Identification and tracing ofEnterococcusspp. by RAPD-PCR in traditional fermented sausages and meat environment

Screening and Genomic Profiling of Antimicrobial Bacteria Sourced from Poultry Slaughterhouse Effluents: Bacteriocin Production and Safety Evaluation

Background/Objectives: Antimicrobial-resistant (AMR) pathogens represent a serious threat to public health, particularly in food production systems where antibiotic use remains widespread. As a result, alternative antimicrobial treatments to antibiotics are essential for effectively managing bacterial infections. This study aimed to identify and characterize novel antimicrobial peptides produced by bacteria, known as bacteriocins, as well as to recognize safe bacteriocin-producing strains, sourced from poultry slaughterhouse effluents. Methods: A total of 864 bacterial isolates were collected across eight stages of a poultry slaughter line and screened for antimicrobial activity against Gram-positive and Gram-negative indicator strains. Whole-genome sequencing (WGS) was performed on 12 selected strains, including Enterococcus faecium (6 isolates), Lactococcus lactis (1 isolate), Lactococcus garvieae (1 isolate) and Escherichia coli (4 isolates). The presence of bacteriocin gene clusters (BGC), antibiotic resistance genes (ARG), and virulence factors (VF) was analyzed. The antimicrobial activity of a novel bacteriocin was further evaluated using in vitro cell-free protein synthesis (IV-CFPS). Results: WGS revealed multiple BGCs, including a novel class IId bacteriocin, lactococcin P1A (LcnP1A), in L. lactis SWD9. LcnP1A showed antimicrobial activity against various indicator strains, including Listeria monocytogenes. While most bacteriocin-encoding strains harbored ARGs and VFs, E. faecium SWG6 was notable for its absence of ARGs and minimal VFs, highlighting its potential as a probiotic. Conclusions: These findings underscore the importance of discovering novel bacteriocins and safer bacteriocin producing strains to address antimicrobial resistance in the food chain. Further research would validate the efficacy of both the novel lactococcin P1A bacteriocin and the E. faecium SWG6 isolate for application in processed food and animal production systems.

Non-faecium non-faecalis enterococci: a review of clinical manifestations, virulence factors, and antimicrobial resistance

SUMMARYEnterococci are a diverse group of Gram-positive bacteria that are typically found as commensals in humans, animals, and the environment. Occasionally, they may cause clinically relevant diseases such as endocarditis, septicemia, urinary tract infections, and wound infections. The majority of clinical infections in humans are caused by two species: Enterococcus faecium and Enterococcus faecalis. However, there is an increasing number of clinical infections caused by non-faecium non-faecalis (NFF) enterococci. Although NFF enterococcal species are often overlooked, studies have shown that they may harbor antimicrobial resistance (AMR) genes and virulence factors that are found in E. faecium and E. faecalis. In this review, we present an overview of the NFF enterococci with a particular focus on human clinical manifestations, epidemiology, virulence genes, and AMR genes.

Genotypic diversity and antagonistic activities of enterococci isolated from pastırma

The biodiversity of enterococci from pastırma (a traditional Turkish dry-cured meat product) by genotypic identification and the antagonistic activities of strains were investigated. Pastırma samples taken from 20 different small-scale factories were subjected to microbiological and physicochemical analysis. A hundred enterococci isolates were identified by 16S rRNA gene sequence analysis. To determine antagonistic activity of strains, Listeria monocytogenes and Staphylococcus aureus were used. The lactic acid bacteria and Micrococcus/Staphylococcus counts were ≥ 6 log cfu/g in 55% of the samples and 75% of the samples, respectively. Enterobacteriaceae was generally below the detectable level (< 2 log cfu/g). The enterococci count was higher than 6 log cfu/g in 30-35% of the samples, depending on the medium used. The enterococci isolates (100 isolates) were identified as E. faecium (80 strains), E. faecalis (19 strains) and E. hirae (1 strain) in genotypic identification. The nine E. faecium strains showed antagonistic activity against L. monocytogenes in the well diffusion test. In contrast, in the same antagonistic activity test, all of the strains had no antagonistic activity against S. aureus. Further studies could be planned to characterize E. faecium strains that show antagonistic activity against L. monocytogenes.

Agarose Gel Electrophoresis-Based RAPD-PCR-An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies

Agarose gel electrophoresis is a well-known tool to detect DNA fragments amplified in polymerase chain reaction (PCR). Its usefulness has also been confirmed for epidemiological studies based on restriction fragments length polymorphism (RFLP), usually performed using pulsed-field gel electrophoresis (PFGE). Little is known on the effectiveness for alert-pathogen epidemiological studies of another less time-consuming and costly technique called randomly amplified polymorphic DNA-PCR (RAPD-PCR). Meanwhile, its usefulness is believed to be comparable to RFLP-PFGE. Therefore, the aim of the study was to establish and optimize the conditions of agarose gel electrophoresis following RAPD-PCR for 19 Enterococcus faecium strains derived from epidemic outbreaks at intensive care units. An application of different PCR primers, primer combinations, and, in particular, agarose gel concentrations and electrophoresis conditions revealed the usefulness of this relatively fast and inexpensive method based on RAPD-PCR for epidemiological studies without a compulsion to use the specialized equipment necessary for RFLP-PFGE.

Complete Genome Sequence of Carotenoid-Producing Enterococcus gilvus CR1, Isolated from Raw Cow's Milk

Enterococcus gilvus CR1, isolated from raw cow's milk, can produce carotenoids. The complete genome sequence of this strain was determined using the PacBio RS II platform. The assembly was found to contain a circular chromosome, including carotenoid biosynthesis genes, and comprises 2,863,043 bp, with a G+C content of 41.86% and three plasmids.

Distribution of species and antimicrobial resistance among enterococci isolated from the fecal microbiota of captive blue-fronted parrot (Amazona aestiva) in Rio de Janeiro, Brazil

Enterococcal strains recovered from fecal samples of captive blue-fronted parrots (Amazona aestiva) assisted at two wild animal screening centers in Rio de Janeiro, Brazil, were identified as Enterococcus hirae (the predominant species; 75.3%), followed by Enterococcus faecalis (17.3%), Enterococcus casseliflavus (4.8%), Enterococcus gallinarum (1.7%), and Enterococcus hermanniensis (0.9%). All strains were susceptible to linezolid and teicoplanin. Rates of nonsusceptibility (including resistant and intermediate categories) to other 16 antimicrobials tested varied from 69.3% to 0.4%, A considerable proportion (48.0%) of the strains was multidrug-resistant and diverse genetic determinants associated with antimicrobial resistance were identified. Tetracycline-resistant strains carried the tet(M) and/or tet(L) genes. Macrolides resistance was associated with the erm(B), erm(A) and mefA genes, while 43.2% of the isolates were negative for the investigated genes. High-level resistance to gentamicin associated with the aac(6')-le-aph(2″)-la gene was detected in one E. faecalis strain. The two strains presenting high-level resistance to streptomycin were negative for the ant(6')-Ia, ant(3')-Ia, ant(9')-Ia and ant(9')-Ib genes. The vat(D) gene was found in all the 47 quinupristin/dalfopristin resistant strains identified as non-E. faecalis. Analysis of PFGE profiles of E. hirae strains after restriction with SmaI demonstrated the occurrence of five clonal groups. The predominant E. hirae clone was distributed among birds in the two institutions, suggesting that this clone was well adapted to the host and environments investigated. The four clonal groups identified among E. faecalis were composed by small numbers of strains and, generally, restricted to birds in the same sector. The occurrence of enterococcal strains exhibiting antimicrobial resistance traits and carrying genetic determinants that represent potential threats to the health of both humans and animals, in the intestinal microbiota of A. aestiva, highlights the need for additional monitoring studies to elucidate the population structure and the dynamics of transmission of these microorganisms among animals, humans and the environment.

Antimicrobial resistance and virulence factor gene profiles of Enterococcus spp. isolates from wild Arctocephalus australis (South American fur seal) and Arctocephalus tropicalis (Subantarctic fur seal)

Enterococci are natural inhabitants of the gastrointestinal tracts in humans and animals. Epidemiological data suggest that enterococci are important reservoirs of antimicrobial resistant genes that may be transmitted from other bacterial species The aim of this study was to investigate the species composition, antimicrobial resistance and virulence genes in enterococci recovered from fecal samples of wild Arctocephalus australis and A. tropicalis found dead along the South Coast of Brazil. From a total of 43 wild fur seals, eleven were selected for this study. Phenotypic and genotypic characterizations were used to classify Enterococcus species. Strains were tested for susceptibility to 10 antibiotics, presence of ace, gelE, asa, cylA, tet(L), tet(M) and erm(B) genes by PCR, and genetic variability using RAPD-PCR. Among the 50 enterococci isolated, 40% were Enterococcus faecalis, 40% E. hirae, 12% E. casseliflavus and 8 % other enterococcal species. Resistance profiles were observed to erythromycin, nitrofurantoin, tetracycline, norfloxacin and ciprofloxacin. The prevalence of virulence genes was ace (68%), gelE (54%), asa (22%) and cylA (4%). In erythromycin- and tetracycline strains, erm(B) and tet(M) were detected, respectively. The RAPD-PCR demonstrated a close phylogenetic relationship between the enterococci isolated from A. australis and A. tropicalis. In conclusion, different enterococcus species showing antimicrobial resistance and virulence determinates were isolated from fecal samples of fur seals. Antibiotic resistant strains in these animals could be related within food chain and aquatic pollutants or linked to environmental resistome, and demonstrates the potential importance of these animals as reservoirs and disseminators of such determinants in marine environmental.

Antibiotic resistance of lactic acid bacteria isolated from dry-fermented sausages

Dry-fermented sausages are meat products highly valued by many consumers. Manufacturing process involves fermentation driven by natural microbiota or intentionally added starter cultures and further drying. The most relevant fermentative microbiota is lactic acid bacteria (LAB) such as Lactobacillus, Pediococcus and Enterococcus, producing mainly lactate and contributing to product preservation. The great diversity of LAB in dry-fermented sausages is linked to manufacturing practices. Indigenous starters development is considered to be a very promising field, because it allows for high sanitary and sensorial quality of sausage production. LAB have a long history of safe use in fermented food, however, since they are present in human gastrointestinal tract, and are also intentionally added to the diet, concerns have been raised about the antimicrobial resistance in these beneficial bacteria. In fact, the food chain has been recognized as one of the key routes of antimicrobial resistance transmission from animal to human bacterial populations. The World Health Organization 2014 report on global surveillance of antimicrobial resistance reveals that this issue is no longer a future prediction, since evidences establish a link between the antimicrobial drugs use in food-producing animals and the emergence of resistance among common pathogens. This poses a risk to the treatment of nosocomial and community-acquired infections. This review describes the possible sources and transmission routes of antibiotic resistant LAB of dry-fermented sausages, presenting LAB antibiotic resistance profile and related genetic determinants. Whenever LAB are used as starters in dry-fermented sausages processing, safety concerns regarding antimicrobial resistance should be addressed since antibiotic resistant genes could be mobilized and transferred to other bacteria.

Prevalence and phenotypic characterization of Enterococcus spp. isolated from food in Brazil

We evaluated the frequency of enterococci from food and found 95.2% of positivity, being E. faecium and E. faecalis the most frequent species. High-level streptomycin resistance was observed, as well as gelatinase and hemolysis activity, showing the potential role of environmental strains as reservoir of virulence and resistance traits.

Role of house flies in the ecology of Enterococcus faecalis from wastewater treatment facilities

Enterococci are important nosocomial pathogens, with Enterococcus faecalis most commonly responsible for human infections. In this study, we used several measures to test the hypothesis that house flies, Musca domestica (L.), acquire and disseminate antibiotic-resistant and potentially virulent E. faecalis from wastewater treatment facilities (WWTF) to the surrounding urban environment. House flies and sludge from four WWTF (1-4) as well as house flies from three urban sites close to WWTF-1 were collected and cultured for enterococci. Enterococci were identified, quantified, screened for antibiotic resistance and virulence traits, and assessed for clonality. Of the 11 antibiotics tested, E. faecalis was most commonly resistant to tetracycline, doxycycline, streptomycin, gentamicin, and erythromycin, and these traits were intra-species horizontally transferrable by in vitro conjugation. Profiles of E. faecalis (prevalence, antibiotic resistance, and virulence traits) from each of WWTF sludge and associated house flies were similar, indicating that flies successfully acquired these bacteria from this substrate. The greatest number of E. faecalis with antibiotic resistance and virulence factors (i.e., gelatinase, cytolysin, enterococcus surface protein, and aggregation substance) originated from WWTF-1 that processed meat waste from a nearby commercial meat-processing plant, suggesting an agricultural rather than human clinical source of these isolates. E. faecalis from house flies collected from three sites 0.7-1.5 km away from WWTF-1 were also similar in their antibiotic resistance profiles; however, antibiotic resistance was significantly less frequent. Clonal diversity assessment using pulsed-field gel electrophoresis revealed the same clones of E. faecalis from sludge and house flies from WWTF-1 but not from the three urban sites close to WWTF-1. This study demonstrates that house flies acquire antibiotic-resistant enterococci from WWTF and potentially disseminate them to the surrounding environment.

Molecular detection of bacterial contamination in gnotobiotic rodent units

Gnotobiotic rodents provide an important technique to study the functional roles of commensal bacteria in host physiology and pathophysiology. To ensure sterility, these animals must be screened frequently for contamination. The traditional screening approaches of culturing and Gram staining feces have inherent limitations, as many bacteria are uncultivable and fecal Gram stains are difficult to interpret. Thus, we developed and validated molecular methods to definitively detect and identify contamination in germ-free (GF) and selectively colonized animals. Fresh fecal pellets were collected from rodents housed in GF isolators, spontaneously contaminated ex-GF isolators, selectively colonized isolators and specific pathogen-free (SPF) conditions. DNA isolated from mouse and rat fecal samples was amplified by polymerase chain reaction (PCR) and subjected to quantitative PCR (qPCR) using universal primers that amplify the 16S rRNA gene from all bacterial groups. PCR products were sequenced to identify contaminating bacterial species. Random amplification of polymorphic DNA (RAPD) PCR profiles verified bacterial inoculation of selectively colonized animals. These PCR techniques more accurately detected and identified GF isolator contamination than current standard approaches. These molecular techniques can be utilized to more definitively screen GF and selectively colonized animals for bacterial contamination when Gram stain and/or culture results are un-interpretable or inconsistent.

Antimicrobial resistance profiles of Enterococcus faecalis and Enterococcus faecium isolated from artisanal food of animal origin in Argentina

Enterococci are part of the indigenous microbiota of human gastrointestinal tract and food of animal origin. Enterococci inhabiting non-human reservoirs play a critical role in the acquisition and dissemination of antimicrobial resistance determinants. The aim of this work was to investigate the antimicrobial resistance in Enterococcus faecalis and Enterococcus faecium strains recovered from artisanal food of animal origin. Samples of goat cheese (n = 42), cow cheese (n = 40), artisanal salami (n = 30), and minced meat for the manufacture of hamburgers (n = 60) were analyzed. Phenotypic and genotypic tests for species-level identification of the recovered isolates were carried out. Minimum inhibitory concentration (MIC) study for in vitro quantitative antimicrobial resistance assessment was performed, and 71 E. faecalis and 22 E. faecium were isolated. The recovered enterococci showed different multi-drug resistance patterns that included tretracycline, erythromycin, ciprofloxacin, linezolid, penicillin, ampicillin, vancomycin, teicoplanin, gentamicin (high-level resistance), and streptomycin (high-level resistance). VanA-type E. faecium were detected. β-lactamase activity was not observed. Artisanal foods of animal origin act as a non-human reservoir of E. faecalis and E. faecuim strains, expressing multi-resistance to antimicrobials. In conclusion, the implementation of a continuous antimicrobial resistance surveillance in enterococci isolated from artisanal food of animal origin is important.

Virulence factors and antibiotic susceptibility in enterococci isolated from oral mucosal and deep infections

OBJECTIVE

This study evaluates the presence of virulence factors and antibiotic susceptibility among enterococcal isolates from oral mucosal and deep infections.

METHODS

Forty-three enterococcal strains from oral mucosal lesions and 18 from deep infections were isolated from 830 samples that were sent during 2 years to Oral Microbiology, University of Gothenburg, for analysis. The 61 strains were identified by 16S rDNA, and characterized by the presence of the virulence genes efa A (endocarditis gene), gel E (gelatinase gene), ace (collagen binding antigen gene), asa (aggregation substance gene), cyl A (cytolysin activator gene) and esp (surface adhesin gene), tested for the production of bacteriocins and presence of plasmids. MIC determination was performed using the E-test method against the most commonly used antibiotics in dentistry, for example, penicillin V, amoxicillin and clindamycin. Vancomycin was included in order to detect vancomycin-resistant enterococci (VRE) strains.

RESULTS

Sixty strains were identified as Enterococcus faecalis and one as Enterococcus faecium. All the virulence genes were detected in more than 93.3% (efa A and esp) of the E. faecalis strains, while the presence of phenotypic characteristics was much lower (gelatinase 10% and hemolysin 16.7%). Forty-six strains produced bacteriocins and one to six plasmids were detected in half of the isolates.

CONCLUSIONS

Enterococcal strains from oral infections had a high virulence capacity, showed bacteriocin production and had numerous plasmids. They were generally susceptible to ampicillins but were resistant to clindamycin, commonly used in dentistry, and no VRE-strain was found.

Enterococci as probiotics and their implications in food safety

Enterococci belong to the lactic acid bacteria (LAB) and they are of importance in foods due to their involvement in food spoilage and fermentations, as well as their utilisation as probiotics in humans and slaughter animals. However, they are also important nosocomial pathogens that cause bacteraemia, endocarditis and other infections. Some strains are resistant to many antibiotics and possess virulence factors such as adhesins, invasins, pili and haemolysin. The role of enterococci in disease has raised questions on their safety for use in foods or as probiotics. Studies on the incidence of virulence traits among enterococcal strains isolated from food showed that some can harbour virulence traits, but it is also thought that virulence is not the result of the presence of specific virulence determinants alone, but is rather a more intricate process. Specific genetic lineages of hospital-adapted strains have emerged, such as E. faecium clonal complex (CC) 17 and E. faecalis CC2, CC9, CC28 and CC40, which are high risk enterococcal clonal complexes. These are characterised by the presence of antibiotic resistance determinants and/or virulence factors, often located on pathogenicity islands or plasmids. Mobile genetic elements thus are considered to play a major role in the establishment of problematic lineages. Although enterococci occur in high numbers in certain types of fermented cheeses and sausages, they are not deliberately added as starter cultures. Some E. faecium and E. faecalis strains are used as probiotics and are ingested in high numbers, generally in the form of pharmaceutical preparations. Such probiotics are administered to treat diarrhoea, antibiotic-associated diarrhoea or irritable bowel syndrome, to lower cholesterol levels or to improve host immunity. In animals, enterococcal probiotics are mainly used to treat or prevent diarrhoea, for immune stimulation or to improve growth. From a food microbiological point of view, the safety of the bacteria used as probiotics must be assured, and data on the major strains in use so far indicate that they are safe. The advantage of use of probiotics in slaughter animals, from a food microbiological point of view, lies in the reduction of zoonotic pathogens in the gastrointestinal tract of animals which prevents the transmission of these pathogens via food. The use of enterococcal probiotics should, in view of the development of problematic lineages and the potential for gene transfer in the gastrointestinal tract of both humans and animals, be carefully monitored, and the advantages of using these and new strains should be considered in a well contemplated risk/benefit analysis.

Volatile profile and microbiological characterization of hollow defect in dry-cured ham

This paper describes the physicochemical and microbiological parameters and volatile profile of the muscles surrounding the coxofemoral joint which are affected with hollow defect when compared to the part of muscles nearby which did not show this defect. Differences of the same parameters between both areas in dry-cured hams without this defect were also analyzed. Gram-positive catalase-positive cocci were the predominant flora in the muscles affected with hollow defect, with the main species being Staphyloccocus equorum, Staphylococcus nepalensis and Staphylococcus xylosus. Lactic acid bacteria, Listeria monocytogenes and Staphylococcus aureus were <2 log CFU g(-1) and Salmonella spp. was not detected. Volatile profile of samples affected with hollow defect had higher amounts of compounds such as esters, pyrazines, sulfurs and furans. There was a positive correlation between the amount of ester compounds and the hollow defect intensity. Moisture content was lower and pH values were higher in affected areas than in unaffected areas.