The marine environment as a reservoir of enterococci carrying resistance and virulence genes strongly associated with clinical strains

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.

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.

Metagenomic Characterization of Microbial Pollutants and Antibiotic- and Metal-Resistance Genes in Sediments from the Canals of Venice

The spread of fecal pollutants and antibiotic resistance in the aquatic environment represents a major public health concern and is predicted to increase in light of climate change consequences and the increasing human population pressure on the lagoon and coastal areas. The city of Venice (Italy) is affected by diverse microbial pollution sources, including domestic wastewaters that, due to the lack of modern sewage treatment infrastructure in the historical city center, are released into canals. The outflowing jets of its tidal inlets thus represent a source of contamination for the nearby beaches on the barrier island separating the lagoon from the sea. Metagenomic analyses of DNA extracted from sediment samples from six sites in the canals of the city’s historic center were undertaken to characterize the microbial community composition, the presence of fecal microbes as well as other non-enteric pathogens, and the content of genes related to antibiotic (AB) and heavy metal (HM) resistance, and virulence. The six sites hosted similar prokaryotic communities, although variations in community composition likely related to oxygen availability were observed. All sites displayed relatively high levels of fecal contamination, including the presence of Fecal Indicator Bacteria, sewage- and alternative feces-associated bacteria. Relatively high levels of other potential pathogens were also found. About 1 in 500 genes identified at these sites are related to AB and HM resistance; conversely, genes related to virulence were rare. Our data suggest the existence of widespread sediment microbial pollution in the canals of Venice, coupled with the prevalence of ARGs to antibiotics frequently used in humans as well as of HMRGs to toxic metals that still persists in the lagoon. All of this evidence raises concerns about the consequences on the water quality of the lagoon and adjacent marine areas and the potential risks for humans, deserving further studies.

Antibiotic Resistance Genes and Potentially Pathogenic Bacteria in the Central Adriatic Sea: Are They Connected to Urban Wastewater Inputs?

Despite last decades’ interventions within local and communitarian programs, the Mediterranean Sea still receives poorly treated urban wastewater (sewage). Wastewater treatment plants (WWTPs) performing primary sewage treatments have poor efficiency in removing microbial pollutants, including fecal indicator bacteria, pathogens, and mobile genetic elements conferring resistance to antimicrobials. Using a combination of molecular tools, we investigated four urban WWTPs (i.e., two performing only mechanical treatments and two performing a subsequent conventional secondary treatment by activated sludge) as continuous sources of microbial pollution for marine coastal waters. Sewage that underwent only primary treatments was characterized by a higher content of traditional and alternative fecal indicator bacteria, as well as potentially pathogenic bacteria (especially Acinetobacter, Coxiella, Prevotella, Streptococcus, Pseudomonas, Vibrio, Empedobacter, Paracoccus, and Leptotrichia), than those subjected to secondary treatment. However, seawater samples collected next to the discharging points of all the WWTPs investigated here revealed a marked fecal signature, despite significantly lower values in the presence of secondary treatment of the sewage. WWTPs in this study represented continuous sources of antibiotic resistance genes (ARGs) ermB, qnrS, sul2, tetA, and blaTEM (the latter only for three WWTPs out of four). Still, no clear effects of the two depuration strategies investigated here were detected. Some marine samples were identified as positive to the colistin-resistance gene mcr-1, an ARG that threatens colistin antibiotics’ clinical utility in treating infections with multidrug-resistant bacteria. This study provides evidence that the use of sole primary treatments in urban wastewater management results in pronounced inputs of microbial pollution into marine coastal waters. At the same time, the use of conventional treatments does not fully eliminate ARGs in treated wastewater. The complementary use of molecular techniques could successfully improve the evaluation of the depuration efficiency and help develop novel solutions for the treatment of urban wastewater.

Transcriptomic and rRNA:rDNA Signatures of Environmental versus Enteric Enterococcus faecalis Isolates under Oligotrophic Freshwater Conditions

The use of enterococci as a fecal indicator bacterial group for public health risk assessment has been brought into question by recent studies showing that “naturalized” populations of Enterococcus faecalis exist in the extraenteric environment. The extent to which these naturalized E. faecalis organisms can confound water quality monitoring is unclear. To determine if strains isolated from different habitats display different survival strategies and responses, we compared the decay patterns of three E. faecalis isolates from the natural environment (environmental strains) against three human gut isolates (enteric strains) in laboratory mesocosms that simulate an oligotrophic, aerobic freshwater environment. Our results showed similar overall decay rates between enteric and environmental isolates based on viable plate and quantitative PCR (qPCR) counts. However, the enteric isolates exhibited a spike in copy number ratios of 16S rRNA gene transcripts to 16S rRNA gene DNA copies (rRNA:rDNA ratios) between days 1 and 3 of the mesocosm incubations that was not observed in environmental isolates, which could indicate a different stress response. Nevertheless, there was no strong evidence of differential gene expression between environmental and enteric isolates related to habitat adaptation in the accompanying mesocosm metatranscriptomes. Overall, our results provide novel information on how rRNA levels may vary over different growth conditions (e.g., standard lab versus oligotrophic) for this important indicator bacteria. We also observed some evidence for habitat adaptation in E. faecalis; however, this adaptation may not be substantial or consistent enough for integration in water quality monitoring.

IMPORTANCE Enterococci are commonly used worldwide to monitor environmental fecal contamination and public health risk for waterborne diseases. However, closely related enterococci strains adapted to living in the extraenteric environment may represent a lower public health risk and confound water quality estimates. We developed an rRNA:rDNA viability assay for E. faecalis (a predominant species within this fecal group) and tested it against both enteric and environmental isolates in freshwater mesocosms to assess whether this approach can serve as a more sensitive water quality monitoring tool. We were unable to reliably distinguish the different isolate types using this assay under the conditions tested; thus, environmental strains should continue to be counted during routine water monitoring. However, this assay could be useful for distinguishing more recent (i.e., higher-risk) fecal pollution because rRNA levels significantly decreased after 1 week in all isolates.

Changes in Antibiotic-Resistance Genes Induced by the Grazing Effect in Three Cladoceran Species

The acquisition of Antibiotic-Resistance Genes (ARGs) by natural bacteria caused by antibiotic abuse is causing serious problems for human and animal welfare. Here, we evaluated the influence of three cladoceran species on Antibiotic-Resistant Bacteria (ARB) and tetracycline-resistance gene (tet(A)) copies, and discussed the effect of these biological interactions on the distribution and diffusion of ARGs in freshwater ecosystems. Bacterial community and tet(A) abundances in water samples collected from wetlands were strongly influenced by cladoceran presence. The presence of Daphnia obtusa dramatically decreased ARB and tet(A) abundance compared to that with other cladoceran species (Chydorus sphaericus and Simocephalus vetulus). Interestingly, we found a high abundance of Flavobacteriales in the microbiomes of cladoceran species. Considering that Flavobacteriales species are potential carriers of the tet(A) gene, their adsorption and assimilation with cladocerans could significantly impact the reduction of tet(A) in water. Field surveys also showed that tet(A) abundance could be low if the dominance of D. obtusa in each wetland was high. This study highlighted the need for ecological interactions and a broad range of niches in the food web when discussing the fate of ARGs in freshwater ecosystems.

Molecular Characteristics of Enterococcus faecalis and Enterococcus faecium from Bulk Tank Milk in Korea

Simple Summary

Enterococci can be an opportunistic pathogen in milk, which can easily disseminate antimicrobial resistance and virulence genes. The purpose of this study was to characterize and compare the enterococci isolates from samples of bulk tank milk obtained from four dairy companies in Korea to prevent the spread of pathogenic and antimicrobial-resistant enterococci in dairy companies. The results demonstrated various degrees of antimicrobial resistance and virulence-factor distribution in enterococci from bulk tank milk in Korea and support the assessment that pathogens from bulk tank milk can also become a reservoir for dissemination of antimicrobial resistance and virulence factors through cross-contamination processes.

Abstract

Enterococci are considered to be environmental mastitis-causing pathogens that can easily spread antimicrobial resistance or virulence genes via horizontal transfer. In this study, the molecular characteristics of enterococci from bulk tank milk were investigated to assess the importance of dairy herd management. A total of 338 enterococci (305 Enterococcus faecalis and 33 Enterococcus faecium) were isolated from 1584 batches of bulk tank milk samples from 396 farms affiliated with four dairy companies in Korea, and significant differences (40.6–79.7%) (p < 0.05) in the prevalence of enterococci were observed in the samples from different companies. Enterococci showed the highest resistance to tetracycline (TET) (73.4%), followed by doxycycline (DOX) (49.7%) and erythromycin (ERY) (46.2%), while two enterococci isolates showed resistance to vancomycin (VAN). Among 146 tetracycline (TET) and ERY-resistant enterococci, each 50 (19.4%) enterococci carried combination-resistance and transposon gene types erm(B) + tet(M) + IntTn and erm(B) + tet(L) + tet(M) + IntTn, respectively. The virulence genes such as ace (99.0%), efaA (97.7%), cad1 (95.7%), and gelE (85.9%) were highly conserved in E. faecalis and significantly predominated over E. faecium (p < 0.001). Our results indicate that pathogens from bulk tank milk can also become a reservoir for the dissemination of antimicrobial resistance and virulence factors through cross-contamination processes.

Fecal indicator bacteria from environmental sources; strategies for identification to improve water quality monitoring

In tropical to temperate environments, fecal indicator bacteria (FIB), such as enterococci and Escherichia coli, can persist and potentially multiply, far removed from their natural reservoir of the animal gut. FIB isolated from environmental reservoirs such as stream sediments, beach sand and vegetation have been termed "naturalized" FIB. In addition, recent research suggests that the intestines of poikilothermic animals such as fish may be colonized by enterococci and E. coli, and therefore, these animals may contribute to FIB concentrations in the aquatic environment. Naturalized FIB that are derived from fecal inputs into the environment, and subsequently adapted to maintain their population within the non-host environment are termed "naturalized enteric FIB". In contrast, an additional theory suggests that some "naturalized" FIB diverged from enteric FIB many millions of years ago and are now normal inhabitants of the environment where they are referred to as "naturalized non-enteric FIB". In the case of the Escherichia genus, the naturalized non-enteric members are identified as E. coli during routine water quality monitoring. An over-estimation of the health risk could result when these naturalized, non-enteric FIB, (that is, not derived from avian or mammalian fecal contamination), contribute to water quality monitoring results. It has been postulated that these environmental FIB belonging to the genera Escherichia and Enterococcus can be differentiated from enteric FIB by genetic methods because they lack some of the genes required for colonization of the host intestine, and have acquired genes that aid survival in the environment. Advances in molecular tools such as next generation sequencing will aid the identification of genes peculiar or "enriched" in particular habitats to discriminate between enteric and environmental FIB. In this appraisal, we have reviewed the research studying "naturalized" FIB, and discussed the techniques for their differentiation from enteric FIB. This differentiation includes the important distinction between enteric FIB derived from fresh and non-recent fecal inputs, and those truly non-enteric environmental microbes, which are currently identified as FIB during routine water quality monitoring. The inclusion of tools for the identification of naturalized FIB (enteric or environmental) would be a valuable resource for future studies assessing water quality.

Antibiotic-Resistant Enterococcus Species in Marine Habitats: A Review

Antibiotic-resistant Enterococcus (ARE) are among leading causes of nosocomial infections worldwide. Enterococcus spp. are ubiquitous in sewage, which can contaminate surface waters via many pathways, providing a route of exposure for humans. This review focuses on ARE in marine and estuarine habitats, including marine animals. Phylogenetic confirmation of the genus Enterococcus and intermediate or full resistance to clinically relevant antibiotics were inclusion criteria. The proportion of resistant isolates varied greatly among antibiotics, for example, 24.2% for ampicillin and 2.4% for vancomycin. The water column contained the highest proportion of ARE observations (18.8%), followed by animal feces and tissues (14.8%), sediment (9.4%), and sand (2.0%). The proportion of multidrug-resistant isolates was the greatest in animal tissue and fecal samples, followed by water and sediments. This review indicates that clinically relevant ARE are present in marine/estuarine habitats and that animals may be important reservoirs.

Tossed 'good luck' coins as vectors for anthropogenic pollution into aquatic environment

Superstition has it that tossing coins into wells or fountains brings good luck, thereby causing a potential accumulation of microbially contaminated metal particles in the water. Here, we characterized the microbiota and the resistance profile in biofilm on such coins and their surrounding sediments. The study site was a tidal marine lake within a touristic center located in a natural reserve area. Notwithstanding the fact that coin-related biofilms were dominated by typical marine taxa, coin biofilms had specific microbial communities that were different from the communities of the surrounding sediment. Moreover, the communities were different depending on whether the coin were made mainly of steel or of copper. Sequences affiliated with putative pathogens were found on every third coin but were not found in the surrounding sediment. Antibiotic resistance genes (ARGs) were detected on most of the coins, and interestingly, sediments close to the area where coins accumulate had a higher frequency of ARGs. We suggest that the surface of the coins might offer a niche for ARGs and faecal bacteria to survive, and, thus, tossed coins are a potential source and vector for ARGs into the surrounding environment.

The vertical distribution of tetA and intI1 in a deep lake is rather due to sedimentation than to resuspension

Lakes are exposed to anthropogenic pollution including the release of allochthonous bacteria into their waters. Antibiotic resistance genes (ARGs) stabilize in bacterial communities of temperate lakes, and these environments act as long-term reservoirs of ARGs. Still, it is not clear if the stabilization of the ARGs is caused by a periodical introduction, or by other factors regulated by dynamics within the water column. Here we observed the dynamics of the tetracycline resistance gene (tetA) and of the class 1 integron integrase gene intI1 a proxy of anthropogenic pollution in the water column and in the sediments of subalpine Lake Maggiore, together with several chemical, physical and microbiological variables. Both genes resulted more abundant within the bacterial community of the sediment compared to the water column and the water-sediment interface. Only at the inset of thermal stratification they reached quantifiable abundances in all the water layers, too. Moreover, the bacterial communities of the water-sediment interface were more similar to deep waters than to the sediments. These results suggest that the vertical distribution of tetA and intI1 is mainly due to the deposition of bacteria from the surface water to the sediment, while their resuspension from the sediment is less important.

Incidence of Virulence Determinants Among Enterococcal Clinical Isolates in Egypt and Its Association with Biofilm Formation

Background: Although Enterococci compromise an essential part of normal gut microbiota of both animals and humans, they have emerged as a leading opportunistic pathogen causing infections. The pathogenesis of enterococci is attributed to an array of virulence determinants. Objectives: This study aims to explore the prevalence and characteristics of enterococcal clinical isolates collected from Mansoura University Hospitals, Egypt, assess their ability to form biofilm, and the correlation with virulence determinants and antimicrobial resistance. Materials and Methods: A total of 70 Enterococcal clinical isolates were collected from different clinical sources between June and December 2016. Biofilm formation capacity was assessed, and characterization of virulence factors and antibiotic susceptibility was performed. Clonal relatedness between isolates was assessed using enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) approach. Results and Conclusion: The molecular analysis demonstrated high genetic diversity among enterococcal clinical isolates. The gelE was the most frequently detected gene (91.4%), followed by asa1 (70%), esp (65.7%), and cylA (17.1%), while hyl was not detected in any isolate. Gelatinase activity was detected in 35.7%, while hemolysin and lipase activity was detected in 12.9% and 78.5%, respectively. Most of the enterococcal isolates were biofilm producers, of which 67.1% were strong/moderate biofilm producers. All linezolid-resistant isolates exhibited strong/moderate biofilm formation capacity. Strong/moderate biofilm formation was more frequently observed among esp-positive (esp+) and gelatinase nonproducing (gelatinase-) enterococcal isolates. Multiple regression analysis denoted that esp (odds ratio [OR] 5.371, p = 0.003) and gelatinase production (OR 0.264, p = 0.015) were associated with strong/moderate biofilm formation capacity. These findings suggest that esp gene positivity and gelatinase production may affect biofilm formation capacity among enterococcal clinical isolates.

Antimicrobial Resistance in Enterococcus spp. of animal origin

Enterococci are natural inhabitants of the intestinal tract in humans and many animals, including food-producing and companion animals. They can easily contaminate the food and the environment, entering the food chain. Moreover, Enterococcus is an important opportunistic pathogen, especially the species E. faecalis and E. faecium, causing a wide variety of infections. This microorganism not only contains intrinsic resistance mechanisms to several antimicrobial agents, but also has the capacity to acquire new mechanisms of antimicrobial resistance. In this review we analyze the diversity of enterococcal species and their distribution in the intestinal tract of animals. Moreover, resistance mechanisms for different classes of antimicrobials of clinical relevance are reviewed, as well as the epidemiology of multidrug-resistant enterococci of animal origin, with special attention given to beta-lactams, glycopeptides, and linezolid. The emergence of new antimicrobial resistance genes in enterococci of animal origin, such as optrA and cfr, is highlighted. The molecular epidemiology and the population structure of E. faecalis and E. faecium isolates in farm and companion animals is presented. Moreover, the types of plasmids that carry the antimicrobial resistance genes in enterococci of animal origin are reviewed.

Assessing antimicrobial resistance gene load in vegan, vegetarian and omnivore human gut microbiota

Massive antimicrobial use in animal farming is considered as the greatest contributor to the presence of antimicrobial-resistant bacteria (ARB) in food of animal origin. Nevertheless, sewage from treated animals may impact on vegetables grown on fertilised fields, but it is largely unknown whether and to what extent ARB are transferred to vegetables and the human gut. It could be hypothesised that food of animal and vegetal origin have a different role in ARB transfer to the human gut and that different diets could be characterised by different antimicrobial resistance gene (ARG) loads. This study included three groups comprising vegans (n = 26), vegetarians (n = 32) and omnivores (n = 43). Metadata regarding food consumption and anthropometric parameters were collected. Gut microbial communities were investigated by 16S rDNA analysis. Four ARGs (sul2, tetA, bla_TEM and strB) were quantified by qPCR. The results showed a lower total load of investigated ARGs in vegan diet (pairwise comparison adjusted results: omnivorous-vegan, P = 0.0119; omnivorous-vegetarian, P = 0.7416; and vegan-vegetarian, P = 0.0119). No significant differences in abundance of each gene separately were found between the three groups. Neither the amount of animal protein nor the occurrence of ARGs was significant in explaining differences in the gut microbial community of individuals, and a large proportion of the differences between community composition (PERMANOVA, 46.87%) was not explained by the analysed variables. The results support the role of omnivorous and vegetarian diets in accumulating ARGs, suggesting a possible role for animal-derived food consumption.

Antibiotic and heavy metal resistance in enterococci from coastal marine sediment

Sediment samples from three coastal sites - two beach resorts (Beach 1 and Beach 2 sites) and an area lying between an oil refinery and a river estuary (Estuarine site) - were analyzed for antibiotic- and heavy metal (HM)-resistant enterococci. A total of 123 enterococci, 36 E. faecium, 34 E. casseliflavus, 33 E. hirae, 5 E. faecalis, 3 E. durans, 3 E. gallinarum, and 9 Enterococcus spp, were recovered. Strains resistant to erythromycin, tetracycline and quinupristin/dalfopristin (Q/D) were recovered from all sites, whereas multidrug-resistant isolates were recovered only from "Beach 2" (14%) and "Estuarine" (3.7%). As regards HM resistance, the strains showed a high frequency (68%) of cadmium and/or copper resistance and uniform susceptibility to mercury. The prevalence of cadmium-resistant strains was significantly higher among erythromycin-resistant than among erythromycin-susceptible strains. A significant association between cadmium or copper resistance and Q/D resistance was also observed at "Estuarine" site. The levels of the two HMs in sediment from all sites were fairly low, ranging from 0.070 to 0.126 μg/g, for cadmium and from 1.00 to 7.64 μg/g for copper. Mercury was always undetectable. These findings are consistent with reports that low HM concentrations may contribute to co-selection of antibiotic-resistant bacterial strains, including enterococci.

Comparative 16SrDNA Gene-Based Microbiota Profiles of the Pacific Oyster (Crassostrea gigas) and the Mediterranean Mussel (Mytilus galloprovincialis) from a Shellfish Farm (Ligurian Sea, Italy)

The pacific oyster Crassostrea gigas and the Mediterranean mussel Mytilus galloprovincialis are two widely farmed bivalve species which show contrasting behaviour in relation to microbial diseases, with C. gigas being more susceptible and M. galloprovincialis being generally resistant. In a recent study, we showed that different susceptibility to infection exhibited by these two bivalve species may depend on their different capability to kill invading pathogens (e.g., Vibrio spp.) through the action of haemolymph components. Specific microbial-host interactions may also impact bivalve microbiome structure and further influence susceptibility/resistance to microbial diseases. To further investigate this concept, a comparative study of haemolymph and digestive gland 16SrDNA gene-based bacterial microbiota profiles in C. gigas and M. galloprovincialis co-cultivated at the same aquaculture site was carried out using pyrosequencing. Bacterial communities associated with bivalve tissues (hemolymph and digestive gland) were significantly different from those of seawater, and were dominated by relatively few genera such as Vibrio and Pseudoalteromonas. In general, Vibrio accounted for a larger fraction of the microbiota in C. gigas (on average 1.7-fold in the haemolymph) compared to M. galloprovincialis, suggesting that C. gigas may provide better conditions for survival for these bacteria, including potential pathogenic species such as V. aestuarianus. Vibrios appeared to be important members of C. gigas and M. galloprovincialis microbiota and might play a contrasting role in health and disease of bivalve species. Accordingly, microbiome analyses performed on bivalve specimens subjected to commercial depuration highlighted the ineffectiveness of such practice in removing Vibrio species from bivalve tissues.

Enterococci populations of a metropolitan river after an extreme flood event: prevalence, persistence and virulence determinants

We investigated the prevalence, persistence and virulence determinants of enterococci populations in water samples collected over three rounds following an extreme flood event in a metropolitan river. Enterococci (n = 482) were typed using the high resolution biochemical fingerprinting method (PhP typing) and grouped into common (C) or single (S) biochemical phenotypes (BPTs). In all, 23 C-BPTs (72.6% of isolates) were found across the sites. A representative isolate of each C-BPT was identified to the species level and tested for the presence of seven virulence genes (VGs), biofilm formation and resistance to 14 antibiotics. The enterococci concentrations in samples collected during the first two rounds were above national recreational water guidelines. By round three, enterococci concentrations decreased significantly (P < 0.05). However, 11 C-BPTs (55.5% of isolates) persisted across all sampling rounds. E. casseliflavus and E. mundtii were the most common enterococci populations comprising of >57% of all isolates. Ten of the 11 most dominant C-BPTs were resistant to multiple antibiotics and harboured one or more VGs. The high prevalence of antibiotic resistance and VGs among enterococci isolates in this catchment not only provides them with niche advantages but also poses a risk to public health.

Interspecies transfer of vancomycin, erythromycin and tetracycline resistance among Enterococcus species recovered from agrarian sources

Background

Enterococci are now well recognised for their ability to transfer antibiotic resistance and for their association with nosocomial infections, but less is known regarding their relevance in the wider environment. Enterococcus faecalis and Enterococcus faecium were isolated from a range of agrarian associated sources (low-flow water, septic tank, poultry litter, high flow water, slurry/soil) and were assessed for latent ability to transfer antimicrobial resistance.

Results

The isolates were tested for phenotypic clumping in the presence of cell-free supernatant from other isolates. Some isolates were identified which demonstrated clumping, indicating that they possessed peptide sex pheromone conjugal machinery. All isolates were also tested for antibiotic resistance phenotypes using both disc diffusion and minimum inhibitory concentration (MIC) assays. These tests revealed that the enterococci demonstrated both phenotypic clumping and antibiotic resistance phenotypes. Based on these selection criteria, the isolates were identified as having the potential for horizontal gene transfer and were used to investigate the transfer of multiple antibiotic resistance phenotypes. Conjugal transfer of antibiotic resistance phenotypes was determined using a solid agar mating method followed by a standard antibiotic selection test resulting in different transfer patterns. An interspecies conjugal transfer of vancomycin resistance from E. faecalis to E. faecium was identified while the remaining reactions were within the same species. Transfer efficiencies ranging from 2 × 10⁻¹ to 2.3 × 10⁻⁵ were determined based on the reactions of three donor isolates (MF06036, MF0410 and MF06035) and two recipient isolates (MW01105^Rif and ST01109^Rif), with the transfer of vancomycin, erythromycin and tetracycline resistance genes.

Conclusions

The conjugation reactions and selection conditions used in this study resulted in a variety of co-transferred resistance phenotypes suggesting the presence of different mobile elements in the set of natural isolates. This study highlights the potential for extensive horizontal gene transfer in a previously neglected reservoir for enterococci.

Virulence Genes among Enterococcus faecalis and Enterococcus faecium Isolated from Coastal Beaches and Human and Nonhuman Sources in Southern California and Puerto Rico

Most Enterococcus faecalis and E. faecium are harmless to humans; however, strains harboring virulence genes, including esp, gelE, cylA, asa1, and hyl, have been associated with human infections. E. faecalis and E. faecium are present in beach waters worldwide, yet little is known about their virulence potential. Here, multiplex PCR was used to compare the distribution of virulence genes among E. faecalis and E. faecium isolated from beaches in Southern California and Puerto Rico to isolates from potential sources including humans, animals, birds, and plants. All five virulence genes were found in E. faecalis and E. faecium from beach water, mostly among E. faecalis. gelE was the most common among isolates from all source types. There was a lower incidence of asa1, esp, cylA, and hyl genes among isolates from beach water, sewage, septage, urban runoff, sea wrack, and eelgrass as compared to human isolates, indicating that virulent strains of E. faecalis and E. faecium may not be widely disseminated at beaches. A higher frequency of asa1 and esp among E. faecalis from dogs and of asa1 among birds (mostly seagull) suggests that further studies on the distribution and virulence potential of strains carrying these genes may be warranted.

Enterococcus faecium ST17 from Coastal Marine Sediment Carrying Transferable Multidrug Resistance Plasmids

The multidrug-resistant Enterococcus faecium 17i48, sequence type 17, from marine sediment, carrying erm(B), tet(M), and tet(L) genes, was analyzed for the presence of antibiotic resistance plasmids and for the ability to transfer resistance genes. The strain was found to harbor the replicon type (repA) of pRE25, pRUM, pHTβ, and the axe-txe toxin-antitoxin (TA) system. In mating experiments, tet(M) and tet(L) were cotransferred with the repA_pRE25, whereas erm(B) was consistently cotransferred with the axe-txe and repA_pRUM, suggesting that tetracycline and erythromycin resistance genes were carried on different elements both transferable by conjugation, likely via pHTβ-mediated mobilization. Hybridization and PCR mapping demonstrated that tet(M) and tet(L) were located in tandem on a pDO1-like plasmid that also carried the repA_pRE25, whereas erm(B) was carried by a pRUM-like plasmid. Sequencing of the latter plasmid showed a high nucleotide identity with pRUM and the presence of cat, aadE, sat4, and a complete aphA resistance genes. These findings show that the genetic features of E. faecium 17i48 are consistent with a hospital-adapted clone and suggest that antibiotic resistance may spread in the environment, also in the absence of antibiotic pressure, due to TA system plasmid maintenance.

Virulence determinants and production of extracellular enzymes in Enterococcus spp. from surface water sources

Virulence factors in Enterococcus may be indicative of potential pathogenicity. The aim of this study was to determine the relationship between the presence of clinically relevant virulence genes, in Enterococcus spp. from environmental water, and their in vitro expression. One hundred and twenty-four Enterococcus isolates (seven species), from five surface water systems in the North West Province, South Africa, were screened for the presence of asa1, cylA, esp, gelE and hyl using polymerase chain reaction. The expression of cylA, hyl and gelE was determined by phenotypic assessments. Sixty-five percent of the isolates were positive for one virulence gene and 13% for two or more. Most frequently detected genes were gelE (32%) and cylA (28%). Enterococcal surface protein was absent in all isolates screened. The presence of virulence genes was correlated with their extracellular enzyme production. The results show that a large percentage of these environmental Enterococcus spp. possess virulence factors that could be expressed in vitro. This is a cause for concern and could have implications for individuals using this water for recreational and cultural purposes. Further investigation is required into the sources of these potential pathogenic Enterococcus isolates and measures to minimize their presence in water sources.

Environmental waters as a source of antibiotic-resistant Enterococcus species in Belgrade, Serbia

Despite the number of studies on antibiotic-resistant enterococci from Serbian clinical settings, there are no data about environmental contamination with these bacteria. Thus, this study investigated the prevalence of antibiotic-resistant enterococci in Belgrade, Serbia. Enterococcus species collected from ten surface water sites, including a lake, two major river systems, and springs, were tested. Among enterococci, we found single (21.7 %), double (17.4 %), and multiple antibiotic resistance patterns (56.3 %). Vancomycin-resistant strains were not found, indicating that their abundance in Belgrade is tightly linked to clinical settings. The multiple drug-resistant strains Enterococcus faecalis, Enterococcus faecium, and Enterococcus mundtii were frequently detected in the lake during the swimming season and in the rivers near industrial zones. We confirmed the presence of ermB, ermC, ant(6)-Ia, tetM, and tetL and mutations in gyrA genes. The phylogenetic analysis of 16S rRNA gene of E. faecium isolates that harbor esp gene classified them into two groups based on high-bootstraps scores in the tree analysis. Pulsed-field gel electrophoresis analysis of antibiotic-resistant enterococci revealed genomic similarity ranging from 75 to 100 %. This study indicates the importance of anthropogenic impact to the spread of antibiotic-resistant enterococci in environmental waters of Belgrade, Serbia.

Prevalence of enterococcus species and their virulence genes in fresh water prior to and after storm events

Enterococcus spp. isolates (n = 286) collected from six surface water bodies in subtropical Brisbane, Australia, prior to and after storm events, were identified to species level and tested for the presence of seven clinically important virulence genes (VGs). Enterococcus faecalis (48%), Enterococcus faecium (14%), Enterococcus mundtii (13%), and Enterococcus casseliflavus (13%) were frequently detected at all sites. The frequency of E. faecium occurrence increased from 6% in the dry period to 18% after the wet period. The endocarditis antigen (efaA), gelatinase (gelE), collagen-binding protein (ace), and aggregation substance (asa1) were detected in 61%, 43%, 43%, and 23% of Enterococcus isolates, respectively. The chances of occurrence of ace, gelE, efaA, and asa1 genes in E. faecalis were found to be much higher compared to the other Enterococcus spp. The observed odds ratio of occurrence of ace and gelE genes in E. faecalis was much higher at 7.96 and 6.40 times, respectively. The hyl gene was 3.84 times more likely to be detected in E. casseliflavus. The presence of multiple VGs in most of the E. faecalis isolates underscores the importance of E. faecalis as a reservoir of VGs in the fresh water aquatic environment. Consequently, if contaminated surface water is to be used for production of potable and nonpotable water some degree of treatment depending upon intended use such as detention in basins prior to use or chlorination is required.