Proteomic Characterization of Virulence Factors and Related Proteins in Enterococcus Strains from Dairy and Fermented Food Products

Abstract

Enterococcus species are Gram-positive bacteria that are normal gastrointestinal tract inhabitants that play a beneficial role in the dairy and meat industry. However, Enterococcus species are also the causative agents of health care-associated infections that can be found in dairy and fermented food products. Enterococcal infections are led by strains of Enterococcus faecalis and Enterococcus faecium, which are often resistant to antibiotics and biofilm formation. Enterococci virulence factors attach to host cells and are also involved in immune evasion. LC-MS/MS-based methods offer several advantages compared with other approaches because one can directly identify microbial peptides without the necessity of inferring conclusions based on other approaches such as genomics tools. The present study describes the use of liquid chromatography–electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS) to perform a global shotgun proteomics characterization for opportunistic pathogenic Enterococcus from different dairy and fermented food products. This method allowed the identification of a total of 1403 nonredundant peptides, representing 1327 proteins. Furthermore, 310 of those peptides corresponded to proteins playing a direct role as virulence factors for Enterococcus pathogenicity. Virulence factors, antibiotic sensitivity, and proper identification of the enterococcal strain are required to propose an effective therapy. Data are available via ProteomeXchange with identifier PXD036435. Label-free quantification (LFQ) demonstrated that the majority of the high-abundance proteins corresponded to E. faecalis species. Therefore, the global proteomic repository obtained here can be the basis for further research into pathogenic Enterococcus species, thus facilitating the development of novel therapeutics.

Rapid Proteomic Characterization of Bacteriocin-Producing Enterococcus faecium Strains from Foodstuffs

“…Here, we used a state-of-the-art shotgun proteomic method such as liquid chromatography coupled to a TimsTOF Pro instrument (Bruker Daltonics, Bremen, Germany) to characterize bacteriocin-producing Efm strains with the potential to be used as probiotics. Our current proteomic workflow does not just characterize the strains within only 24h, but it also increases by over 100 times the protein resolution compared with previous proteomic studies [30,31]. The resulting proteome explained the antibiotic resistance phenotypes that Hosseini et al reported [21], and identified new resistance traits to fluoroquinolones and aminoglycosides.…”

High-Resolution Comparative and Quantitative Proteomics of Biogenic-Amine-Producing Bacteria and Virulence Factors Present in Seafood

“…This study involved nine different bacterial species, found in seafood, that produce either histamine or other BAs (Table ). The peptides analyzed for these bacteria were prepared by trypsin treatment and loaded in an LTQ-Orbitrap Elite instrument, as designated before. − , This produced a total of 35,621 peptide spectrum matches (PSMs), identified as belonging to 20,792 nonredundant peptides; their sequences correlated with 4621 annotated proteins present in the Proteobacteria UniProt/TrEMBL database (August 2022) (Supporting Information, Data S1). The MS/MS-based proteomics results were submitted to the ProteomeXchange Consortium, through the Proteomics Identification Database (PRIDE depository) and were issued the data set identifier PXD043997 .…”

“…VanZ is another interesting peptide identified; it confers resistance to the glycopeptide teicoplanin, a natural lipoglycopeptide antibiotic. Additional proteins, involved in antimicrobial resistance, identified include β-lactamases, penicillin-binding protein activators LpoA and LpoB, and a penicillin amidase, also known as peptidase S45, and MarR, a regulator of several proteins involved in antibiotic resistance. , Further polypeptides identified include multidrug resistance proteins and multidrug efflux systems, such as the multidrug ABC transporter, multidrug DMT transporter permease, modulator of drug activity B, and RND family efflux transporter MFP. Additional proteins, comprising TerD, TerY, TehB, TerB, TerD, and Ter, were identified as implicated in the resistance to toxic substances, such as tellurite, cadmium, copper, zinc, magnesium, and mercury.…”

ComI inhibits transformation inBacillus subtilisby selectively killing competent cells

“…Additionally, Enterococci are lagging other Gram-positive pathogens in molecular biology because of restrictions in DNA transfer (41). Enterococci contain elements necessary for natural competence, and it was suggested that they could play an alternative role in host colonization and immune invasion, but there has been no evidence for natural competence (42). It’s possible that non-competent bacteria containing orthologs of competence genes may contain an inhibitor, like comI , that integrates competence physiology with inhibitor activity to achieve transformation inhibition.…”