Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE)

Abstract

Vancomycin-resistant enterococci (VRE), due to their intrinsic resistance to various commonly used antibiotics and their malleable genome, make the treatment of infections caused by these bacteria less effective. The aims of this work were to characterize isolates of Enterococcus spp. that originated from processed meat, through phenotypic and genotypic techniques, as well as to detect putative antibiotic resistance biomarkers. The 19 VRE identified had high resistance to teicoplanin (89%), tetracycline (94%), and erythromycin (84%) and a low resistance to kanamycin (11%), gentamicin (11%), and streptomycin (5%). Based on a Next-Generation Sequencing NGS technique, most isolates were vanA-positive. The most prevalent resistance genes detected were erm(B) and aac(6’)-Ii, conferring resistance to the classes of macrolides and aminoglycosides, respectively. MALDI-TOF mass spectrometry (MS) analysis detected an exclusive peak of the Enterococcus genus at m/z (mass-to-charge-ratio) 4428 ± 3, and a peak at m/z 6048 ± 1 allowed us to distinguish Enterococcus faecium from the other species. Several statistically significant protein masses associated with resistance were detected, such as peaks at m/z 6358.27 and m/z 13237.3 in ciprofloxacin resistance isolates. These results reinforce the relevance of the combined and complementary NGS and MALDI-TOF MS techniques for bacterial characterization.

Enterococci, from Harmless Bacteria to a Pathogen

“…In addition to food-producing animals, VRE and their resistance genes have been reported and detected in foods at retail (meat, vegetables, cheese, and milk) [ 74 , 75 , 76 , 77 ]. This is a cause for enormous concern since it favors the dissemination of antimicrobial resistance organisms, consequently reducing therapeutic options [ 78 ].…”

“…This is a cause for enormous concern since it favors the dissemination of antimicrobial resistance organisms, consequently reducing therapeutic options [ 78 ]. In Portugal, only a few studies have reported the presence of VRE in food such as cheese, poultry carcasses, and processed meat [ 74 , 79 , 80 , 81 , 82 , 83 , 84 ].…”

Prevalence of Vancomycin-Resistant Enterococcus (VRE) in Companion Animals: The First Meta-Analysis and Systematic Review

“…Interestingly, prior to the restriction on avoparcin use in 1997 [ 44 ], 8 studies reported the prevalence of VRE in companion animals, while 27 studies reported the prevalence of VRE in companion animals after the avoparcin ban. As seen in our analysis, the prevalence was gradually rising prior to the ban but continued to fluctuate after the avoparcin ban.…”

Applied Proteomics in ‘One Health’

“…Another application of proteomics techniques is the precise and accurate identification of bacterial strains and is used additionally in microbiological studies. A relevant example is the differentiation of Enterococcus faecium from other bacterial species from processed meat samples [ 274 ].…”