Mass Spectrometry to Unlock the Challenges of Microbial Identification and Antimicrobial Susceptibility Testing

Abstract

MALDI-TOF mass spectrometry has revolutionized clinical microbiology diagnostics by delivering accurate, fast, and reliable identification of microorganisms. It is conventionally based on the detection of intracellular molecules, mainly ribosomal proteins, for identification at the species-level and/or genus-level. Nevertheless, for some microorganisms (e.g., for mycobacteria) extensive protocols are necessary in order to extract intracellular proteins, and in some cases a protein-based approach cannot provide sufficient evidence to accurately identify the microorganisms within the same genus (e.g., Shigella sp. vs E. coli and the species of the M. tuberculosis complex). Consequently lipids, along with proteins are also molecules of interest. Lipids are ubiquitous, but their structural diversity delivers complementary information to the conventional protein-based clinical microbiology matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based approaches currently used. Lipid modifications, such as the ones found on lipid A related to polymyxin resistance in Gram-negative pathogens (e.g., phosphoethanolamine and aminoarabinose), not only play a role in the detection of microorganisms by routine MALDI-TOF mass spectrometry but can also be used as a read-out of drug susceptibility. In this review, we will demonstrate that in combination with proteins, lipids are a game-changer in both the rapid detection of pathogens and the determination of their drug susceptibility using routine MALDI-TOF mass spectrometry systems.

Combination of MALDI-TOF Mass Spectrometry and Machine Learning for Rapid Antimicrobial Resistance Screening: The Case of Campylobacter spp.

“…As well, the application of MALDI-TOF MS in microbiology for lipid investigation has conceptualized several breakthroughs for AMR screening (Bruker, 2019;Furniss et al, 2019;Dortet et al, 2020). In case of the ability of such method to distinct microbial lipids directly from body fluids such as serum, blood, and urine, there will be no need of a culture step (Solntceva et al, 2021). So far, only the last-line treatment for multidrug-resistant Gramnegative bacteria, i.e., polymyxin, has been investigated without a ML approach.…”

Use of Fourier-Transform Infrared Spectroscopy With IR Biotyper® System for Legionella pneumophila Serogroups Identification

“…Considering that the differentiation into 15 serogroups is given by different fatty acid components, it will be interesting to focus new studies on the evaluation of lipid profile adsorption. The IR Biotyper® is already able to perform it on other microorganisms, characterizing several differences on fatty acid and lipidic profile that are able to differentiate them also at species level (e.g., for Mycobacteria; Solntceva et al, 2021 ).…”

Model architectures for bacterial membranes

“…Lipids in bacterial membranes serve as important structural and functional constituents and have important roles in membrane organisation, cell recognition, membrane fluidity, energy storage, direct modulation, membrane stability, cell signalling, and membrane formation (Solntceva et al 2020;Carvalho and Caramujo 2018;Willdigg and Helmann 2021). To perform such complex and diverse functions, bacterial membranes are composed of approximately equivalent proportions of lipids and proteins and are complex structures with a high degree of organisation and variation between bacterial species and their GN and GP classifications (Strahl and Errington 2017;Epand and Epand 2009a;Sohlenkamp and Geiger 2016).…”

“…Numerous glycolipids, which are composed of a carbohydrate attached by a glycosidic bond containing 1-2 fatty acid units, are also typical constituents in the membranes of GN and GP bacteria (Bertani and Ruiz 2018;Reichmann and Gründling 2011). In addition to the aforementioned common lipid species, bacteria can also possess species-specific lipids (Solntceva et al 2020).…”

“…Teichoic acids, including LTA, thread through the murein layers to anchor the murein wall to the membrane and regulate cell envelope function and structure (Malanovic and Lohner 2016;Silhavy et al 2010). LTA is an alditol phosphate polymer linked by a glycolipid anchor that secures it to the lipid membrane (Solntceva et al 2020;Percy and Gründling 2014). The structure of LTA varies significantly between GP bacterial species whereby there are five types of LTA (types I-V) that differ in core structure and glycolipid anchor (Percy and Gründling 2014;Shiraishi et al 2013).…”