Species distribution, antibiotic resistance and virulence traits in canine and feline enterococci in Tunisia

Molecular characterization of tetracycline and vancomycin-resistant Enterococcus faecium isolates from healthy dogs in Egypt: a public health threat

BACKGROUND

Vancomycin-resistant enterococci (VRE) are among the most common causative pathogens for nosocomial infections worldwide. Moreover, strains of VRE have been isolated from several domestic livestock in Egypt.

METHODS

This study examined if healthy dogs are a potential source of VRE infection by isolating and characterizing Enterococcus faecium strains from stool samples on a morphological basis and biochemical activities. Subsequently, it was confirmed by genotypic characterization using polymerase chain reaction (PCR), followed by the detection of antibiotic resistance genes, virulence determinants, and genes contributing to enterocin production by PCR. Furthermore, the phylogenetic relationships among vanB and tetL genes were analyzed.

RESULTS

All ten fecal samples were identified as E. faecium and confirmed by PCR. In addition, 90% of the isolates tested were positive for the virulence genes gelE and esp, and all the isolates tested were positive for the antibiotic resistance genes tetL and vanB. Only three of the five enterocin genes examined were detected. Ent As-48, bacteriocin 31, and Ent L50 were identified in 100%, 80%, and 60% of the samples, respectively.

CONCLUSION

Dogs should be regarded as a reservoir of E. faecium that carries vancomycin resistance and virulence determinants that may affect public health in Egypt, considering a "One Health" task force approach to restrict their spread.

Antimicrobial and Biocide Resistance among Canine and Feline Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii Isolates from Diagnostic Submissions

A total of 215 isolates from infections of dogs and cats, including 49 Enterococcus faecalis, 37 Enterococcus faecium, 59 Escherichia coli, 56 Pseudomonas aeruginosa, and 14 Acinetobacter baumannii, were investigated for their susceptibility to 27 (Gram-positive bacteria) or 20 (Gram-negative bacteria) antimicrobial agents/combinations of antimicrobial agents by broth microdilution according to the recommendations of the Clinical and Laboratory Standards Institute. Moreover, all isolates were analysed for their susceptibility to the biocides benzalkonium chloride, chlorhexidine, polyhexanide, and octenidine by a recently published broth microdilution biocide susceptibility testing method. While the E. faecalis isolates did not show expanded resistances, considerable numbers of the E. faecium isolates were resistant to penicillins, macrolides, tetracyclines, and fluoroquinolones. Even a single vancomycin-resistant isolate that carried the vanA gene cluster was detected. Expanded multiresistance phenotypes were also detected among the E. coli isolates, including a single carbapenem-resistant, blaOXA-48-positive isolate. In addition, multiresistant A. baumannii isolates were detected. The minimal inhibitory concentrations of the biocides showed unimodal distributions but differed with respect to the biocide and the bacterial species investigated. Although there were no indications of a development of biocide resistance, some P. aeruginosa isolates exhibited benzalkonium MICs higher than the highest test concentration.

Characterization and Comparison of Enterococcus spp. Isolates from Feces of Healthy Dogs and Urine of Dogs with UTIs

Simple Summary

Infections caused by Enterococcus spp. represent a serious threat to human and animal health due to difficulties in treatment. Indeed, these bacteria are a very able “trafficker” of antimicrobial resistance genes and for this reason they are often resistant to many antimicrobials. In this study we explored the role of pet dogs as possible carriers and targets of antimicrobial resistant and virulent enterococci. Isolates collected from feces of healthy animals and urine of dogs suffering with UTIs were characterized and compared. Strains resulted as resistant to many of the antimicrobials tested and almost of them were multidrug-resistant. Diffuse resistance was recorded for compounds routinely employed in human and pet therapy. Genes responsible for antimicrobial resistance were widely detected. E. faecalis and E. faecium resulted as equally distributed in stool samples, while E. faecalis prevailed among UTI isolates; virulence genes were more often detected in bacteria belonging to this species. Our data confirm that enterococci inhabitant of the gut flora probably represent the main source of UTI in dogs. Furthermore, healthy and sick pet dogs could be spreaders of antimicrobial and virulent enterococci, representing a possible hazard for other animals and owners.

Abstract

Enterococcus spp. are opportunistic pathogens of both humans and animals characterized by high resistance to antimicrobials. Dogs could be intestinal carriers or suffer from Enterococcus infections, mainly urinary tract infections (UTIs). This study aimed to analyze and compare Enterococcus spp. isolated from healthy dog stools and sick dog urine. Overall, 51 isolates (29 from stools and 22 from UTI) were characterized at species level and tested for antimicrobial resistance, biofilm production and presence of resistance and virulence genes. E. faecium and E. faecalis resulted as equally distributed in stools samples, while E. faecalis predominated among UTI isolates. HLAR phenotype was detected in 47.1% isolates; 64.7% isolates were resistant to ampicillin (47.1% with a MIC ≥ 64 µg/mL). High levels of resistance were recorded for fluoroquinolones (enrofloxacin 74.5%, ciprofloxacin 66.7%), clindamycin (84.3%), tetracycline (78.4%) and quinupristin–dalfopristin (78.4%). No vancomycin resistant strains were detected. All but one isolate were multidrug-resistant. Most detected resistance genes were tetM (70.5%), pbp4 (52.9%) and aph(3′)-IIIa (39.2%). All isolates were able to produce biofilm, but isolates from UTIs and belonging to E. faecalis more frequently resulted in strong biofilm producers. Most detected virulence genes were asa1 (52.9%), gelE (41.2%), cylA (37.3%) and esp (35.3%); all of them resulted as more frequently associated to E. faecalis. No particular differences emerged between isolates from feces and UTI, considering all evaluated aspects. Our results confirm pet dogs as carriers of multidrug-resistant enterococci; stool microflora could be considered as the most probable source of enterococcal UTI and E. faecalis carried by dogs seems to be more virulent than E. faecium, justifying its more frequent involvement in urinary tract infections.

Industrial dog food is a vehicle of multidrug-resistant enterococci carrying virulence genes often linked to human infections

The increase in the number of pets in recent years has been followed by an exponential growth of the industrial pet food sector, which has been accompanied by new food safety risks, namely antibiotic resistance. The aim of this study was to investigate whether dog food commercially available in Portugal is a reservoir of clinically-relevant antibiotic resistant Enterococcus. Fifty-five samples (25 brands; 22 wet, 14 raw frozen, 8 dry, 7 treats and 4 semi-wet) were collected on 9 commercial surfaces in the Porto region (September 2019 to January 2020). Most samples were obtained from brands that are commercialized worldwide (n = 21/25). Sample (25 g) processing included pre-enrichment and enrichment steps in culture media without/with 3 antibiotics, and then plating into selective media without/with the same antibiotics. Susceptibility was studied for 13 antibiotics (disk diffusion; Etest; microdilution) according to EUCAST/CLSI. Clinically-relevant species (E. faecium and E. faecalis), antibiotic resistance (vanA, vanB, optrA, poxtA) and virulence (e.g. ptsD, esp, sgrA) genes were identified by PCR. Other species of Enterococcus were identified by MALDI-TOF MS. Clonality was established by MLST in selected isolates. Enterococcus (n = 184; 7 species; >85% E. faecium and E. faecalis) were detected in 30 samples (54%) of different types (14 raw, 16 heat treated-7 dry, 6 wet, 3 treats). E. faecium and E. faecalis were more frequent in dry and wet samples, respectively. More than 40% of enterococci recovered were resistant to erythromycin, tetracycline, quinupristin-dalfopristin, streptomycin, gentamicin, chloramphenicol, ampicillin or ciprofloxacin, and to a lesser extent to linezolid (23%; optrA, poxtA) or vancomycin and teicoplanin (2% each; vanA). Multidrug-resistant isolates (31%), including to vancomycin and linezolid, were obtained mostly from raw foods, although also detected in wet samples or treats, and mainly from culture media supplemented with antibiotics. Samples subjected to thermal treatment mostly carried non-MDR isolates. The variety of clones observed included strains previously identified in hospitalized patients (E. faecium ST17/ST80; E. faecalis ST40), farm animals, pets and environmental strains. This study shows that dog food from international brands is a vehicle of clinically-relevant enterococci carrying resistance to last resort antibiotics and relevant virulence genes, thus positioning pet food as an important source of antibiotic resistance spread within the One Health context. The high incidence of Enterococcus in a variety of dog food samples indicates the need to review selection of raw materials, manufacturing and hygiene practices in an emerging food sector growing worldwide.

Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces

Background

Long-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the mobile genetic elements, which are usually missed with short-reads. We applied long-read metagenomics with Nanopore sequencing to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample.

Results

We used nanopore long-read metagenomics and frameshift aware correction on a canine fecal sample and retrieved eight single-contig HQ MAGs, which were > 90% complete with < 5% contamination, and contained most ribosomal genes and tRNAs. At the technical level, we demonstrated that a high-molecular-weight DNA extraction improved the metagenomics assembly contiguity, the recovery of the rRNA operons, and the retrieval of longer and circular contigs that are potential HQ MAGs. These HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Catenibacterium, Blautia, and Enterococcus genera. Linking our results to previous gastrointestinal microbiome reports (metagenome or 16S rRNA-based), we found that some bacterial species on the gastrointestinal tract seem to be more canid-specific –Succinivibrio, Prevotellamassilia, Phascolarctobacterium, Blautia_A sp900541345–, whereas others are more broadly distributed among animal and human microbiomes –Sutterella, Catenibacterium, Enterococcus, and Blautia sp003287895. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Moreover, we show that long reads are essential to detect mobilome functions, usually missed in short-read MAGs.

Conclusions

We recovered eight single-contig HQ MAGs from canine feces of a healthy dog with nanopore long-reads. We also retrieved relevant biological insights from these specific bacterial species previously missed in public databases, such as complete ribosomal operons and mobilome functions. The high-molecular-weight DNA extraction improved the assembly’s contiguity, whereas the high-accuracy basecalling, the raw read error correction, the assembly polishing, and the frameshift correction reduced the insertion and deletion errors. Both experimental and analytical steps ensured the retrieval of complete bacterial genomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07607-0.

Multidrug Resistance in Enterococci Isolated From Wild Pampas Foxes (Lycalopex gymnocercus) and Geoffroy's Cats (Leopardus geoffroyi) in the Brazilian Pampa Biome

Enterococci are ubiquitous microorganisms present in various environments and within the gastrointestinal tracts of humans and other animals. Notably, fecal enterococci are suitable indicators for monitoring antimicrobial resistance dissemination. Resistant bacterial strains recovered from the fecal samples of wild animals can highlight important aspects of environmental disturbances. In this report, we investigated antimicrobial susceptibility as well as resistance and virulence genes in fecal enterococci isolated from wild Pampas foxes (Lycalopex gymnocercus) (n = 5) and Geoffroy's cats (Leopardus geoffroyi) (n = 4) in the Brazilian Pampa biome. Enterococci were isolated from eight out of nine fecal samples and Enterococcus faecalis was identified in both animals. However, E. faecium and E. durans were only detected in Pampas foxes, while E. hirae was only detected in Geoffroy's cats. Antimicrobial susceptibility analysis showed resistance to rifampicin (94%), erythromycin (72.6%), ciprofloxacin/norfloxacin (40%), streptomycin (38%), and tetracycline (26%). The high frequency of multidrug-resistant enterococci (66%) isolated in this study is a matter of concern since these are wild animals with no history of therapeutic antibiotic exposure. The tetM/tetL and msrC/ermB genes were detected in most tetracycline- and erythromycin-resistant enterococci, respectively. The gelE, ace, agg, esp, and clyA virulence genes were also detected in enterococci. In conclusion, our data suggest that habitat fragmentation and anthropogenic activities in the Pampa biome may contribute to high frequencies of multidrug-resistant enterococci in the gut communities of wild Pampas foxes and Geoffroy's cats. To the best of the authors' knowledge, this is the first report of antimicrobial-resistant enterococci in the Pampa biome.

Reversible myelosuppression suspected to be secondary to linezolid in a cat with infected subcutaneous ureteral bypass systems

CASE SUMMARY

A 5-year-old castrated male domestic shorthair cat was presented for a multidrug-resistant Enterococcus faecium urinary tract infection within its bilateral subcutaneous ureteral bypass systems. After considerable consultation, the cat was treated with oral linezolid (10 mg/kg q12h) for two separate 2-week courses over 5 weeks. Over this time period, the cat became progressively neutropenic and thrombocytopenic, but was otherwise clinically stable. Upon cessation of the linezolid, the bicytopenia resolved within 12 days.

RELEVANCE AND NOVEL INFORMATION

The reversible myelosuppression in this case is suspected to be secondary to linezolid administration. While previously reported in people, this effect has not been reported at therapeutic doses in veterinary species. This report demonstrates the potential for adverse drug reaction development in cats treated with prolonged linezolid therapy and highlights the need for extreme caution when utilizing linezolid in patients with renal insufficiency. Linezolid is the only drug currently approved by the Food and Drug Administration to treat vancomycin-resistant enterococci infections in people; however, resistance to this antibiotic appears to be increasing. Multidrug-resistant organisms continue to be a real global public health threat in both human and veterinary medicine. Third-tier antibiotics should only be considered under extreme circumstances and after considerable consultation with a specialist. Please note that the authors of this manuscript followed American Veterinary Medical Association policies on stewardship and International Society for Companion Animal Infectious Diseases guidelines, and do not promote or encourage the use in daily practice.

Molecular epidemiology and mechanisms of antibiotic resistance in Enterococcus spp., Staphylococcus spp., and Streptococcus spp. in Africa: a systematic review from a One Health perspective

A systematic review of antibiotic-resistant Gram-positive bacteria in Africa from a One Health perspective is lacking. Here, we report result from a search for English-language articles on the resistance mechanisms and clonality of Gram-positive bacteria in Africa between 2007 and 2019 reported in PubMed, Web of Science, ScienceDirect, and African Journals OnLine; 172 studies from 22 different African countries were identified. Resistance genes, such as mecA, erm(B), erm(C), tet(M), tet(K), tet(L), vanB, vanA, vanC, and tet(O), were found to be common. Staphylococcus spp., Enterococcus spp., and Streptococcus spp. were the main species reported by the studies, with clones such as Staphylococcus aureus ST5 (n = 218 isolates), ST8 (n = 127 isolates), ST80 (n = 133 isolates), and ST88 (n = 117 isolates), and mobile genetic elements such as IS16 (n = 28 isolates), IS256 (n = 96), Tn916 (n = 107 isolates), and SCCmec (n = 4437 isolates) identified. SCCmec IV (n = 747 isolates) was predominant, followed by SCCmec III (n = 305 isolates), SCCmec II (n = 163 isolates), SCCmec V (n = 135 isolates), and SCCmec I (n = 79 isolates). Resistance to penicillin (n = 5926 isolates), tetracycline (n = 5300 isolates), erythromycin (n = 5151 isolates), rifampicin (n = 3823 isolates), gentamycin (n = 3494 isolates), sulfamethoxazole/trimethoprim (n = 3089 isolates), and ciprofloxacin (n = 2746 isolates) was common in most reports from 22 countries. Clonal dissemination of resistance across countries and between humans, animals, and the environment was observed. Resistance rates ranged from 1.4% to 100% for 15 of the studies; 10 were One Health-related studies. Strict infection control measures, antimicrobial stewardship, and periodic One Health epidemiological surveillance studies are needed to monitor and contain the threat of increasing antibiotic resistance in Africa.

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.

Prevalence of virulence genes in Enterococcus species isolated from companion animals and livestock

Enterococcus species have developed from being commensal bacteria to leading pathogens that cause infections in humans and animals. The gastrointestinal tract of mammals is the normal habitat of these species. Virulence factors are proteins that are produced by the bacterium which are used to enhance their pathogenicity. The objectives of this study were to isolate Enterococcus spp. from livestock and companion animals, differentiate between the different sub-species and detect the presence of important virulence genes. Rectal and saliva swabs were collected from dogs and cats, whereas only rectal swabs were collected from cattle and cloacal swabs from chickens. Presumptive Enterococcus was selected using Bile Esculin Azide (BEA) agar, and Enterococcus species were confirmed using the polymerase chain reaction (PCR) by amplifying the tuf gene. In order to differentiate between E. faecalis and E. faecium, a multiplex PCR was used to detect the SodA gene. The genes responsible for gelatinase production (gelE) and for conjugation (ccf) were also detected using PCR. Out of 211 animal swabs, 182 (86%) were positive for the tuf gene. Overall, there were 55 isolates of E. faecalis (30%) compared to 22 isolates of E. faecium (12%). The virulence genes had a prevalence of 52% and 36% for gelE and ccf, respectively, in all animal hosts. The results demonstrated that chicken cloacal samples had the highest prevalence for E. faecalis, gelE and ccf genes compared to all the other isolates detected from other animal hosts. The results also demonstrated a statistically significant (p < 0.05) association between the prevalence of virulence genes (gelE and ccf) and animal species from which Enterococcus spp. was isolated. We provided evidence that healthy livestock and companion animals can harbour pathogenic Enterococcus that can be transferred via the food chain as well as through close association such as petting and licking of humans. This study partially demonstrated that Enterococci spp. are capable of evolving from being simple commensal bacteria to becoming pathogens that cause infection in humans and animals through the acquisition of virulence factors through mobile genetic elements.

Water supply and feed as sources of antimicrobial-resistant Enterococcus spp. in aquacultures of rainbow trout (Oncorhyncus mykiss), Portugal

The role of European fish farms in the spread of antimicrobial-resistance in the environment and food chain, as well as possible sources of their contamination by clinically relevant antimicrobial-resistance bacteria is scarcely known. This study aimed to assess the contribution of Portuguese rural trout farms on dispersion of Enterococcus with antimicrobial-resistance and putative virulence genes in the environment and food chain, as well as to identify farms contamination sources. We also assessed the presence of Enterococcus with low-levels of antimicrobial-resistance using epidemiological cut-offs (ECOFFs). Enterococcus spp. (n=391) from water/sediment recovered upstream, within and downstream trout tanks, feed, trout (2 aquacultures; no antibiotic use) and marketed trout (8 supermarkets) showed variable resistance to tetracycline, erythromycin, ciprofloxacin, chloramphenicol, quinupristin-dalfopristin, nitrofurantoin or aminoglycosides. Antimicrobial-resistance rates were similar among upstream, within and downstream trout tank samples (P>0.05), positioning water-supplying aquacultures as a source of multidrug-resistant (MDR) strains. Nevertheless, predominance of MDR E. faecium in feed, trout tanks and trout comparing to upstream samples, suggests feed as an additional aquaculture contamination source. The observation of E. faecium and E. faecalis susceptible to ampicillin and gentamicin by clinical breakpoints but with low-levels of resistance to those antimicrobials by ECOFFs breakpoints is of concern, as they might evolve throughout secondary genetic events to resistance levels with human clinical impact. Multiple MDR clones carrying copper tolerance (tcrB/cueO), putative virulence or other genes often associated with clinical strains (e.g. E. faecium with IS16/ptsD/sgrA) were observed, some in distinct samples (e.g. upstream and within trout tanks). They included major human and animal Enterococcus lineages, suggesting human and non-aquatic animal origins. The results highlight the need to define the maximum acceptance level of antimicrobial-resistance genes/bacteria to assess water quality and to monitor antimicrobial-resistance strains on feed, essential requirements to maintain a sustainable aquaculture production.