Dairy Products: A Potential Source of Multidrug-Resistant Enterococcus faecalis and Enterococcus faecium Strains

Molecular characterization of histidine and tyrosine decarboxylating Enterococcus species isolated from some milk products

BACKGROUND

Fermented foods can cause adverse effects on human health because of the biogenic amines (BAs) accumulating through amino acid decarboxylation. This study investigated the presence of BAs including tyramine and histamine in 240 samples of some cheese and fermented milk samples using high-performance liquid chromatography. Another aim of this study is to isolate and identify Enterococcus spp. as the most important and frequent BA producer in the examined samples. The isolated Enterococcus spp. was investigated phenotypically for their capacity to produce amino acid decarboxylase enzyme using decarboxylase microplate assay, and genotypically through molecular detection of some genes encoding amino acid decarboxylation (tyrdc and hdc). Biogenic amines producing enterococci were then investigated for their antimicrobial resistance, biofilm production as well as their virulence determinants.

RESULTS

Tyramine and histamine could be detected in 86.7 and 87.9% of the investigated samples with 52.9% being contaminated with Enterococcus spp. Significant correlation between the incidence of Enterococci enterococci and BAs formed in the examined samples (P < 0.0001). tyrdc and hdc genes were detected in 85 and 5% of amino acid decarboxylating Enterococcus spp., respectively. A high percentage of Enterococcus isolates (57.5%) were multidrug-resistant and resistance against penicillin was widespread among isolates followed by tetracycline, vancomycin, erythromycin and linezolid. Also, 77.5% of the isolates were capable of forming biofilms and a highly significant correlation (P < 0.0001) was found between biofilm formation and multidrug resistance. The results showed that the rates of most virulence genes gelE, esp, ace, asa1, and cylA were 77.5. 47.5, 47.5, 35 and 7.5%, respectively, while the hyl gene was not detected in any isolates.

CONCLUSION

The study highlights the significant presence of BAs (TYM and HIS) in cheese and fermented milk samples, with a strong correlation between enterococci contamination and TYM production. The high prevalence of tyramine-producing Enterococcus species poses a notable public health concern especially with the high prevalence of multidrug-resistant, biofilm production and virulence in BAs producing Enterococcus spp. in dairy products, emphasizing the urgent need for improved antimicrobial stewardship among food producers and veterinarians to mitigate the risk of transferring resistant strains to humans.

Relationship Between CRISPR-Cas Systems and Acquisition of Tetracycline Resistance in Non-Clinical Enterococcus Populations in Bulgaria

Non-clinical enterococci are relatively poorly studied by means of acquired antibiotic resistance to tetracycline and by the distribution, functionality and role of their CRISPR systems. Background: In our study, 72 enterococcal strains, isolated from various non-clinical origins, were investigated for their phenotypic and genotypic (tet(M), tet(O), tet(S), tet(L), tet(K), tet(T) and tet(W)) tetracycline resistance. Methods: The genetic determinants for HGT (MGEs (Int-Tn and prgW), inducible pheromones (cpd, cop and cff), aggregation substances (agg, asa1, prgB and asa373) and CRISPR-Cas systems were characterized by PCR and whole-genome sequencing. Results: Four tet genes (tetM, tetO, tetS and tetT) were detected in 39% (n = 28) of our enterococcal population, with tetM (31%) being dominant. The gene location was linked to the Tn6009 transposon. All strains that contained tet genes also had genes for HGT. No tet genes were found in E. casseliflavus and E. gilvus. In our study, 79% of all tet-positive strains correlated with non-functional CRISPR systems. The strain E. faecalis BM15 was the only one containing a combination of a functional CRISPR system (cas1, cas2, csn2 and csn1/cas9) and tet genes. The CRISPR subtype repeats II-A, III-B, IV-A2 and VI-B1 were identified among E. faecalis strains (CM4-II-A, III-B and VI-B1; BM5-IV-A2, II-A and III-B; BM12 and BM15-II-A). The subtype II-A was the most present. These repeats enclosed a great number of spacers (1-10 spacers) with lengths of 31 to 36 bp. One CRISPR locus was identified in plasmid (p.Firmicutes1 in strain E. faecalis BM5). We described the presence of CRISPR loci in the species E. pseudoavium, E. pallens and E. devriesei and their lack in E. gilvus, E. malodoratus and E. mundtii. Conclusions: Our findings generally describe the acquisition of foreign DNA as a consequence of CRISPR inactivation, and self-targeting spacers as the main cause.

Antibiotic Resistance in Fermented Foods Chain: Evaluating the Risks of Emergence of Enterococci as an Emerging Pathogen in Raw Milk Cheese

Fermented foods, particularly fermented dairy products, offer significant health benefits but also present serious concerns. Probiotic bacteria, such as lactic acid bacteria (LAB), found in these foods have been strongly linked to the selection and dissemination of antibiotic resistance genes (ARGs). This study aims to examine the potential risks associated with fermented foods, despite their importance in human nutrition, by analyzing the entire production chain from raw material acquisition to storage. Focusing on cheese production as a key fermented food, the study will investigate various aspects, including dairy farm management, milk acquisition, milk handling, and the application of good manufacturing practices (GMP) and good hygiene practices (GHP) in cheese production. The findings of this review highlight that ARGs found in LAB are similar to those observed in hygiene indicator bacteria like E. coli and pathogens like S. aureus. The deliberate use of antibiotics in dairy farms and the incorrect use of disinfectants in cheese factories contribute to the prevalence of antibiotic-resistant bacteria in cheeses. Cheese factories, with their high frequency of horizontal gene transfer, are environments where the microbiological diversity of raw milk can enhance ARG transfer. The interaction between the raw milk microbiota and other environmental microbiotas, facilitated by cross-contamination, increases metabolic communication between bacteria, further promoting ARG transfer. Understanding these bacterial and ARG interactions is crucial to ensure food safety for consumers.

Etiology and antimicrobial resistance of subclinical mastitis pathogens Staphylococcus aureus, Streptococcus spp. and Enterococcus spp. in sheep milk

The present study investigates the prevalence and etiology of subclinical mastitis in Țurcana sheep flocks located in south-western Romania. Milchtest and California Mastitis Test (CMT), were used for the detection of subclinical mastitis. A number of 360 milk samples across three lactation phases were analyzed. Subclinical mastitis was identified in 146 (40.6%) of sheep milk samples. Only milk samples (n = 146) collected from sheep diagnosed with subclinical mastitis were considered for microbiological analyses. Thus, Staphylococcus aureus (129/146; 88.4%) was identified as the predominant pathogen followed by Streptococcus spp. (14/146; 9.6%) Enterococcus spp. (7/146; 4.8%), Pseudomonas aeruginosa (6/146; 4.1%) and Klebsiella pneumoniae (5/146; 3.4%). Antimicrobial susceptibility of isolated strains of Staphylococcus aureus, Streptococcus spp. and Enterococcus spp. was also tested. The results showed varying resistance patterns depending on the farm and microorganism. In heard A the highest resistance of Staphylococcus aureus was identified to polymyxin B (79.7%) followed by novobiocin (73.4%) and tetracycline (45.3%); Streptococcus spp. to streptomycin (100%), novobiocin (100%), tetracycline (100%) and Enterococcus spp. to tylosin (100%), streptomycin (75.0%) and tetracycline (75.0%). In herd B, Staphylococcus aureus showed high resistance rates to polymyxin B (86.3%), novobiocin (74.5%) and cloxacillin (39.2%); Streptococcus spp. strains to streptomycin (100%), novobiocin (100%), tetracycline (100%) and Enterococcus spp. to gentamicin (100%), streptomycin (66.7%) and erythromycin (66.7%). The obtained preliminary results indicate a potential risk that future treatments of sheep mastitis may not be effective, and demonstrated that raw unpasteurized milk can harbor antimicrobial resistance pathogens posing a threat to public health. However, further investigations involving molecular research on resistance genes are required to draw comprehensive conclusions.

Phenotypic and genotypic characterization of antimicrobial resistances reveals the effect of the production chain in reducing resistant lactic acid bacteria in an artisanal raw ewe milk PDO cheese

Antimicrobial resistance (AMR) is a significant public health threat, with the food production chain, and, specifically, fermented products, as a potential vehicle for dissemination. However, information about dairy products, especially raw ewe milk cheeses, is limited. The present study analysed, for the first time, the occurrence of AMRs related to lactic acid bacteria (LAB) along a raw ewe milk cheese production chain for the most common antimicrobial agents used on farms (dihydrostreptomycin, benzylpenicillin, amoxicillin and polymyxin B). More than 200 LAB isolates were obtained and identified by Sanger sequencing (V1-V3 16S rRNA regions); these isolates included 8 LAB genera and 21 species. Significant differences in LAB composition were observed throughout the production chain (P ≤ 0.001), with Enterococcus (e.g., E. hirae and E. faecalis) and Bacillus (e.g., B. thuringiensis and B. cereus) predominating in ovine faeces and raw ewe milk, respectively, along with Lactococcus (L. lactis) in whey and fresh cheeses, while Lactobacillus and Lacticaseibacillus species (e.g., Lactobacillus sp. and L. paracasei) prevailed in ripened cheeses. Phenotypically, by broth microdilution, Lactococcus, Enterococcus and Bacillus species presented the greatest resistance rates (on average, 78.2 %, 56.8 % and 53.4 %, respectively), specifically against polymyxin B, and were more susceptible to dihydrostreptomycin. Conversely, Lacticaseibacillus and Lactobacillus were more susceptible to all antimicrobials tested (31.4 % and 39.1 %, respectively). Thus, resistance patterns and multidrug resistance were reduced along the production chain (P ≤ 0.05). Genotypically, through HT-qPCR, 31 antimicrobial resistance genes (ARGs) and 6 mobile genetic elements (MGEs) were detected, predominating Str, StrB and aadA-01, related to aminoglycoside resistance, and the transposons tnpA-02 and tnpA-01. In general, a significant reduction in ARGs and MGEs abundances was also observed throughout the production chain (P ≤ 0.001). The current findings indicate that LAB dynamics throughout the raw ewe milk cheese production chain facilitated a reduction in AMRs, which has not been reported to date.

Pathogenic Potential and Antibiotic Susceptibility: A Comprehensive Study of Enterococci from Different Ecological Settings

The pathway and the lifestyle of known enterococcus species are too complicated. The aim of the present study is to trace the path of pathogenicity of enterococci isolated from seven habitats (Cornu aspersum intestine; Bulgarian yoghurt; goat and cow feta cheese-mature and young, respectively; Arabian street food-doner kebab; cow milk; and human breast milk) by comparing their pathogenic potential. In total, 72 enterococcal strains were isolated and identified by MALDI-TOF, sequencing, and PCR. Hemolytic and gelatinase activity were biochemically determined. PCR was carried out for detection of virulence factors (cylB, esp, gls24, nucl, psaA, agg, gelE, and ace) and antibiotic resistance (erm, ermB, blaZ, vanA, aphA, mefA, gyrA, catpIP501, and aac6'-aph2″). Phenotypic antibiotic resistance was assigned according to EUCAST. Eleven representatives of the genus Enterococcus were identified: E. mundtii, E. casseliflavus, E. gilvus, E. pseudoavium, E. pallens, E. malodoratus, E. devriesei, E. gallinarum, E. durans, E. faecium, and E. faecalis. Twenty-two strains expressed α-hemolysis. Thirteen strains had the cylB gene. Only two strains expressed α-hemolysis and possessed the cylB gene simultaneously. Positive amplification for gelE was found in 35% of the isolates, but phenotypic gelatinase activity was observed only in three strains. All isolates showed varying antibiotic resistance. Only E. faecalis BM15 showed multiple resistance (AMP-HLSR-RP). Correlation between genotypic and phenotypic macrolide resistance was revealed for two E. faecalis strains.

Enterococcal Phages: Food and Health Applications

Enterococcus is a diverse genus of Gram-positive bacteria belonging to the lactic acid bacteria (LAB) group. It is found in many environments, including the human gut and fermented foods. This microbial genus is at a crossroad between its beneficial effects and the concerns regarding its safety. It plays an important role in the production of fermented foods, and some strains have even been proposed as probiotics. However, they have been identified as responsible for the accumulation of toxic compounds-biogenic amines-in foods, and over the last 20 years, they have emerged as important hospital-acquired pathogens through the acquisition of antimicrobial resistance (AMR). In food, there is a need for targeted measures to prevent their growth without disturbing other LAB members that participate in the fermentation process. Furthermore, the increase in AMR has resulted in the need for the development of new therapeutic options to treat AMR enterococcal infections. Bacteriophages have re-emerged in recent years as a precision tool for the control of bacterial populations, including the treatment of AMR microorganism infections, being a promising weapon as new antimicrobials. In this review, we focus on the problems caused by Enterococcus faecium and Enterococcus faecalis in food and health and on the recent advances in the discovery and applications of enterococcus-infecting bacteriophages against these bacteria, with special attention paid to applications against AMR enterococci.