Antimicrobial Resistance, Virulence Determinants, and Biofilm Formation of Enterococcus Species From Ready-to-Eat Seafood

Commercial Day-Old Chicks in Nigeria Are Potential Reservoirs of Colistin- and Tigecycline-Resistant Potentially Pathogenic Escherichia coli

Background: Frequent use of colistin (COL) and tetracyclines in the Nigerian poultry sector potentially triggers bacterial resistance against COL and tigecycline (TIG), which are last-line antibiotics used to treat multidrug-resistant infections. Aim/Objectives: This study aimed to isolate COL- and TIG-resistant E. coli from commercial day-old chicks distributed to poultry farmers in Nsukka Southeastern Nigeria, assess the production of extended-spectrum β-lactamase (ESBL) and carbapenemase by the isolates, and establish their pathogenic potentials. Materials and Methods: Non-duplicate cloacal swabs were systematically collected from 250 randomly selected day-old chicks. MacConkey agar with 1 µg/mL of COL and 16 µg/mL of tetracycline was used for the isolation of putative COL- and tetracycline-resistant E. coli, respectively. E. coli isolates were confirmed biochemically using the API20E Gram-negative identification kit and molecularly by polymerase chain reaction targeting the uidA gene. Phenotypic COL resistance was established using COL agar and COL disc elution tests, while TIG insusceptibility was determined with disc diffusion. ESBL and carbapenemase production was assessed by double-disc synergy and modified carbapenem inactivation methods, respectively. Pathogenic potentials were determined using phenotypic methods. Results: COL- and TIG-resistant E. coli was recovered from 95 (38.0%) and 62 (24.8%) swabs from the 250 chicks, respectively. None of the isolates were potential ESBL or carbapenemase producers. The COL-resistant isolates displayed pathogenic potentials such as biofilm formation, haemagglutination, cell surface hydrophobicity, surface layer, and gelatinase activities at rates of 30.7%, 8.4%, 33.7%, 23.5%, and 17.6%, respectively. Meanwhile, the TIG-resistant isolates exhibited their respective potentials at rates of 47.0%, 21.0%, 35.5%, 58.1%, and 43.6%. Red, dry, and rough (RDAR) was the predominant curli fimbriae, and the cellulose morphotype portrayed by both the COL- and TIG-unsusceptible potential biofilm-producing isolates. Conclusions: This study demonstrates that a significant percentage of commercial day-old chicks distributed to farmers in Nsukka, southeastern Nigeria, are colonized by potentially pathogenic COL- and TIG-resistant E. coli, which could spread to humans and the environment.

Curcuma longa rhizome extract: a potential antibiofilm agent against antibiotic-resistant foodborne pathogens

The traditional medicinal value of Curcuma longa (turmeric) and its potential relevance in modern healthcare suggests that traditional remedies and natural products can provide valuable solutions to contemporary challenges, such as combating biofilms and antibiotic-resistant pathogens, potentially offering new strategies for addressing health and safety issues in the fields of food and medicine. This study assessed the antibiofilm and antibacterial characterization of Curcuma longa rhizome extract against antibiotic-resistant foodborne pathogens. Gas Chromatography-Mass Spectrometry (GC-MS) and Fourier-transform infrared (FTIR) analysis were determined to check for the compounds, functional groups, and constituents of the plant extract. In-vitro antibiofilm and antibacterial bioassay of the extract were determined using standard bacteriological procedures. Potential mechanisms of the plant extract were also studied using standard biological methods. The important chemical constituents from the GC-MS extract of C. longa are arturmerone, cinnamyl angelate, tumerone, γ-atlantone, atlantone, α-atlantone, γ-atlantone and curlone. The FTIR analysis of the extract comprises alkyl halides, bromoalkanes, alkanes, ethylene molecules, arenes, amines, alcohols, sulfones, carboxylic acids and their derivatives, aromatic compounds, and phenols. The MIC of C. longa crude extract ranges from ethanol extract (0.03125 - 0.5 mg/mL) and acetone extract (0.0625 - 0.5 mg/mL). The MBC range is as follows: ethanol extract (0.125 - 1 mg/mL), acetone extract (0.125 - 1 mg/mL). The time-kill kinetics showed significant cell reduction with time. The bacterial isolates' nucleic acids and protein leakage were consistent with increased extract concentration and time. There was a reduction in the biofilm cell on the shrimp surface and EPS with increased concentration and time. C. longa exerted significant anti-biofilm activity by removing existing biofilms, disrupting cell connections, and decreasing cells in biofilms. These findings can aid food protection from microbial contamination and prevent biofilms-related infections.

Assessment of prevalence, antibiotic resistance, and virulence profiles of biofilm-forming Enterococcus faecalis isolated from raw seafood in Bangladesh

Enterococcus faecalis are often resistant to different classes of antibiotics, harbor virulence determinants, and produce biofilm. The presence of E. faecalis in raw seafood exhibits serious public health significance. This study aimed to identify antibiotic resistance patterns and virulence factors in biofilm-forming E. faecalis strains extracted from seafood in Bangladesh. A total of 150 samples of raw seafood, comprising 50 shrimps, 25 crabs, and 75 fish, were collected and subjected to culturing, biochemical, and PCR assays to detect E. faecalis. The biofilm-forming abilities of the isolates were determined by Congo Red agar (CRA) plate and Crystal Violet Micro-titer Plate (CVMP) tests. Antibiotic resistance profiles were evaluated using the disk diffusion method. Virulence genes of the isolates were detected by PCR assay. The occurrence of E. faecalis was 29.3 % (44/150), which was higher in crabs and fish (36 %) than in shrimps (16 %). In CRA and CVMP tests, biofilm-forming abilities were observed in 88.64 % of the isolates, whereas 11 (25 %) and 28 (63.6 %) were strong- and intermediate-biofilm formers, respectively. All the isolates contained at least two virulence genes, including pil and ace (97.7 %), sprE (95.5 %), gelE (90.9 %), fsrB (79.6 %), agg (70.5 %), fsrA (68.2 %), and fsrC (61.4 %). All the isolates were phenotypically resistant to penicillin, followed by ampicillin and rifampicin (86.4 %), erythromycin (13.7 %), and tetracycline, vancomycin, norfloxacin, and linezolid (2.3 %). Resistant gene bla TEM was found in 61.4 % of the isolates. Moreover, the study found that E. faecalis strains with strong biofilm-forming capabilities had significantly higher levels of virulence genes and antibiotic resistance (p < 0.05) compared to those with intermediate and/or no biofilm-forming abilities. To the best of our knowledge, this research represents the first instance in Bangladesh of assessing antibiotic resistance and identifying virulence genes in biofilm-forming E. faecalis strains isolated from seafood samples. Our study revealed that seafood is a carrier of antibiotic-resistant, virulent, and biofilm-forming E. faecalis, demonstrating a potential public health threat.

Phenotypic and genotypic characterization of Enterococcus faecalis and Enterococcus faecium isolated from fish, vegetables, and humans

Enterococci, common hospital-acquired infections in immunocompromised patients, have garnered attention in clinical microbiology. To determine the clinical relevance of enterococci as food-borne pathogens, 116 fish, 90 vegetables, and 120 human diarrheal samples were tested for E. faecalis and E. faecium pathogenicity. Conventionally, 69 of 326 (21.17%) samples were positive for Enterococcus species, 52 (15.95%) of which were molecularly classified as E. faecalis and 13 (3.99%) as E. faecium. The E. faecalis contamination percentage of fresh fish (19.70%) was higher than frozen fish (4%). Cauliflower had the highest E. faecalis percentage (16.67%) when fish and vegetable samples didn't harbor the E. faecium atpA gene. 23.33% and 10.83% of participants' samples were molecularly confirmed as E. faecalis and E. faecium positive, respectively. E. faecalis isolates had all virulence genes, with gels being the most common (65.38%), while cylA and asa1 genes couldn't be detected in E. faecium isolates. E. faecalis showed the highest resistance against vancomycin and tetracycline (69.23%), whereas E. faecium extremely resisted tetracycline (76.92%) and erythromycin (69.23%) with the recognition of MDR among 44.2% of E. faecalis and 38.5% of E. faecium isolates. The great similarity of our isolates showed the clinical importance of food-borne antibiotic-resistant enterococci.

Analysis of Antibiotic Resistance Genes (ARGs) across Diverse Bacterial Species in Shrimp Aquaculture

There is little information available on antibiotic resistance (ABR) within shrimp aquaculture environments. The aim of this study was to investigate the presence of antibiotic resistance genes (ARGs) in shrimp farming operations in Atacames, Ecuador. Water samples (n = 162) and shrimp samples (n = 54) were collected from three shrimp farming operations. Samples were cultured and a subset of isolates that grew in the presence of ceftriaxone, a third-generation cephalosporin, were analyzed using whole-genome sequencing (WGS). Among the sequenced isolates (n = 44), 73% of the isolates contained at least one ARG and the average number of ARGs per isolate was two, with a median of 3.5 ARGs. Antibiotic resistance genes that confer resistance to the β-lactam class of antibiotics were observed in 65% of the sequenced isolates from water (20/31) and 54% of the isolates from shrimp (7/13). We identified 61 different ARGs across the 44 sequenced isolates, which conferred resistance to nine antibiotic classes. Over half of all sequenced isolates (59%, n = 26) carried ARGs that confer resistance to more than one class of antibiotics. ARGs for certain antibiotic classes were more common, including beta-lactams (26 ARGs); aminoglycosides (11 ARGs); chloramphenicol (three ARGs); and trimethoprim (four ARGs). Sequenced isolates consisted of a diverse array of bacterial orders and species, including Escherichia coli (48%), Klebsiella pneumoniae (7%), Aeromonadales (7%), Pseudomonadales (16%), Enterobacter cloacae (2%), and Citrobacter freundii (2%). Many ARGs were shared across diverse species, underscoring the risk of horizontal gene transfer in these environments. This study indicated the widespread presence of extended-spectrum β-lactamase (ESBL) genes in shrimp aquaculture, including blaCTX-M, blaSHV, and blaTEM genes. Increased antibiotic resistance surveillance of shrimp farms and identification of aquaculture operation-level risk factors, such as antibiotic use, will likely be important for mitigating the spread of ARGs of clinical significance.

Enterococcus spp. in fish: Analysis of the presence and resistance in samples from Tri-City, Poland

The growing concern over antibiotic resistance in foodborne pathogens necessitates comprehensive assessments of its prevalence and associated risks in various food products. The present study aimed to assess the occurrence of Enterococcus spp. in samples of fish purchased at various points of sale in the Tricity region. The selection of products (n = 74) was based on their availability and included both fish caught in the Baltic region and products imported from, Vietnam, China, Norway, and European Union (EU) countries. For bacterial isolation, samples were inoculated into selective broth, and the growth of enterococci was assessed based on turbidity. Positive cultures were confirmed by a change in color in bromocresol purple broth and were isolated on Slanetz-Bartley agar. Bacteria were present in all tested samples regardless of the degree of raw material processing as follows: frozen (F)- 55%, fresh/raw (FS)- 70.6%, thawed (DF)- 30%, smoked (S)- 50%, and the packaging methods, modified atmosphere packaging (MAP)- 34.4%, unit packaging (UP)- 75%, and sold in bulk (SB)- 76.9%, with an overall frequency of occurrence of 58.1%. The number of bacteria ranged from not detected to 4.28-log cfu/g, with the lowest mean values for thawed fish and those packed in MAP. Tests conducted on 24 strains isolated from samples showed their varied sensitivity to tetracyclines. Single cases of multidrug resistance of the tested strains were also observed. The conducted statistical analysis did not show statistically significant differences in the count of enterococci based on the origin, degree of processing, or packaging (p < 0.05). Moreover, differences in strain sensitivity to ampicillin were observed. Detected cases of resistance, especially to tetracycline, require careful monitoring and action to limit the health risks associated with resistant bacterial strains in food products.

Dissemination, virulence characteristic, antibiotic resistance determinants of emerging linezolid and vancomycin-resistant Enterococcus spp. in fish and crustacean

Enterococci are emerging nosocomial pathogens. Their widespread distribution causes them to be food contaminants. Furthermore, Enterococci can colonize various ecological niches and diffuse into the food chain via contaminated animals and foods because of their remarkable tolerance to unfavorable environmental circumstances. Due to their potential dissemination to humans, antimicrobial-resistant Enterococci in fish are a worldwide health issue. This study characterized AMR, ARGs, VAGs, gelatinase activity, and biofilm formation in Enterococcus spp. recovered from fish and seafood and evaluated potential correlations. 54 Enterococcus spp. strains(32.73 %)were isolated from 165 samples (75 Oreochromis niloticus, 30 Argyrosomus regius, and 60 Shrimp), comprising 30 Enterococcus faecalis (55.6 %) and 24 Enterococcus faecium (44.4 %) with total 32.73 % (54/165), The maximum prevalence rate of Enterococcus spp. was observed in Nile tilapia (34/54; 63 %), followed by shrimp (14/54; 25.9 %) and Argyrosomus regius (6/54; 11.1 %). The maximum prevalence rate of E. faecalis was observed in Nile tilapia (22/30; 73.3 %), followed by shrimp (8/30; 26.7 %) with significant differences. The prevalence rate of E. faecium was observed in Nile tilapia (12/24; 50 %), followed by shrimp (6/24,25 %). E. faecium is only isolated from Argyrosomus regius (6/24,25 %). Isolates exhibited high resistance against both tetracycline (90.7 %) and erythromycin(88.9 %), followed by gentamycin (77.8 %), ciprofloxacin (74.1 %), levofloxacin (72.2 %), penicillin (44.4 %), vancomycin (37 %), and linezolid (20.4 %). 50 strains (92.6 %) exhibited resistance to more than two antibiotics, 5 strains (10 %) were XDR, and the remaining 45 strains (90 %) were classified as MDR. 92.6 % of the isolates had MARindices >0.2, indicating they originated in settings with a high risk of contamination. Additionally, ten ARGs were identified, with tet(M) 92.6 %, followed by erm(B) (88.9 %), aac(6')-Ie-aph(2″)-Ia(77.8 %), tet(K) (75.9 %), gyrA (74.1 %), blaZ (48.1 %), vanA (37 %), vanB (31.5 %), optrA (20.4 %), and catA(3.7 %). Biofilm formation and gelatinase activity were observed in 85.2 %, and 61.1 % of the isolates, respectively. A total of 11 VAGs were detected, with gelE as the most prevalent (83.3 %) followed by agg(79.6 %), pil (74.1 %), both sprE and asa1 (72.2 %), hyl (70.4 %), eps(68.5 %), EF3314 (57.4 %), ace (50 %), and cylA (35.2 %) with no detection of cylB. In conclusion, the emergence of linezolid-resistant -vancomycin-resistant enterococci recovered from Egyptian fish and shrimp, suggests that fish and seafood might participate a fundamental part in the emergence of antimicrobial resistance among humans.

Species prevalence, virulence genes, and antibiotic resistance of enterococci from food-producing animals at a slaughterhouse in Turkey

Healthy cattle, sheep, and goats can be reservoirs for gastrointestinal pathogenic fecal enterococci, some of which could be multidrug-resistant to antimicrobials. The objective of this study was to determine the prevalence and diversity of Enterococcus species in healthy sheep, goat, and cattle carcasses, as well as to analyze the antimicrobial resistance phenotype/genotype and the virulence gene content. During 2019-2020, carcass surface samples were collected from 150 ruminants in a slaughterhouse. A total of 90 enterococci, comprising five species, were obtained. The overall prevalence of enterococci was found to be 60%, out of which 37.7% were identified as Enterococcus (E.) hirae, 33.3% as E. casseliflavus, 15.5% as E. faecium, 12.2% as E. faecalis, and 1.1% as E. gallinarum. Virulence-associated genes of efaA (12.2%) were commonly observed in the Enterococcus isolates, followed by gelE (3.3%), asaI (3.3%), and ace (2.2%). High resistance to quinupristin-dalfopristin (28.8%), tetracycline (21.1%), ampicillin (20%), and rifampin (15.5%) was found in two, four, four, and five of the Enterococcus species group, respectively. The resistance of Enterococcus isolates to 11 antibiotic groups was determined and multidrug resistant (MDR) strains were found in 18.8% of Enterococcus isolates. Characteristic resistance genes were identified by PCR with an incidence of 6.6%, 2.2%, 1.1%, 1.1%, 1.1%, and 1.1% for the tetM, ermB, ermA, aac(6')Ie-aph(2")-la, VanC1, and VanC2 genes in Enterococcus isolates, respectively. Efflux pump genes causing multidrug resistance were detected in Enterococcus isolates (34.4%). The results showed that there were enterococci in the slaughterhouse with a number of genes linked to virulence that could be harmful to human health.

Assessment of Zn and Cu in piglets' liver and kidney: impact in fecal Enterococcus spp.?

Zinc and copper have been used as growth promotors in alternative to antibiotics in pig's diet. The aim was the ascertainment of the Zn and Cu concentrations in piglets' liver and kidney and their impact in the reduced susceptibility to Zn, Cu, and antibiotics in enterococci, used as microbiota biomarker. Zn and Cu were determined in the livers and kidneys of 43 piglets slaughtered in Portugal, by flame atomic absorption spectrometry. Enterococci were isolated from feces for determining the identification of species (E. faecalis, E. faecium, and Enterococcus spp.); susceptibility to vancomycin, ciprofloxacin, linezolid, tigecycline, ampicillin, imipenem, and metals; and Cu tolerance genes. In piglets with Zn and Cu high or toxic levels, enterococci had reduced susceptibility to ions, reinforced by the presence of Cu tolerance genes and by resistance to antibiotics. The study relevance is to show the relationship between these metals' levels and decreased susceptibility to Cu, Zn, and antibiotics by enterococci. From the results, it could be supposed that the piglets were being fed with high doses of Zn and Cu which could select more resistant bacteria to both antibiotics and metals that could spread to environment and humans.

An insights into emerging trends to control the threats of antimicrobial resistance (AMR): an address to public health risks

Antimicrobial agents are used to treat microbial ailments, but increased use of antibiotics and exposure to infections in healthcare facilities and hospitals as well as the excessive and inappropriate use of antibiotics at the society level lead to the emergence of multidrug-resistant (MDR) bacteria. Antimicrobial resistance (AMR) is considered a public health concern and has rendered the treatment of different infections more challenging. The bacterial strains develop resistance against antimicrobial agents by limiting intracellular drug accumulation (increasing efflux or decreasing influx of antibiotics), modification and inactivation of drugs and its targets, enzymatic inhibition, and biofilm formation. However, the driving factors of AMR include the sociocultural and economic circumstances of a country, the use of falsified and substandard medicines, the use of antibiotics in farm animals, and food processing technologies. These factors make AMR one of the major menaces faced by mankind. In order to promote reciprocal learning, this article summarizes the current AMR situation in Pakistan and how it interacts with the health issues related to the COVID-19 pandemic. The COVID-19 pandemic aids in illuminating the possible long-term impacts of AMR, which are less immediate but not less severe since their measures and effects are equivalent. Impact on other sectors, including the health industry, the economy, and trade are also discussed. We conclude by summarizing the several approaches that could be used to address this issue.

Biofilms as Battlefield Armor for Bacteria against Antibiotics: Challenges and Combating Strategies

Bacterial biofilms are formed by communities, which are encased in a matrix of extracellular polymeric substances (EPS). Notably, bacteria in biofilms display a set of 'emergent properties' that vary considerably from free-living bacterial cells. Biofilms help bacteria to survive under multiple stressful conditions such as providing immunity against antibiotics. Apart from the provision of multi-layered defense for enabling poor antibiotic absorption and adaptive persistor cells, biofilms utilize their extracellular components, e.g., extracellular DNA (eDNA), chemical-like catalase, various genes and their regulators to combat antibiotics. The response of biofilms depends on the type of antibiotic that comes into contact with biofilms. For example, excessive production of eDNA exerts resistance against cell wall and DNA targeting antibiotics and the release of antagonist chemicals neutralizes cell membrane inhibitors, whereas the induction of protein and folic acid antibiotics inside cells is lowered by mutating genes and their regulators. Here, we review the current state of knowledge of biofilm-based resistance to various antibiotic classes in bacteria and genes responsible for biofilm development, and the key role of quorum sensing in developing biofilms and antibiotic resistance is also discussed. In this review, we also highlight new and modified techniques such as CRISPR/Cas, nanotechnology and bacteriophage therapy. These technologies might be useful to eliminate pathogens residing in biofilms by combating biofilm-induced antibiotic resistance and making this world free of antibiotic resistance.

Antimicrobial Resistance in Bacteria from Meat and Meat Products: A One Health Perspective

According to the 2030 Agenda of the United Nations, one of the sustainable development goals is to ensure sustainable consumption and production patterns. The need to ensure food safety includes, other than microbiological hazards, concerns with antimicrobial-resistant (AMR) bacteria. The emergence of resistant bacteria in the food industry is essentially due to the abusive, and sometimes incorrect, administration of antimicrobials. Although not allowed in Europe, antimicrobials are often administered to promote animal growth. Each time antimicrobials are used, a selective pressure is applied to AMR bacteria. Moreover, AMR genes can be transmitted to humans through the consumption of meat-harbouring-resistant bacteria, which highlights the One Health dimension of antimicrobial resistance. Furthermore, the appropriate use of antimicrobials to ensure efficacy and the best possible outcome for the treatment of infections is regulated through the recommendations of antimicrobial stewardship. The present manuscript aims to give the current state of the art about the transmission of AMR bacteria, particularly methicillin-resistant S. aureus, ESBL-producing Enterobacteriaceae, and vancomycin-resistant Enterococcus spp., along with other ESKAPE bacteria, from animals to humans through the consumption of meat and meat products, with emphasis on pork meat and pork meat products, which are considered the most consumed worldwide.

Safety evaluation of enterococci isolated from raw milk and artisanal cheeses made in Slovenia and Serbia

Enterococci represent a significant part of the non-starter LAB microbiota of artisanal cheeses produced mainly from raw milk. Common approaches to safety evaluation of enterococci isolates include assessment of antimicrobial resistance and virulence potential. Hence, a collection of 47 (n = 22, Serbia; n = 25, Slovenia) dairy enterococcal isolates, of which E. faecalis (n = 28), E. faecium (n = 11), E. durans (n = 5), E. casseliflavus (n = 2), and E. gallinarum (n = 1), was analyzed. The susceptibility to 12 antimicrobials was tested using a broth microdilution method, and the presence of the selected antimicrobial resistance and virulence genes was investigated using PCR. Isolates were resistant to tetracycline (TET) (25.5%), erythromycin (ERY) (17.0%), gentamycin and chloramphenicol (CHL) (∼6%). No resistance to ampicillin (AMP), ciprofloxacin (CIP), daptomycin (DAP), linezolid (LZD), teicoplanin (TEI), tigecycline (TGC) and vancomycin (VAN) was detected. Among all the resistance determinants analyzed, ermB gene was detected most frequently. All 10 virulence genes analyzed were detected with a distribution of cpd (72.3%), cob and ccf (70.2%), gelE (68.1%), hyl (59.6%), agg (53.2%) and esp (46.8%). The genes encoding cytolysin (cylA, cylM and cylB) were amplified to a lesser extent (21.3%, 21.3% and 12.8%, respectively). However, due to the limited number of enterococci isolates analyzed in the present study, further studies are still required in order to better document the safety status of dairy enterococci.

Resistance Profiles and Virulence Determinants in Biofilm-Forming Enterococcus faecium Isolated from Raw Seafood in Bangladesh

Pathogenic, antibiotic-resistant, and biofilm-forming bacteria can be transferred to humans through the consumption of contaminated seafood. The present study was carried out to determine antibiotic resistance profiles and virulence determinants in biofilm-forming Enterococcus faecium isolated from seafood in Bangladesh. A total of 150 seafood samples, including shrimp (n = 50), crabs (n = 25), and marine fish (n = 75), were screened using cultural, staining, biochemical, polymerase chain reaction (PCR), Congo red (CR), and disk diffusion (DD) assays. In PCR, E. faecium was detected in 27.3% (41/150; CI95% 20.8; 34.9) of samples, where marine fish (34.7%, CI95% 24.9; 45.9) had the highest prevalence (p < 0.05) compared to crabs (32%, CI95% 17.2; 51.6) and shrimp (14%, CI95% 7.0; 26.1). Thirty-two (78.1%, CI95% 63.3; 88.0) of the E. faecium isolates were determined to be biofilm formers in the CR test, where 43.9% (18/41, CI95% 29.9; 59.0) and 34.2% (14/41, CI95% 21.6; 49.5) of the isolates were strong and intermediate biofilm formers, respectively. In PCR, virulence genes, i.e., pil (100%), ace (92.7%), agg (68.3%), fsrA (65.9%), gelE (63.4%), sprE (53.7%), fsrB (51.2%), and fsrC (43.9%), were detected in E. faecium isolates. All the E. faecium isolates were phenotypically resistant to ≥3 antimicrobial categories and ≥3 antibiotics, including WHO-classified reserve antibiotics linezolid (70.7%) and fosfomycin (19.5%). Moreover, the multiple antibiotic resistance index ranged up to 0.8, showing resistance to ten antibiotics and eight antibiotic classes. In this study, the prevalence of virulence genes and antibiotic resistance was significantly greater (p < 0.05) in strong biofilm-forming E. faecium strains as compared to strains with intermediate and non-biofilm-forming abilities. As far as we know, this study, for the first time in Bangladesh, determined antibiotic resistance and detected virulence genes in biofilm-forming E. faecium isolated from seafood samples. The data from this study could play a significant role in evaluating potential health hazards linked to the ingestion of uncooked or minimally processed seafood.

Prevalence and antimicrobial resistance profiles of Vibrio spp. and Enterococcus spp. in retail shrimp in Northern California

Shrimp is one of the most consumed seafood products globally. Antimicrobial drugs play an integral role in disease mitigation in aquaculture settings, but their prevalent use raises public health concerns on the emergence and spread of antimicrobial resistant microorganisms. Vibrio spp., as the most common causative agents of seafood-borne infections in humans, and Enterococcus spp., as an indicator organism, are focal bacteria of interest for the monitoring of antimicrobial resistance (AMR) in seafood. In this study, 400 samples of retail shrimp were collected from randomly selected grocery stores in the Greater Sacramento, California, area between September 2019 and June 2020. The prevalence of Vibrio spp. and Enterococcus spp. was 60.25% (241/400) and 89.75% (359/400), respectively. Subsamples of Vibrio (n = 110) and Enterococcus (n = 110) isolates were subjected to antimicrobial susceptibility testing (AST). Vibrio isolates had high phenotypic resistance to ampicillin (52/110, 47.27%) and cefoxitin (39/110, 35.45%). Enterococcus were most frequently resistant to lincomycin (106/110, 96.36%), quinupristin-dalfopristin (96/110, 87.27%), ciprofloxacin (93/110, 84.55%), linezolid (86/110, 78.18%), and erythromycin (58/110, 52.73%). For both Vibrio and Enterococcus, no significant associations were observed between multidrug resistance (MDR, resistance to ≥3 drug classes) in isolates from farm raised and wild caught shrimp (p > 0.05) and in isolates of domestic and imported origin (p > 0.05). Whole genome sequencing (WGS) of a subset of Vibrio isolates (n = 42) speciated isolates as primarily V. metschnikovii (24/42; 57.14%) and V. parahaemolyticus (12/42; 28.57%), and detected 27 unique antimicrobial resistance genes (ARGs) across these isolates, most commonly qnrVC6 (19.05%, 8/42), dfrA31 (11.90%, 5/42), dfrA6 (9.5%, 4/42), qnrVC1 (9.5%, 4/42). Additionally, WGS predicted phenotypic resistance in Vibrio isolates with an overall sensitivity of 11.54% and specificity of 96.05%. This study provides insights on the prevalence and distribution of AMR in Vibrio spp. and Enterococcus spp. from retail shrimp in California which are important for food safety and public health and exemplifies the value of surveillance in monitoring the spread of AMR and its genetic determinants.

Analysis of Antibiotic-Resistant and Virulence Genes of Enterococcus Detected in Calf Colostrum-One Health Perspective

Enterococci are considered among the most prevalent global multidrug-resistant microorganisms globally. Their dissemination is a global concern, particularly by food-producing animals for both animals and humans. The aim of this study was to identify the species and investigate the antibiotic resistance and virulence profile of Enterococcus in bovine colostrum. Out of 88 presumptive Enterococcus isolates, species identification and susceptibility to 14 antimicrobials were tested using the disk diffusion method. An analysis of the antibiotic resistance and virulence genes was performed on the most prevalent species, using specific PCR assays. Enterococcus faecalis (54.5%), E. faecium (14.8%) and E. gallinarum (6.8%) were the identified species. To the best of our knowledge, this is the first report of E. gallinarum in bovine colostrum. The majority of the isolates showed resistance to quinupristin-dalfopristin (95.9%), erythromycin (80.7%), tetracycline (80.7%) and streptomycin (58%). Ninety-two percent of isolates were classified as multidrug-resistant. The most frequently detected resistance genes were tet(K) (61.1%), tet(M) (75.9%), tet(L) (90.7%), erm(B) (55.6%) and ant(6)-Ia (46.3%). The most prevalent virulence factors were cpd, esp, agg and cylL_L. Enterococcus faecium showed a higher probability of carrying the erm(C), tet(M), ace and gel(E) genes (p < 0.05). These results demonstrated that colostrum can constitute an important reservoir and vehicle for the dissemination of antibiotic resistance and virulence genes to the three niches included in a One Health perspective (humans, animals and the environment), highlighting the importance of hygiene sanitary measures to mitigate colostrum microbial contamination.

Molecular characterization of five novel plasmids from Enterococcus italicus SD1 isolated from fermented milk: An insight into understanding plasmid incompatibility

Enterococcal plasmids have attracted considerable interest because of their indispensable role in the pathogenesis and dissemination of multidrug-resistance. In this work, five novel plasmids pSRB2, pSRB3, pSRB4, pSRB5 and pSRB7 have been identified and characterised, coexisting in Eneterococcus italicus SD1 from fermented milk. The plasmids pSRB2, pSRB3 and pSRB5 were found to replicate via theta mode of replication while pSRB4 and pSRB7 were rolling-circle plasmids. Comparative analysis of SD1-plasmids dictated that the plasmids are mosaic with novel architecture. Plasmids pSRB2 and pSRB5 are comprised of a typical iteron-based class-A theta type origin of replication, whereas pSRB3 has a Class-D theta type replication origin like pAMβ1. The plasmids pSRB4 and pSRB7 shared similar ori as in pWV01. The SD1 class-A theta type plasmids shared significant homology between their replication proteins with differences in their DNA-binding domain and comprises of distinct iterons. The differences in their iterons and replication proteins restricts the "handcuff" formation for inhibition of plasmid replication, rendering to their compatibility to coexist. Similarly, for SD1 rolling circle plasmids the differences in the replication protein binding site in the origin and the replication protein supports their coexistence by inhibiting the crosstalk between the origins and replication proteins. The phylogenetic tree of their replication proteins revealed their distant kinship. The results indicate that the identified plasmids are unique to E. italicus SD1, providing further opportunities to study their utility in designing multiple gene expression systems for the simultaneous production of proteins in enterococci with the renewed concept of plasmid incompatibility.

Epidemiological profiles and pathogenicity of Vancomycin-resistant Enterococcus faecium clinical isolates in Taiwan

The emerging Vancomycin-resistant Enterococcus faecium (VRE-fm) is an opportunistic pathogen causing nosocomial infections. The identification of VRE-fm is important for successful prevention and control in healthcare settings. VRE-fm clinical isolates obtained from regional hospitals in northern Taiwan were characterized for antimicrobial susceptibility, virulence genes and biofilm production. Most isolates exhibited multi-drug resistance and carried the virulence genes, esp and hyl. While all isolates produce biofilms, those isolates that carried esp exhibited greater biofilm production. Isolates with different virulence gene carriages were examined for pathogenicity by using a nematode model, Caenorhabditis elegans, for determining microbial-host interactions. The survival assay showed that C. elegans was susceptible to Linezolid-resistant VRE-fm isolates with hyl. Combining the molecular epidemiological profiles regarding pathogenesis in C. elegans can serve as a guide for physicians in limiting opportunistic infections caused by VRE-fm.

Biofilm Formation Capacity and Presence of Virulence Determinants among Enterococcus Species from Milk and Raw Milk Cheeses

Bacterial biofilm is one of the major hazards facing the food industry. Biofilm-forming ability is one of the most important virulence properties of enterococci. The genus Enterococcus includes pathogenic, spoilage, and pro-technological bacteria. The presence of enterococci in milk and dairy products is usually associated with inadequate hygiene practices. The study examined the isolates' capacity for biofilm formation and identification of the genetic determinants of its formation among 85 Enterococcus strains isolated from raw milk (n = 49) and soft-ripened cheeses made from unpasteurized milk (n = 36). E. faecalis and E. faecium were the dominant species. The obtained results showed that 41.4% isolates from milk and 50.0% isolates from cheeses were able to form biofilm. All of the isolates analyzed had at least one of the studied genes. As regards the isolates from raw milk, the most prevalent gene was the gelE (85.6%), followed by the asa1 (66.7%). None of the isolates from cheeses showed the presence of cylA and sprE. The most prevalent gene among the strains from this source was the epbC (94.4%), followed by the gelE (88.9%). In isolates from both sources, the presence of proteins from the Fsr group was noted the least frequently. Nevertheless, results showed that were no significant differences between the biofilm-producing Enterococcus spp. and non-biofilm-producing isolates in term of occurrences of tested virulence genes. The ability to produce a biofilm by enterococci isolated from raw milk or ready-to-eat products emphasizes the need for continuous monitoring of the mechanisms of microbial adhesion.

Staphylococcus aureus in Horses in Nigeria: Occurrence, Antimicrobial, Methicillin and Heavy Metal Resistance and Virulence Potentials

Staphylococcus aureus was isolated from a total of 360 nasal and groin skin swabs from 180 systematic randomly-selected horses slaughtered for meat at Obollo-Afor, Enugu State, Southeast Nigeria and antimicrobial, methicillin and heavy metal resistance profile and virulence potentials of the isolates established. Baird-Parker agar with egg yolk tellurite was used for S. aureus isolation. S. aureus isolates were confirmed biochemically and serologically using a specific S. aureus Staphytect Plus™ latex agglutination test kit. The antimicrobial resistance profile, methicillin, vancomycin and inducible clindamycin resistance, and β-lactamase production of the isolates were determined with disc diffusion. Tolerance to Copper, Cadmium, Lead and Zinc was assessed using the agar dilution method and virulence potentials were determined using phenotypic methods. Forty-three (23.9%) of the 180 horses harbored S. aureus. Some 71 S. aureus were recovered from the 360 samples. Two (2.8%) of the 71 S. aureus were methicillin-resistant S. aureus (MRSA) and 69 (97.2%) were methicillin-susceptible. MRSA was recovered from 2 (1.1%) of the 180 horses. Some 9.4% of the isolates were multiple drug-resistant (MDR). The mean multiple antibiotic resistance indices (MARI) for the isolates was 0.24. Heavy metal resistance rate of the isolates ranged between 35.4-70.4%. The isolates, including the MRSA strains, displayed virulence potentials as clumping factor and catalase, gelatinase, caseinase, heamolysin, and biofilm was at the rate of 100%, 53.5%, 43.7%, 18.3% and 23.9%, respectively. This study showed that a considerable percentage of horses slaughtered in Obollo-Afor Southeastern Nigeria are potential reservoirs of virulent multiple drug- and heavy metal-resistant S. aureus, including MRSA, that could spread to humans and the environment.

Culture-dependent examination of the bacteriological quality of ready-to-eat African salads in Enugu metropolis, Nigeria and antibiotic resistance profile of associated bacteria

This study investigated the bacteriological quality of ready-to-eat (RTE) African salads in Enugu metropolis, Enugu, Nigeria. A total of 10 samples of African salad were purchased from 10 different vendors in Enugu metropolis. The samples were purchased from Agbani Road, Ogbete, Mayor, Uwani, Kenyatta, Achara Layout, Obiagu and Timber. Isolation and enumeration of bacterial isolates were done using Nutrient agar, Eosin Methylene Blue (EMB) agar, Thiosulphate-citrate-bile salts-sucrose (TCBS) agar, Salmonella-Shigella Agar (SSA) and MacConkey agar, following standard methods. Identification of the bacterial isolates were done through biochemical tests and the Analytical Profile Index (API 20E) test kit. The antibiotic sensitivity of the bacterial isolates was also done using the Kirby Bauer disc diffusion method. Total culturable heterotrophic count was above 300 colonies across the samples. The highest bacterial counts recorded on EMB, SSA and TCBS across the samples were 6.3 × 10⁶ CFU/g, 7.4 × 10⁶ CFU/g and 1.21 × 10⁷ CFU/g respectively. The identities of the organisms were; Salmonella spp., Staphylococcus aureus, Escherichia coli, Vibrio mimicus, Vibrio fluvialis, Vibrio cholerae, Vibrio parahaemolyticus and Vibrio hollisae. The prevalent organism across the samples was Vibrio spp. The antibiotic sensitivity test suggested that Vibrio spp. was resistant to Ampiclox and Amoxycillin but sensitive to Erythromycin, Pefloxacin and Septrin. From this study, it was discovered that consumers of RTE African salad from majority of the vendors across Enugu metropolis are at risk of severe food poisoning.

Meta-analysis of the global prevalence of Enterococcus spp. in foods: Antibiotic resistance profile of Enterococcus faecalis and Enterococcus faecium

Aim: The objective of this study was to evaluate the prevalence and diversity of Enterococcus spp. and antibiotic-resistant Enterococcus faecalis and Enterococcus faecium isolates in different foods worldwide.

Method and Result: This study used meta-analytical methods. Besides, Web of Science (n= 705), Medline (n= 6), and Scopus (n= 1.338) were searched for studies in the years 1995-2021 using related keywords. Results showed that the pooled prevalence for Enterococcus spp. and antibiotic-resistant of E. faecalis and E. faecium isolates were found 0.41 (95% C.I. 0.34-0.47), 0.25 (95% C.I. 0.13-0.38), respectively. According to the results of the subgroup analysis, the lowest and highest prevalence of Enterococcus spp. in food types were calculated for red meat (0.56), and fermented foods (0.29). Also, as a result of subgroup analyses by country the highest prevalence of Enterococcus spp. was calculated in studies conducted in Slovakia (0.74). In contrast, the lowest prevalence was calculated in studies conducted in Georgia (0.07).

Conclusion: The meta-analyses improved our understanding of the prevalence of Enterococcus spp. and the antibiotic resistance of E. faecalis and E. faecium isolates in different foods and provided results that can be useful as input for quantitative microbiological risk evaluation modeling.

Significance and Impact of Study: We demonstrated the antibiotic resistance of E. faecalis and E. faecium in foods and gaps that could be addressed in the future. Therefore, it is believed that the results compiled herein will contribute to the epidemiological surveillance of the presence and antibiotic resistance of E. faecalis and E. faecium in foods.

Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia

Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in the dissemination and modification of the antibiotic-resistant phenotype. To that end, we leveraged fully resolved Enterococcus faecium and Enterococcus faecalis genomes of isolates collected over 5 days from an inpatient with prolonged bacteraemia. Isolates from both species harboured similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events and IS-mediated excision events in plasmids of E. faecium isolates. We also characterize a novel arrangement of the ISs in a Tn1546-like transposon in E. faecalis isolates likely implicated in a vancomycin genotype–phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in liaSR genes and a putative composite transposon in E. faecium, offering a new paradigm for the study of daptomycin resistance and novel insights into its dissemination. In conclusion, our study highlights the role ISs and other transposable elements play in the rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.

Anti-Biofilm and Antibacterial Activities of Cycas media R. Br Secondary Metabolites: In Silico, In Vitro, and In Vivo Approaches

Enterococcus species possess many virulence factors that have an essential role in exacerbating the infections caused by them. The current study aimed to evaluate the effect of the secondary metabolites ginkgetin (GINK) and sotetsuflavone (SOTE), isolated from Cycas media R. Br dichloromethane fraction, on Enterococcus faecalis (E. faecalis) isolates for the first time. The antibacterial and antivirulence activities of the isolated compounds were investigated using docking studies and in vitro by determination of the minimum inhibitory concentrations (MICs). Additionally, flow cytometry and scanning electron microscope (SEM) were utilized to assess the effect of SOTE on the tested bacteria. Moreover, crystal violet assay and qRT-PCR were used to test the effect of SOTE on the biofilm-forming ability of E. faecalis isolates. In addition, a systemic infection model was utilized in vivo to investigate the antibacterial activity of SOTE. We found that both GINK and SOTE showed a good affinity for the five proteins enrolled in the virulence of E. faecalis, with SOTE being the highest, suggesting the possible mechanisms for the antivirulence activity of both ligands. In addition, SOTE exhibited a higher antibacterial activity than GINK, as the values of the MICs of SOTE were lower than those of GINK. Thus, we performed the in vitro and in vivo assays on SOTE. However, they did not exhibit any significant variations (p > 0.05) in the membrane depolarization of E. faecalis isolates. Moreover, as evaluated by SEM, SOTE caused distortion and deformation in the treated cells. Regarding its impact on the biofilm formation, it inhibited the biofilm-forming ability of the tested isolates, as determined by crystal violet assay and qRT-PCR. The in vivo experiment revealed that SOTE resulted in a reduction of the inflammation of the liver and spleen with an increase in the survival rate. SOTE also improved the liver-function tests and decreased tumor necrosis factor-alpha using immunostaining and the inflammation markers, interleukins (IL-1β and IL-6), using ELISA. Thus, we can conclude that SOTE could be a promising compound that should be investigated in future preclinical and clinical studies.

Antibiotic resistance and virulence genes in Enterococcus species isolated from raw and processed seafood

This study evaluated the antibiotic resistance characteristics and virulence genes of enterococci isolated from raw and processed seafood sold in the Marmara Region, Turkey. In this context, the enterococcal load was determined as between 1.0 and 2.5 log CFU/g in 39 of a total of 397 samples. It was determined that 117 strains isolated from the samples belonged to Enterococcus gallinarum, E. casseliflavus, E. durans, E. faecium, and E. faecalis species. Erythromycin, tetracycline, streptomycin, and gentamicin resistance was observed, whereas the tetM, ermB, aac(6')-aph(2'')-la genes were found in a majority of the isolates. It was also determined that the isolates carried the agg2 and gelE virulence genes. When all these results are evaluated, the presence of these isolates in aquatic products may pose a risk in terms of food safety and public health.

Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain

The presence of multi-drug resistant (MDR) bacteria in ready-to-eat foods comprises a threat for public health due to their ability to acquire and transfer antibiotic-resistant determinants that could settle in the microbiome of the human digestive tract. In this study, Enterococcus faecium UC7251 isolated from a fermented dry sausage was characterized phenotypically and genotypically to hold resistance to multiple antibiotics including aminoglycosides, macrolides, β-lactams, and tetracyclines. We further investigated this strain following a hybrid sequencing and assembly approach (short and long reads) and determined the presence of various mobile genetic elements (MGEs) responsible of horizontal gene transfer (HGT). On the chromosome of UC7251, we found one integrative and conjugative element (ICE) and a conjugative transposon Tn916-carrying tetracycline resistance. UC7251 carries two plasmids: one small plasmid harboring a rolling circle replication and one MDR megaplasmid. The latter was identified as mobilizable and containing a putative integrative and conjugative element-like region, prophage sequences, insertion sequences, heavy-metal resistance genes, and several antimicrobial resistance (AMR) genes, confirming the phenotypic resistance characteristics. The transmissibility potential of AMR markers was observed through mating experiments, where Tn916-carried tetracycline resistance was transferred at intra- and inter-species levels. This work highlights the significance of constant monitoring of products of animal origin, especially RTE foodstuffs, to stimulate the development of novel strategies in the race for constraining the spread of antibiotic resistance.

Processed ready-to-eat (RTE) foods sold in Yenagoa Nigeria were colonized by diarrheagenic Escherichia coli which constitute a probable hazard to human health

The study aimed to recover diarrheagenic Escherichia coli strains from processed ready-to-eat (RTE) foods in Yenagoa, Nigeria and characterize them using culture-based and molecular methods. Three hundred RTE food samples were collected randomly from different food outlets between February 2021 and August 2021 and assessed for the occurrence of E. coli using standard bacteriological procedures. The virulence factor formation and antibiotic susceptibility profile of the isolates was carried out using standard microbiological procedures. Polymerase chain reaction (PCR) was used to confirm the identity of the isolates via specific primers and further used to assay the diarrheagenic determinants of the E. coli isolates. The prevalence of E. coli positive samples based on the proliferation of E. coli on Chromocult coliform agar forming purple to violet colonies was 80(26.7%). The population density of E. coli from the RTE foods ranged from 0–4.3 × 10⁴ ± 1.47 CFU/g. The recovered E. coli isolates (n = 62) were resistant to antibiotics in different proportions such as ampicillin 62(100%), aztreonam 47(75.81%) and chloramphenicol 43(69.35%). All the recovered E. coli isolates were resistant to ≥ 2 antibiotics. The multiple antibiotic-resistant index (MARI) ranged from 0.13–0.94 with 47(75.8%) of isolates having MARI >2. A total of 48(77.4%) of the isolates were multidrug-resistant (MDR). The proportion of extracellular virulence factor formation is as follows: protease 12(19.35%), curli 39(62.9%), cellulose 21(33.89%), ornithine decarboxylase 19(30.65%) and aesculin hydrolysis 14(22.58%). The overall proportion of diarrheagenic E. coli was 33/62(53.2%). The distributions of typical diarrheagenic E. coli includes: tETEC 9(14.5%), tEPEC 13(20.9%), tEAEC 6(9.7%), tEIEC 2(3.2%) and tEHEC 3(4.8%). The proportions of atypical strains include aETEC 10(16.1%), aEAEC 5(8.1%), aEPEC 1(1.6%) and aEIEC 3(4.8%). This study demonstrated that some RTE foods sold in Yenagoa, Nigeria, are contaminated and constitute a probable human health hazard. Thus, there is a need for intensive surveillance of this isolate in RTE foods variety to spot evolving AMR phenotypes and avert food-borne infections.

Designing of a Recombinant Multi-Epitopes Based Vaccine against Enterococcus mundtii Using Bioinformatics and Immunoinformatics Approaches

Enterococcus species are an emerging group of bacterial pathogens that have a significant role in hospital-associated infections and are associated with higher mortality and morbidity rates. Among these pathogens, Enterococcus mundtii is one of the causative agents of multiple hospital associated infections. Currently, no commercially available licensed vaccine is present, and multi-drug resistant strains of the pathogen are prominent. Due to several limitations of experimental vaccinology, computational vaccine designing proved to be helpful in vaccine designing against several bacterial pathogens. Herein, we designed a multi-epitope-based vaccine against E. mundtii using in silico approaches. After an in-depth analysis of the core genome, three probable antigenic proteins (lytic polysaccharide monooxygenase, siderophore ABC transporter substrate-binding protein, and lytic polysaccharide monooxygenase) were shortlisted for epitope prediction. Among predicted epitopes, ten epitopes-GPADGRIAS, TTINHGGAQA, SERTALSVTT, GDGGNGGGEV, GIKEPDLEK, KQADDRIEA, QAIGGDTSN, EPLDEQTASR, AQWEPQSIEA, QPLKFSDFEL-were selected for multi-epitope vaccine construct designing. The screened B- and T-cell epitopes were joined with each other via specific linkers and linked to the cholera toxin B subunit as an adjuvant to enhance vaccine immune protection efficacy. The designed vaccine construct induced cellular and humoral immune responses. Blind docking with immune cell receptors, followed by molecular dynamic simulation results confirms the good binding potency and stability of the vaccine in providing protection against the pathogen.

Molecular characterization and antimicrobial resistance of Enterococcus faecalis isolated from seafood samples

Background

Enterococcus faecalis is considered an opportunistic foodborne pathogen. The present study aimed to assess the prevalence, antimicrobial resistance, virulence characters, and molecular typing of E. faecalis strains isolated from seafood samples.

Methods

Two hundred and seventy‐six seafood samples were collected. E. faecalis was isolated from samples using bacterial culture. Furthermore, the disk diffusion assessed their antimicrobial resistance. Also, the distribution of virulence factors was determined using polymerase chain reaction (PCR) assay. Random amplified polymorphic DNA (RAPD) method was used for their molecular typing.

Results

Fifty‐six of 276 (20.2%) seafood samples were contaminated with E. faecalis. Fish harboured the highest contamination rate (30.0%). Isolates harboured the highest resistance rate towards oxacillin (100%), tetracycline (100%), erythromycin (100%), cefoxitin (89.2%), cefazolin (87.5%), trimethoprim‐sulfamethoxazole (85.7%), rifampin (69.6%), clindamycin (69.6%), and gentamicin (64.2%) antimicrobials. Efa (100%), ebpA (89.2%), ebpB (58.9%), ebpC (53.5%), and esp (51.7%) were the most commonly detected virulence factors among E. faecalis isolates. RAPD–PCR analysis showed 11 different molecular clusters considering the closeness of more than 80%.

Conclusion

Seafood samples were considered reservoirs of virulence and resistant E. faecalis strains. Different molecular clusters of isolates may reflect their diverse sources of contamination.

Molecular characterization of antimicrobial resistance and virulence factors of Enterococcus faecalis from ducks at slaughterhouses

This study investigated the prevalence of antimicrobial resistant Enterococcus faecalis (E. faecalis) from ducks at slaughterhouses, analyzed antimicrobial resistance genes and virulence-associated genes of the isolates. Multilocus sequence typing (MLST) was performed to characterize their molecular characteristics. A total of 227 E. faecalis isolates (67.8%) were obtained from cecum (n = 114), cloaca (n = 50), skin (n = 59), and rinsed water (n = 4). These E. faecalis exhibited high level of resistance against tetracycline (95.6%), doxycycline (94.3%), linezolid (75.8%), erythromycin (72.2%), followed by norfloxacin (56.8%), vancomycin (38.3%), penicillin (36.1%), teicoplanin (30.8%). Lower level of resistance was found to high-level streptomycin (19.8%), imipenem (15.9%) and high-level gentamicin (5.7%). The vast majority of isolates (90.3%) were multidrug resistant (MDR). Moreover, the commonly observed resistance genes were optrA (90.7%) and ermB (90.3%), followed by aph(3’)-Ⅲ (86.8%), tetM (84.6%), acc(6’)-aph(2) (77.5%), blaZ (76.7%) and aac(6’)-Ie-aph(2”)-Ia (75.8%). The less frequently observed genes were vanC (19.8%), blaTEM (4.8%), vanM (2.6%), and vanA (0.4%). None of the strains carried aph(2”)-Ic and vanB genes. Furthermore, a high prevalence of ten virulence determinants was identified, and efaA (99.1%) was predominant, followed by eep (97.4%), srtA (96.9%), asa1 (95.6%), fsrB (92.1%), sprE (89.9%), aggA (63.9%), gelE (56.4%), esp (33.9%), and cylL (15.4%). Eleven isolates (4.9%) co-carried all of the tested virulence-associated genes. MLST analysis demonstrated that, E. faecalis isolates consisted of 12 known STs and 5 new STs, among which 6 of the identified STs were associated with nosocomial infection. Our data indicated that retail ducks serve as an important source of MDR E. faecalis with high pathogenicity potential, and suggested that transmission to humans could not be excluded.

Diversity and health risk potentials of the Enterococcus population in tropical coastal water impacted by Hurricane Lane

Hurricane-caused stormwater runoffs transport diverse terrestrial pollutants, adversely impact microbiological water quality, and introduce fecal and other pathogens to coastal water environments. This study investigated the genotypic diversity, phylogenetic composition, antibiotic resistance patterns, and virulence gene repertoire of the Enterococcus population in the Hilo Bay coastal water after the immediate impact of Hurricane Lane. DNA fingerprinting of Enterococcus isolates exhibited large genotypic diversity, while 16S rRNA gene sequencing identified four major species, including E. faecalis (34.7%), E. faecium (22.4%), E. hirae (22.4%), and E. durans (18.4%). Four common enterococcal virulence genes (cylA, esp, asa1, and gelE) were detected in the Enterococcus population, with significant portions of E. durans (33.3%), E. faecalis (41.2%), E. faecium (36.4%), and E. hirae (27.3%) isolates possessing two or more virulence genes. Considerable antibiotic resistance to rifampin, erythromycin, tetracycline, and nitrofurantoin was detected in the Enterococcus population, with one E. durans isolate showing vancomycin resistance. The results indicate considerable health implications associated with Enterococcus spp. in the hurricane-impacted tropical coastal water, illustrating the needs for more comprehensive understanding of the microbiological risks associated with storm-impacted coastal water.

Effects of osmotic and high pressure stress on expression of virulence factors among Enterococcus spp. isolated from food of animal origin

The aim of study was to determine the occurrence of virulence factors and virulence-related genes among enterococci isolated from food of animal origin and effects of osmotic and high pressure stress on expression of virulence-related genes. The number of 78 isolates were analyzed. None of them showed a strong ability to form biofilm, 38.5% (n = 30) had the slime production ability, 41% (n = 32) had gelatinase activity, γ -type hemolysis was observed in 55% of isolates, and α-type hemolysis in 45%. All of the isolates carried 1-13 virulence-related genes. The most common genes were gelE (85.9%), sprE (78.2%) and asa1 (75.6%). There were also observed changes in the expression of the gelE, esp, asa1 and cylL genes in response to various NaCl concentration and high pressure processing. Results obtained in this study indicate that enterococci isolated from food may act as reservoirs of virulence genes. The presence of virulence factors among enterococci, especially the ability to biofilm formation is important for food safety and the protection of public health. The results presented in our work demonstrate that stress that can occur during food preservation and food processing can induce the changes in the virulence-related genes expression.

Antimicrobial resistance, virulence genes and biofilm formation in Enterococcus species isolated from milk of sheep and goat with subclinical mastitis

This study is designed to discuss the antimicrobial resistance, virulence determinants and biofilm formation capacity of Enterococcus spp. isolated from milk of sheep and goat with subclinical mastitis in Qena, Egypt. The obtained isolates were identified by the VITEK2 system and 16S rDNA sequencing as E. faecalis, E. faecium, E. casseliflavus and E. hirae. Overall, E. faecalis and E. faecium were the dominant species recovered from mastitic milk samples. The antimicrobial susceptibility test evidenced multidrug resistance of the isolates against the following antimicrobials: oxacillin (89.2.%), followed by vancomycin (75.7%) and linezolid (70.3%). Also, most of these isolates (73%) could form biofilms. For example, 18.9% of Enterococcus strains formed strong biofilm, whereas 32.4% of isolates formed moderate biofilm and 21.6% of isolates formed weak biofilm. The most prevalent resistance genes found in our isolates were blaZ (54%), vanA (40%), ermB (51.4%), tetM (13.5%) and optrA (10.8%). Moreover, asa1 (37.8%), cylA (42.3%), gelE (78.4%), esp (32.4%), EF3314(48.6%) and ace (75.5%) were the most common virulence genes. A significant correlation was found between biofilm formation, multidrug resistance and virulence genes of the isolates. This study highlights several aspects of virulence and harmfulness of Enterococcus strains isolated from subclinical mastitic milk, which necessitates continuous inspection and monitoring of dairy animals.

Prevalence and Characterization of Food-Borne Vibrio parahaemolyticus From African Salad in Southern Nigeria

The demand for minimally processed vegetables (African salad) has increased partly due to its inclusion in ready-to-eat foods. Nevertheless, the associated risk of the presence of emergent foodborne pathogens, such as Vibrio parahaemolyticus might be underestimated. The present study was designed to isolate and characterize foodborne V. parahaemolyticus from minimally processed vegetables using culture-based methods and molecular approach. A total of 300 samples were examined from retail outlets between November 2018 and August 2019 from Southern Nigeria. The prevalence of vibrios from the overall samples based on the colonial proliferation of yellow, blue-green and/or green colonies on thiosulfate citrate bile salts sucrose agar was 74/300 (24.6%). An average of two green or blue-green colonies from respective plates was screened for V. parahaemolyticus using analytical profile index (API) 20 NE. Polymerase chain reaction further confirmed the identity of positive V. parahaemolyticus. The counts of V. parahaemolyticus ranged from 1.5 to 1,000 MPN/g. A total of 63 recovered V. parahaemolyticus were characterized further. The resistance profile of the isolates include ampicillin 57/63 (90.5%), cefotaxime 41/63 (65.1%), ceftazidime 30/63 (47.6%), amikacin 32/63 (50.8%), kanamycin 15/63 (23.8%), and oxytetracycline 16/63 (25.4%). The multiple antibiotic index ranged from 0–0.81. The formation of biofilm by the isolates revealed the following: strong formation 15/63 (23.8%), moderate formation 31/63 (49.2%), weak formation 12/63 (19.1%), and no formation 5/63 (7.9%). A total of 63/63 (100%), 9/63 (14.3%), and 20/63 (31.8%) of the isolates harbored the tox R gene, TDH-related hemolysin (trh) and thermostable direct hemolysin (tdh) determinants respectively. The isolates with O2 serogroup were most prevalent via PCR. Isolates that were resistant to tetracycline, kanamycin, and chloramphenicol possessed resistant genes. The presence of multidrug-resistant vibrios in the minimally processed vegetables constitutes a public health risk and thus necessitates continued surveillance.

Occurrence of multidrug-resistant Enterococcus faecium isolated from environmental samples

Enterococcus species are present in the microbiota of humans and animals and have also been described in the environment. Among the species, Enterococcus faecium is one of the main pathogens associated with nosocomial infections worldwide. Enterococcus faecium isolates resistant to different classes of antimicrobials have been increasingly reported, including multidrug-resistant (MDR) isolates in environmental sources, which is worrying. Therefore, this study aimed to characterize E. faecium isolates obtained from soil and water samples regarding antimicrobial resistance and virulence determinants. A total 40 E. faecium isolates were recovered from 171 environmental samples. All isolates were classified as MDR, highlighting the resistance to the fluoroquinolones class, linezolid and vancomycin. Furthermore, high-level aminoglycoside resistance and high-level ciprofloxacin resistance were detected in some isolates. Several clinically relevant antimicrobial resistance genes were found, including vanC1, ermB, ermC, mefAE, tetM, tetL, ant(6')-Ia, ant(4')-Ia, aph(3')-IIIa and aac(6')-Ie-aph(2″)-Ia. Three virulence genes were detected among the MDR E. faecium isolates, such as esp, gelE and ace. The results of this study contribute to a better understanding of MDR E. faecium isolates carrying antimicrobial resistance and virulence genes in environmental sources and report for the first time in the world the presence of vanC1-producing E. faecium isolated from soil.

Phylogenetic characterization and multidrug resistance of bacteria isolated from seafood cocktails

The continual increase in resistance to antibacterial drugs has become a major public health problem, and their indiscriminate use in agriculture, aquaculture, and the treatment of human and animal diseases has severely contributed to the occurrence and spread of multidrug resistance genes. This study phylogenetically characterized multidrug-resistant bacteria isolated from seafood cocktails. Seafood cocktail dishes from 20 establishments on public roads were sampled. Samples were grown on TCBS agar and blood agar. Forty colonies with different macro- and microscopic characteristics were isolated. The 16S rRNA gene V4 and V6 hypervariable regions were amplified, sequenced and phylogenetically analyzed. Antibacterial drug resistance was determined by disk diffusion assay. Isolated bacteria were identical to species of the genera Enterococcus, Proteus, Vibrio, Staphylococcus, Lactococcus, Vagococcus, Micrococcus, Acinetobacter, Enterobacter, and Brevibacterium, with 75-100% presenting resistance or intermediate resistance to dicloxacillin, ampicillin, and penicillin; 50-70% to cephalosporins; 30-67.5% to amikacin, netilmicin and gentamicin; 40% to nitrofurantoin and other antibacterial drugs; 25% to chloramphenicol; and 2.5% to trimethoprim with sulfamethoxazole. In general, 80% of the bacteria showed resistance to multiple antibiotics. The high degree of bacterial resistance to antibacterial drugs indicates that their use in producing raw material for marine foods requires established guidelines and the implementation of good practices.

Global Prevalence of Vancomycin-Resistant Enterococci in Food of Animal Origin: A Meta-Analysis

Vancomycin-resistant enterococci (VRE) are a leading cause of nosocomial infections in patients worldwide. VRE contamination in food of animal origin may create a risk for human health. This study was conducted to estimate the pooled prevalence of VRE in food of animal origin worldwide, to assess the result heterogeneity, and to determine cumulative evidence and the trend of the prevalence over time. Relevant studies were retrieved from PubMed, Scopus, and Web of Science. A random-effects model was used to calculate the pooled prevalence of VRE in food of animal origin. Subgroup meta-analysis was used to assess the heterogeneity of the results. A cumulative meta-analysis and meta-regression were conducted to determine cumulative evidence and the trend of the prevalence of VRE in food of animal origin over time, respectively. Of the 1352 retrieved studies, 50 articles were included. The pooled prevalence of VRE in food of animal origin was 11.7% (95% confidence interval [95% CI] = 8.4 to 16.0). Subgroup meta-analyses showed a significant difference in the prevalence of VRE for two characteristics. First, for the source of food, the prevalence of VRE was highest in aquatic food (43.4% [95% CI = 28.4 to 59.7]) and lowest in dairy food (4.1% [95% CI = 1.7 to 9.8]). Second, for continents, the prevalence of VRE was highest in Africa (18.5% [95% CI = 12.8 to 26.1]) and lowest in North America (0.3% [95% CI = 0.1 to 1.1]). Cumulative evidence showed two distinct features in two different periods. The pooled prevalence of VRE rapidly decreased from 79.3% in 1998 to 13.1% in 2003; it has slightly fluctuated between 10.5% and 20.5% since 2004. The results of the meta-regression indicated that the prevalence gradually decreased over time. In conclusion, the estimate of overall VRE prevalence worldwide in food of animal origin was ∼12%, indicating the burden of VRE contamination in food of animal origin.

Characterization of a novel theta-type plasmid pSM409 of Enterococcus faecium RME isolated from raw milk

Enterococcal plasmids have generated renewed interest for their indispensable role in pathogenesis and dissemination of multidrug-resistance. Recently, a novel plasmid pSM409 (4303-bp, GC% = 33.6%), devoid of antibiotic-resistance and virulence genes, has been identified in Enterococcus faecium RME, isolated from raw milk by us. pSM409 contains six open reading frames encoding a replication initiator protein (RepB) and five accessory proteins: antitoxin epsilon, bacteriocin immunity protein, HsdS, and two hypothetical proteins. Comparative sequence analysis of pSM409 reveals a mosaic pattern of similarity with different loci obtained from different theta plasmids, which dictates the plasmid to be heterogeneous or mosaic, possibly due to recombination. The pSM409 comprised of a typical theta-type origin of replication with four and a half direct repeats (iterons) of 22 nucleotides. The pSM409-RepB shared 76-82% homology with the RepB of reported theta plasmids from different genera, with dissimilarities mostly in its DNA-binding and C-terminal domain. The RepB sequence-based phylogenetic tree revealed its distinct position relative to the reported ones. The RepB grouped in the same clade has identical DNA-binding domains and their cognate iterons, possibly due to their sequence-specific interaction to initiate plasmid replication. Comparative analysis of the pSM409-iteron reveals that the repeats markedly differed from their closest homologues. This clade-specific relationship provides a new concept of classifying theta plasmids. The theta-type replicon identified in pSM409 has been found to be unique to E. faecium RME, prompting us to further investigate its utility as a vector for genetic manipulation of enterococci for health and industry.

Antimicrobial Resistance Gene Detection and Plasmid Typing Among Multidrug Resistant Enterococci Isolated from Freshwater Environment

In this study, mechanisms of antimicrobial resistance (AR) as well as the abundance and diversity of plasmids were determined among multidrug resistant (MDR) enterococci from surface water in GA, USA. A total of 51 enterococci isolates were screened for the presence of 27 AR genes conferring resistance to ciprofloxacin, erythromycin, tylosin, kanamycin, streptomycin, lincomycin, Quinupristin/Dalfopristin (Q/D), and tetracycline. A plasmid classification system based on replication genes was used to detect 19 defined Gram-positive plasmid replicon families. Twelve genes were identified as conferring resistance to erythromycin and tylosin (erm(B) and erm(C)), kanamycin (aph(3′)-IIIa), streptomycin (ant(6)-Ia), lincomycin (lnu(B)), Q/D (vat(E)), ciprofloxacin (qnr_{E. faecalis}), and tetracycline (tet(K), tet(L), tet(M), tet(O) and tet(S)). Twelve different rep-families were identified in two-thirds of the isolates. While AR genes commonly found in human and animals were detected in this study among environmental enterococci, resistance genes could not be determined for many of the isolates, which indicates that diverse AR mechanisms exist among enterococci, and the understanding of AR mechanisms for environmental enterococci is limited. Diverse rep-families were identified among the enterococci recovered from the aquatic environment, and these rep-families appear to be quite different from those recovered from other sources. This work expands knowledge of AR gene reservoirs and enterococcal plasmids across a wider range of environments.

Vancomycin-Resistant Enterococci (VRE) in Nigeria: The First Systematic Review and Meta-Analysis

Vancomycin-Resistant Enterococci (VRE) are on the rise worldwide. Here, we report the first prevalence of VRE in Nigeria using systematic review and meta-analysis. International databases MedLib, PubMed, International Scientific Indexing (ISI), Web of Science, Scopus, Google Scholar, and African journals online (AJOL) were searched. Information was extracted by two independent reviewers, and results were reviewed by the third. Two reviewers independently assessed the study quality using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) checklist. OpenMeta analyst was used. The random effect was used, and publication bias was assessed using a funnel plot. Between-study heterogeneity was assessed, and the sources were analysed using the leave-one-out meta-analysis, subgroup analysis, and meta-regression. Nineteen studies met the eligibility criteria and were added to the final meta-analysis, and the study period was from 2009–2018. Of the 2552 isolates tested, 349 were VRE, and E. faecalis was reported the most. The pooled prevalence of VRE in Nigeria was estimated at 25.3% (95% CI; 19.8–30.8%; I² = 96.26%; p < 0.001). Between-study variability was high (t² = 0.011; heterogeneity I² = 96.26% with heterogeneity chi-square (Q) = 480.667, degrees of freedom (df) = 18, and p = 0.001). The funnel plot showed no publication bias, and the leave-one-out forest plot did not affect the pooled prevalence. The South-East region had a moderate heterogeneity though not significant (I² = 51.15%, p = 0.129). Meta-regression showed that all the variables listed contributed to the heterogeneity except for the animal isolate source (p = 0.188) and studies that were done in 2013 (p = 0.219). Adherence to proper and accurate antimicrobial usage, comprehensive testing, and continuous surveillance of VRE are required.

Antimicrobial Resistance, Virulence Genes, and Biofilm Formation Capacity Among Enterococcus species From Yaks in Aba Tibetan Autonomous Prefecture, China

Yaks provide necessities such as meat and milk for Tibetans living at high altitudes on and around the Qinghai-Tibetan Plateau. Enterococci are ubiquitous members of the animal gut microbiota that can cause biofilm-associated opportunistic infections. Meanwhile, multidrug-resistant Enterococcus also poses a serious threat to public health. This study aims to characterize antibiotic resistance, virulence genes, and biofilm formation of enterococci from yaks. From April 2018 to July 2019, we collected 395 fecal samples of yaks in Aba Tibetan Autonomous Prefecture, China. Enterococci isolated from the samples were identified and classified according to the 16S rDNA sequence. The antibiotic resistance of each isolate was detected according to the Kirby-Bauer disk diffusion method, and antibiotic resistance genes were detected by polymerase chain reaction (PCR) and sequencing. Enterococcal biofilms were assessed using standard procedures. Different virulence genes were detected by PCR and sequencing. In total, 381 enterococci strains were recovered, with Enterococcus faecalis (41.99%) and Enterococcus faecium (37.80%) being the predominant species. Many isolates were multidrug- resistant (60.37%) and showed a high resistance rate to rifampicin (64.30%) and tetracycline (61.54%). We also detected various antimicrobial resistance (AMR) genes in the tested strains. The E. faecalis strains had higher frequency of biofilm formation and virulence genes than other enterococcal species. This is the first report that shows yaks are repositories for drug-resistant enterococci with virulent determinants and biofilms that may spread into humans and to environment. This study also provides useful data suggesting that enterococci may pose a potential health risk to yaks. Therefore, active surveillance of AMR and pathogenesis in enterococci from yaks is urgently warranted.

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

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.