Detection of vancomycin-resistant enterococci from faecal samples of Iberian wolf and Iberian lynx, including Enterococcus faecium strains of CC17 and the new singleton ST573

Genomic analysis of enterococci carrying optrA, poxtA, and vanA resistance genes from wild boars, Italy

AIMS

To investigate enterococci carrying linezolid and vancomycin resistance genes from fecal samples recovered from wild boars.

METHODS AND RESULTS

Florfenicol- and vancomycin-resistant enterococci, isolated on selective agar plates, were screened by PCR for the presence of linezolid and vancomycin resistance genes. Five isolates carried optrA or poxtA linezolid resistance genes; one strain was resistant to vancomycin for the presence of vanA gene. All isolates were tested for their antibiotic susceptibility and subjected to Whole Genome Sequencing (WGS) analysis. In Enterococcus faecalis (E. faecalis) V1344 and V1676, the optrA was located on the new pV1344-optrA and pV1676-optrA plasmids, respectively, whereas in Enterococcus faecium (E. faecium) V1339 this gene was on a 22 354-bp chromosomal genetic context identical to the one detected in a human E. faecium isolate. In both E. faecium V1682 and E. durans V1343, poxtA was on the p1818-c plasmid previously found in a human E. faecium isolate. In E. faecium V1328, the vanA gene was on the Tn1546 transposon in turn located on a new pV1328-vanA plasmid. Only E. faecium V1682 successfully transferred the poxtA gene to an enterococcal recipient in filter mating assays.

CONCLUSIONS

The occurrence of genetic elements carrying linezolid and vancomycin resistance genes in enterococci from wild boars is a matter of concern, moreover, the sharing of plasmids and transposons between isolates from wild animals, human, and environment indicates an exchange of genetic material between these settings.

Antimicrobial Resistance Among Clinically Significant Bacteria in Wildlife: An Overlooked One Health Concern

Antimicrobial resistance (AMR) has emerged as a critical global health challenge. However, the significance of AMR is not limited to humans and domestic animals but extends to wildlife and the environment. Based on the analysis of > 200 peer-reviewed papers, this review provides comprehensive and current insights into the detection of clinically significant antimicrobial resistant bacteria and resistance genes in wild mammals, birds and reptiles worldwide. The review also examines the overlooked roles of wildlife in AMR emergence and transmission. In wildlife, AMR is potentially driven by anthropogenic activity, agricultural and environmental factors, and natural evolution. This review highlights the significance of AMR surveillance in wildlife, identifies species and geographical foci and gaps, and demonstrates the value of multifaceted One Health strategies if further escalation of AMR globally is to be curtailed.

Hiding in plain sight - Wildlife as a neglected reservoir and pathway for the spread of antimicrobial resistance: A narrative review

Antimicrobial resistance represents a global health problem, with infections due to pathogenic antimicrobial resistant bacteria (ARB) predicted to be the most frequent cause of human mortality by 2050. The phenomenon of antimicrobial resistance has spread to and across all ecological niches, and particularly in livestock used for food production with antimicrobials consumed in high volumes. Similarly, hospitals and other healthcare facilities are recognized as significant “hotspots” of ARB and antimicrobial resistance genes (ARGs); however, over the past decade, new and previously overlooked ecological niches are emerging as hidden reservoirs of ARB/ARGs. Increasingly extensive and intensive industrial activities, degradation of natural environments, burgeoning food requirements, urbanization, and global climatic change have all dramatically affected the evolution and proliferation of ARB/ARGs, which now stand at extremely concerning ecological levels. While antimicrobial resistant bacteria and genes as they originate and emanate from livestock and human hosts have been extensively studied over the past 30 years, numerous ecological niches have received considerably less attention. In the current descriptive review, the authors have sought to highlight the importance of wildlife as sources/reservoirs, pathways and receptors of ARB/ARGs in the environment, thus paving the way for future primary research in these areas.

Prevalence, antibiotic resistance and virulence of Enterococcus spp. from wastewater treatment plant effluent and receiving waters in South Africa

Poorly operating wastewater treatment plants (WWTPs) result in faecal pollution of receiving waters, posing a health risk to humans and animals. The aim of this study was to determine the antimicrobial resistance patterns and presence of virulent genes in Enterococcus spp. isolated from three WWTPs' final effluent and receiving waters in the North West Province, South Africa. Sixty-three Enterococcus spp. were identified and their antimicrobial susceptibility, as well as the presence of five virulence genes, determined. The antibiotic inhibition zone diameter data were subject to cluster analysis. Sixty-eight percent of the screened Enterococcus spp. were resistant to three or more antibiotics and harboured plasmids. Five virulence genes were detected and six multi-virulence profiles observed. Cluster analysis indicated groupings of isolates from all three effluent points downstream together, and between plants 1 and 2 together. The findings of this study have demonstrated that Enterococcus spp. harbouring virulence factors and plasmids that mediate multiple antibiotic resistance are present in effluent and receiving water systems that support various social needs. This is a cause for concern and it is recommended that Enterococcus be used as an additional faecal indicator when microbiological quality of water is assessed.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

Antibiotic Susceptibility and Virulence Genes in Enterococcus Isolates from Wild Mammals Living in Tuscany, Italy

Drug resistance is of great importance to human and animal health, but wild environments are still poorly understood in terms of their function as reservoirs of dangerous microbes and resistance determinants. The aim of the study was to determine the antibiotic susceptibility and virulence factors of Enterococcus bacteria from wildlife in Tuscany, Italy. Of the 36 mammalian fecal samples, 52 isolates were derived and classified as Enterococcus faecium (46% of isolates), Enterococcus hirae (19%), Enterococcus faecalis (13%), Enterococcus gallinarum (8%), Enterococcus casseliflavus (6%), Enterococcus durans (4%), Enterococcus mundtii (2%), and Enterococcus canintestini (2%) using both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and methods based on analysis of genetic material. The isolates tested showed the most frequent resistance to tetracycline (36.5% isolates), ciprofloxacin (36.5%), and erythromycin (25%). Three isolates showed high level of resistance (minimal inhibitory concentration ≥1,024 μg/mL) to vancomycin and teicoplanin, and 15% of the isolates demonstrated multidrug resistance. No isolate resistant to ampicillin, linezolid, or streptomycin was found. Among resistance genes, aac(6)-Ii (50% isolates), msrA/B (48%), msrC (42%), and tetM (31%) were identified most frequently. All E. faecium and E. faecalis isolates were positive for the efaAfm and efaAfs genes, respectively. Other virulence-associated genes, that is, gelE, cylA, asa1, esp, ace, orf1481, ptsD, and sgrA, were found in the majority of E. faecalis and several E. faecium isolates. Multilocus sequence typing analysis performed for selected isolates revealed three new sequence types. The results obtained indicate that wild mammals might act as reservoirs of resistance and virulence determinants that could be transferred between different ecosystems.

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.

A Decade-Long Commitment to Antimicrobial Resistance Surveillance in Portugal

Antimicrobial resistance (AMR) is a worldwide problem with serious health and economic repercussions. Since the 1940s, underuse, overuse, and misuse of antibiotics have had a significant environmental downside. Large amounts of antibiotics not fully metabolized after use in human and veterinary medicine, and other applications, are annually released into the environment. The result has been the development and dissemination of antibiotic-resistant bacteria due to many years of selective pressure. Surveillance of AMR provides important information that helps in monitoring and understanding how resistance mechanisms develop and disseminate within different environments. Surveillance data is needed to inform clinical therapy decisions, to guide policy proposals, and to assess the impact of action plans to fight AMR. The Functional Genomics and Proteomics Unit, based at the University of Trás-os-Montes and Alto Douro in Vila Real, Portugal, has recently completed 10 years of research surveying AMR in bacteria, mainly commensal indicator bacteria such as enterococci and Escherichia coli from the microbiota of different animals. Samples from more than 75 different sources have been accessed, from humans to food-producing animals, pets, and wild animals. The typical microbiological workflow involved phenotypic studies followed by molecular approaches. Throughout the decade, 4,017 samples were collected and over 5,000 bacterial isolates obtained. High levels of AMR to several antimicrobial classes have been reported, including to β-lactams, glycopeptides, tetracyclines, aminoglycosides, sulphonamides, and quinolones. Multi-resistant strains, some relevant to human and veterinary medicine like extended-spectrum β-lactamase-producing E. coli and vancomycin-resistant enterococci, have been repeatedly isolated even in non-synanthropic animal species. Of particular relevance are reports of AMR bacteria in wildlife from natural reserves and endangered species. Future work awaits as this threatening yet unsolved problem persists. GRAPHICAL ABSTRACTSummary diagram of the antimicrobial resistance surveillance work developed by the UTAD Functional Genomics and Proteomics Unit.

Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer

Ampicillin resistance has greatly contributed to the recent dramatic increase of a cluster of human adapted Enterococcus faecium lineages (ST17, ST18, and ST78) in hospital-based infections. Changes in the chromosomal pbp5 gene have been associated with different levels of ampicillin susceptibility, leading to protein variants (designated as PBP5 C-types to keep the nomenclature used in previous works) with diverse degrees of reduction in penicillin affinity. Our goal was to use a comparative genomics approach to evaluate the relationship between the diversity of PBP5 among E. faecium isolates of different phylogenomic groups as well as to assess the pbp5 transferability among isolates of disparate clonal lineages. The analyses of 78 selected E. faecium strains as well as published E. faecium genomes, suggested that the diversity of pbp5 mirrors the phylogenomic diversification of E. faecium. The presence of identical PBP5 C-types as well as similar pbp5 genetic environments in different E. faecium lineages and clones from quite different geographical and environmental origin was also documented and would indicate their horizontal gene transfer among E. faecium populations. This was supported by experimental assays showing transfer of large (≈180–280 kb) chromosomal genetic platforms containing pbp5 alleles, ponA (transglycosilase) and other metabolic and adaptive features, from E. faecium donor isolates to suitable E. faecium recipient strains. Mutation profile analysis of PBP5 from available genomes and strains from this study suggests that the spread of PBP5 C-types might have occurred even in the absence of a significant ampicillin resistance phenotype. In summary, genetic platforms containing pbp5 sequences were stably maintained in particular E. faecium lineages, but were also able to be transferred among E. faecium clones of different origins, emphasizing the growing risk of further spread of ampicillin resistance in this nosocomial pathogen.

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.

Acquired antibiotic resistance among wild animals: the case of Iberian Lynx (Lynx pardinus)

The selective pressure generated by the clinical misuse of antibiotics has been the major driving force leading to the emergence of antibiotic resistance among bacteria. Antibiotics or even resistant bacteria are released into the environment and contaminate the surrounding areas. Human and animal populations in contact with these sources are able to become reservoirs of these resistant organisms. Then, due to the convergence between habitats, the contact of wild animals with other animals, humans, or human sources is now more common and this leads to an increase in the exchange of resistance determinants between their microbiota. Indeed, it seems that wildlife populations living in closer proximity to humans have higher levels of antibiotic resistance. Now, the Iberian Lynx (Lynx pardinus) is a part of this issue, being suggested as natural reservoir of acquired resistant bacteria. The emerging public health concern regarding microbial resistance to antibiotics is becoming true: the bacteria are evolving and are now affecting unintentional hosts.

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.

Potential impact of antimicrobial resistance in wildlife, environment and human health

Given the significant spatial and temporal heterogeneity in antimicrobial resistance distribution and the factors that affect its evolution, dissemination, and persistence, it is important to highlight that antimicrobial resistance must be viewed as an ecological problem. Monitoring the resistance prevalence of indicator bacteria such as Escherichia coli and enterococci in wild animals makes it possible to show that wildlife has the potential to serve as an environmental reservoir and melting pot of bacterial resistance. These researchers address the issue of antimicrobial-resistant microorganism proliferation in the environment and the related potential human health and environmental impact.

Epidemic Escherichia coli ST131 and Enterococcus faecium ST17 in coastal marine sediments from an Italian beach

Fecal indicator bacteria (FIB) are used worldwide to assess water quality in coastal environments, but little is known about their genetic diversity and pathogenicity. This study examines the prevalence, antimicrobial resistance, virulence, and genetic diversity of FIB isolated from marine sediments from a central Adriatic seaside resort. FIB, recovered from 6 out of 7 sites, were significantly more abundant at sampling stations 300 m offshore than close to the shore. Escherichia coli accounted for 34.5% of fecal coliforms, and Enterococcus faecalis accounted for 32% of enterococci. Most isolates (27% of E. coli and 22% of enterococci) were recovered from the sediments that had the highest organic content. Multidrug-resistant E. coli (31%) and enterococci (22%) were found at nearly all sites, whereas 34.5% of E. coli and 28% of enterococci harboring multiple virulence factors were recovered from just two sites. Pulsed-field gel electrophoresis typing showed wide genetic diversity among isolates. Human epidemic clones ( E. coli ST131 and Enterococcus faecium ST17) were identified for the first time by multilocus sequence typing in an area where bathing had not been prohibited. These clones were from sites far removed from riverine inputs, suggesting a wide diffusion of pathogenic FIB in the coastal environment and a high public health risk.

Vancomycin resistant enterococci: from the hospital effluent to the urban wastewater treatment plant

Vancomycin is an important antibiotic to treat serious nosocomial enterococci infections. Human activities, in particular those related with clinical practices performed in hospitals, can potentiate the transfer and selection of clinically-relevant resistant bacteria such as vancomycin resistant enterococci (VRE). Indeed, previous studies demonstrated the occurrence of VRE in urban wastewater treatment plants and related environments (e.g. sewage, rivers). In this study, the occurrence of VRE in a hospital effluent and in the receiving urban wastewater treatment plant was investigated. Vancomycin and ciprofloxacin resistant bacteria occurred in the hospital effluent and in raw municipal inflow at densities of 10(3) to 10(2) CFU mL(-1), being significantly more prevalent in the hospital effluent than in the urban wastewater. Most of the VRE isolated from the hospital effluent belonged to the species Enterococcus faecalis and Enterococcus faecium and presented multidrug-resistance phenotypes to ciprofloxacin, tetracycline, erythromycin, and high-level gentamicin. The same pattern was observed in clinical isolates and in enterococci isolated from the final effluent of the urban wastewater treatment plant. These results show that hospital effluents discharged into urban wastewater treatment plants may be a relevant source of resistance spread to the environment.