High prevalence of tetracycline resistance in Enterococcus isolates from broilers carrying the erm(B) gene

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

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

The Genetic Landscape of Antimicrobial Resistance Genes in Enterococcus cecorum Broiler Isolates

Enterococcus cecorum is associated with bacterial chondronecrosis with osteomyelitis (BCO) in broilers. Prophylactic treatment with antimicrobials is common in the poultry industry, and, in the case of outbreaks, antimicrobial treatment is needed. In this study, the minimum inhibitory concentrations (MICs) and epidemiological cutoff (ECOFF) values (COWT) for ten antimicrobials were determined in a collection of E. cecorum strains. Whole-genome sequencing data were analyzed for a selection of these E. cecorum strains to identify resistance determinants involved in the observed phenotypes. Wild-type and non-wild-type isolates were observed for the investigated antimicrobial agents. Several antimicrobial resistance genes (ARGs) were detected in the isolates, linking phenotypes with genotypes for the resistance to vancomycin, tetracycline, lincomycin, spectinomycin, and tylosin. These detected resistance genes were located on mobile genetic elements (MGEs). Point mutations were found in isolates with a non-wild-type phenotype for enrofloxacin and ampicillin/ceftiofur. Isolates showing non-wild-type phenotypes for enrofloxacin had point mutations within the GyrA, GyrB, and ParC proteins, while five amino acid changes in penicillin-binding proteins (PBP2x superfamily) were observed in non-wild-type phenotypes for the tested β-lactam antimicrobials. This study is one of the first that describes the genetic landscape of ARGs within MGEs in E. cecorum, in association with phenotypical resistance determination.

Multidrug-resistant Enterococcus faecium strains enter the Norwegian marine environment through treated sewage

This study aimed to understand the antibiotic resistance prevalence among Enterococcus spp. from raw and treated sewage in Bergen city, Norway. In total, 517 Enterococcus spp. isolates were obtained from raw and treated sewage from five sewage treatment plants (STPs) over three sampling occasions, with Enterococcus faecium as the most prevalent (n = 492) species. E. faecium strains (n = 307) obtained from the influent samples, showed the highest resistance against quinupristin/dalfopristin (67.8%). We observed reduced susceptibility to erythromycin (30.6%) and tetracycline (6.2%) in these strains. E. faecium strains (n = 185) obtained from the effluent samples showed highest resistance against quinupristin/dalfopristin (68.1%) and reduced susceptibility to erythromycin (24.9%) and tetracycline (8.6%). We did not detect resistance against last-resort antibiotics, such as linezolid, vancomycin, and tigecycline in any of the strains. Multidrug-resistant (MDR) E. faecium strains were detected in both influent (2.3%) and effluent (2.2%) samples. Whole genome sequencing of the Enterococcus spp. strains (n = 25) showed the presence of several antibiotic resistance genes, conferring resistance against aminoglycosides, tetracyclines, and macrolides, as well as several virulence genes and plasmid replicons. Two sequenced MDR strains from the effluents belonged to the hospital-associated clonal complex 17 and carried multiple virulence genes. Our study demonstrates that clinically relevant MDR Enterococcus spp. strains are entering the marine environment through treated sewage.

Genetic characterization of MDR genomic elements carrying two aac(6')-aph(2″) genes in feline-derived clinical Enterococcus faecalis isolate

Multidrug-resistant Enterococcus faecalis (E. faecalis) often cause intestinal infections in cats. The aim of this study was to investigate a multidrug-resistant E. faecalis isolate for plasmidic and chromosomal antimicrobial resistance and their genetic environment. E. faecalis strain ESC1 was obtained from the feces of a cat. Antimicrobial susceptibility testing was carried out using the broth microdilution method. Conjugation experiments were performed using Escherichia coli and Staphylococcus aureus as receptors. Complete sequences of chromosomal DNA and plasmids were generated by whole genome sequencing (WGS) and bioinformatics analysis for the presence of drug resistance genes and mobile elements. Multidrug-resistant E. faecalis ESC1 contained a chromosome and three plasmids. The amino acid at position 80 of the parC gene on the chromosome was mutated from serine to isoleucine, and hence the amino acid mutation at this site led to the resistance of ESC1 strain to fluoroquinolones. Eleven antibiotic resistance genes were located on two plasmids. We identified a novel composite transposon carrying two aminoglycoside resistance genes aac(6')-aph(2″). This study reported the coexistence of a novel 5.4 kb composite transposon and a resistance plasmid with multiple homologous recombination in an isolate of E. faecalis ESC1. This data provides a basis for understanding the genomic signature and antimicrobial resistance mechanisms of this pathogen.

Comparative Metagenomic and Metatranscriptomic Analyses Reveal the Response of Black Soldier Fly (Hermetia illucens) Larvae Intestinal Microbes and Reduction Mechanisms to High Concentrations of Tetracycline

Black soldier fly (Hermetia illucens L) larvae (BSFL) possess remarkable antibiotic degradation abilities due to their robust intestinal microbiota. However, the response mechanism of BSFL intestinal microbes to the high concentration of antibiotic stress remains unclear. In this study, we investigated the shift in BSFL gut microbiome and the functional genes that respond to 1250 mg/kg of tetracycline via metagenomic and metatranscriptomic analysis, respectively. The bio-physiological phenotypes showed that the survival rate of BSFL was not affected by tetracycline, while the biomass and substrate consumption of BSFL was slightly reduced. Natural BSFL achieved a 20% higher tetracycline degradation rate than the germ-free BSFL after 8 days of rearing. Metagenomic and metatranscriptomic sequencing results revealed the differences between the entire and active microbiome. Metatranscriptomic analysis indicated that Enterococcus, Vagococcus, Providencia, and Paenalcaligenes were the active genera that responded to tetracycline. Furthermore, based on the active functional genes that responded to tetracycline pressure, the response mechanisms of BSFL intestinal microbes were speculated as follows: the Tet family that mediates the expression of efflux pumps expel tetracycline out of the microbes, while tetM and tetW release it from the ribosome. Eventually, tetracycline was degraded by deacetylases and novel enzymes. Overall, this study provides novel insights about the active intestinal microbes and their functional genes in insects responding to the high concentration of antibiotics.

Antibiotic Resistance among Gastrointestinal Bacteria in Broilers: A Review Focused on Enterococcus spp. and Escherichia coli

Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. Furthermore, some clonal lineages, such as ST16, ST194, and ST195 in Enterococcus spp. and ST117 in E. coli, have been identified in humans and animals. These data suggest that consuming contaminated animal-source food, direct contact with animals, or environmental exposure can lead to the transmission of antimicrobial-resistant bacteria. Therefore, this review focused on Enterococcus spp. and E. coli from the broiler industry to better understand how antibiotic-resistant strains have emerged, which antibiotic-resistant genes are most common, what clonal lineages are shared between broilers and humans, and their impact through a One Health perspective.

Curcumin Attenuates Damage to Rooster Spermatozoa Exposed to Selected Uropathogens

Artificial insemination, as an essential pillar of the modern poultry industry, primarily depends on the quality of semen collected from stud roosters. Since the collection and storage of ejaculates is not a sterile process, antimicrobial agents have become essential supplements to semen extenders. While the use of traditional antibiotics has been challenged because of rising bacterial resistance, natural biomolecules represent an appealing alternative because of their antibacterial and antioxidant properties. As such, this study strived to compare the effects of 50 μmol/L curcumin (CUR) with 31.2 µg/mL kanamycin (KAN) as a conventional antibiotic on rooster sperm quality in the presence of Salmonella enterica, Escherichia coli and Pseudomonas aeruginosa. Changes in sperm structural integrity and functional activity were monitored at 2 and 24 h of culture. Computer-assisted semen analysis revealed significant sperm motility preservation following treatment with KAN, particularly in the case of Salmonella enterica and Pseudomonas aeruginosa (p < 0.001) after 24 h. On the other hand, CUR was more effective in opposing ROS overproduction by all bacteria (p < 0.05), as determined by luminol-based luminometry, and maintained sperm mitochondrial activity (p < 0.001 in the case of Salmonella enterica; p < 0.05 with respect to Escherichia coli and Pseudomonas aeruginosa), as assessed by the fluorometric JC-1 assay. The TUNEL assay revealed that CUR readily preserved the DNA integrity of rooster sperm exposed to Salmonella enterica (p < 0.01) and Escherichia coli (p < 0.001). The bacteriological analysis showed higher efficiency of KAN in preventing the growth of all selected bacterial species (p < 0.0001) as opposed to CUR. In conclusion, CUR provided protection to rooster spermatozoa against alterations caused by uropathogens, most likely through its antioxidant activity. Hence, CUR supplementation to poultry semen extenders in combination with properly selected antibacterial substances may become an interesting strategy in the management of bacterial contamination during semen storage.

Emergence and Genomic Characterization of the First Reported optrA-Carrying Linezolid-Resistant Enterococci Isolated from Retail Broiler Meat in the United Arab Emirates

The foodborne transfer of resistant genes from enterococci to humans and their tolerance to several commonly used antimicrobials are of growing concern worldwide. Linezolid is a last-line drug for managing complicated illnesses resulting from multidrug-resistant Gram-positive bacteria. The optrA gene has been reported in enterococci as one of the acquired linezolid resistance mechanisms. The present study uses whole-genome sequencing analysis to characterize the first reported isolates of linezolid-resistant E. faecium (n = 6) and E. faecalis (n = 10) harboring the optrA gene isolated from samples of supermarket broiler meat (n = 165) in the United Arab Emirates (UAE). The sequenced genomes were used to appraise the study isolates’ genetic relatedness, antimicrobial resistance determinants, and virulence traits. All 16 isolates carrying the optrA gene demonstrated multidrug-resistance profiles. Genome-based relatedness classified the isolates into five clusters that were independent of the isolate sources. The most frequently known genotype among the isolates was the sequence type ST476 among E. faecalis (50% (5/10)). The study isolates revealed five novel sequence types. Antimicrobial resistance genes (ranging from 5 to 13) were found among all isolates that conferred resistance against 6 to 11 different classes of antimicrobials. Sixteen different virulence genes were found distributed across the optrA-carrying E. faecalis isolates. The virulence genes in E. faecalis included genes encoding invasion, cell adhesion, sex pheromones, aggregation, toxins production, the formation of biofilms, immunity, antiphagocytic activity, proteases, and the production of cytolysin. This study presented the first description and in-depth genomic characterization of the optrA-gene-carrying linezolid-resistant enterococci from retail broiler meat in the UAE and the Middle East. Our results call for further monitoring of the emergence of linezolid resistance at the retail and farm levels. These findings elaborate on the importance of adopting a One Health surveillance approach involving enterococci as a prospective bacterial indicator for antimicrobial resistance spread at the human–food interface.

A comprehensive review on genomics, systems biology and structural biology approaches for combating antimicrobial resistance in ESKAPE pathogens: computational tools and recent advancements

In recent decades, antimicrobial resistance has been augmented as a global concern to public health owing to the global spread of multidrug-resistant strains from different ESKAPE pathogens. This alarming trend and the lack of new antibiotics with novel modes of action in the pipeline necessitate the development of non-antibiotic ways to treat illnesses caused by these isolates. In molecular biology, computational approaches have become crucial tools, particularly in one of the most challenging areas of multidrug resistance. The rapid advancements in bioinformatics have led to a plethora of computational approaches involving genomics, systems biology, and structural biology currently gaining momentum among molecular biologists since they can be useful and provide valuable information on the complex mechanisms of AMR research in ESKAPE pathogens. These computational approaches would be helpful in elucidating the AMR mechanisms, identifying important hub genes/proteins, and their promising targets together with their interactions with important drug targets, which is a crucial step in drug discovery. Therefore, the present review aims to provide holistic information on currently employed bioinformatic tools and their application in the discovery of multifunctional novel therapeutic drugs to combat the current problem of AMR in ESKAPE pathogens. The review also summarizes the recent advancement in the AMR research in ESKAPE pathogens utilizing the in silico approaches.

Enterococcus Virulence and Resistant Traits Associated with Its Permanence in the Hospital Environment

Enterococcus are opportunistic pathogens that have been gaining importance in the clinical setting, especially in terms of hospital-acquired infections. This problem has mainly been associated with the fact that these bacteria are able to present intrinsic and extrinsic resistance to different classes of antibiotics, with a great deal of importance being attributed to vancomycin-resistant enterococci. However, other aspects, such as the expression of different virulence factors including biofilm-forming ability, and its capacity of trading genetic information, makes this bacterial genus more capable of surviving harsh environmental conditions. All these characteristics, associated with some reports of decreased susceptibility to some biocides, all described in this literary review, allow enterococci to present a longer survival ability in the hospital environment, consequently giving them more opportunities to disseminate in these settings and be responsible for difficult-to-treat infections.

Dissemination of Quinupristin-Dalfopristin and Linezolid resistance genes among hospital environmental and healthy volunteer fecal isolates of Enterococcus faecalis and Enterococcus faecium

BACKGROUND

Streptogramins and linezolid are important in the treatment of infections caused by vancomycin-resistant enterococci.

PURPOSE

Then, we aimed to evaluate the resistance rates against these drugs and the prevalence of genes involved in hospital environmental and fecal normal-flora isolates of Enterococcus faecalis and Enterococcus faecium.

METHODS AND RESULTS

The strains were isolated from the stool samples and hospital environments by culturing on M-Enterococcus (ME) agar, and identified by phenotypic and genotypic microbiological tests. The disk agar diffusion method was used to identify the antimicrobial susceptibility pattern of the isolates. The genomic DNA extraction was done by the alkaline lysis method, and the PCR test was used to detect the resistance genes. A total of 145 enterococci isolates were taken, from which 84 (57.9%) isolates were detected as E. faecalis and 61 (42.06%) isolates were E. faecium. Moreover, 70 (83.33), 4 (4.76%), 1 (1.19%), and 40 (47.61%) isolates of E. faecalis and 20 (32.78%), 1 (1.63%), 4 (6.55%), and 26 (42.62%) E. faecium isolates were resistant against quinupristin-dalfopristin, linezolid, vancomycin, and erythromycin, respectively. Also, 112 (77.24%), 50 (34.48%), 39 (26.89%), 27 (18.62%), 19 (13.1%), 4 (2.75%), and 1 (0.68%) isolates were contained LsaA, vatD, vgbB, vatE, cfr, lsaE and optrA genes, respectively. None of the isolates carried the vgbA gene.

CONCLUSIONS

High-level streptogramin resistance rate and high prevalence of resistance genes in enterococci isolated from the stool of healthy persons and the hospital environment indicates the importance of possible transmission of resistance genes from these isolates to clinical ones.

Antimicrobial Resistance, Biofilm Formation, and Virulence Genes in Enterococcus Species from Small Backyard Chicken Flocks

Backyard birds are small flocks that are more common in developing countries. They are used for poultry meat and egg production. However, they are also implicated in the maintenance and transmission of several zoonotic diseases, including multidrug-resistant bacteria. Enterococci are one of the most common zoonotic bacteria. They colonize numerous body sites and cause a wide range of serious nosocomial infections in humans. Therefore, the objective of the present study was to investigate the diversity in Enterococcus spp. in healthy birds and to determine the occurrence of multidrug resistance (MDR), multi-locus sequence types, and virulence genes and biofilm formation. From March 2019 to December 2020, cloacal swabs were collected from 15 healthy backyard broiler flocks. A total of 90 enterococci strains were recovered and classified according to the 16S rRNA sequence into Enterococcus faecalis (50%); Enterococcus faecium (33.33%), Enterococcus hirae (13.33%), and Enterococcus avium (3.33%). The isolates exhibited high resistance to tetracycline (55.6%), erythromycin (31.1%), and ampicillin (30%). However, all of the isolates were susceptible to linezolid. Multidrug resistance (MDR) was identified in 30 (33.3%) isolates. The enterococci AMR-associated genes ermB, ermA, tetM, tetL, vanA, cat, and pbp5 were identified in 24 (26.6%), 11 (12.2%), 39 (43.3%), 34 (37.7%), 1 (1.1%), 4 (4.4%), and 23 (25.5%) isolates, respectively. Of the 90 enterococci, 21 (23.3%), 27 (30%), and 36 (40%) isolates showed the presence of cylA, gelE, and agg virulence-associated genes, respectively. Seventy-three (81.1%) isolates exhibited biofilm formation. A statistically significant correlation was obtained for biofilm formation versus the MAR index and MDR. Multi-locus sequence typing (MLST) identified eleven and eight different STs for E. faecalis and E. faecium, respectively. Seven different rep-family plasmid genes (rep1–2, rep3, rep5–6, rep9, and rep11) were detected in the MDR enterococci. Two-thirds (20/30; 66.6%) of the enterococci were positive for one or two rep-families. In conclusion, the results show that healthy backyard chickens could act as a reservoir for MDR and virulent Enterococcus spp. Thus, an effective antimicrobial stewardship program and further studies using a One Health approach are required to investigate the role of backyard chickens as vectors for AMR transmission to humans.

Microbiological quality analysis of inoculants based on Bradyrhizobium spp. and Azospirillum brasilense produced "on farm" reveals high contamination with non-target microorganisms

The use of inoculants carrying diazotrophic and other plant growth-promoting bacteria plays an essential role in the Brazilian agriculture, with a growing use of microorganism-based bioproducts. However, in the last few years, some farmers have multiplied microorganisms in the farm, known as "on farm" production, including inoculants of Bradyrhizobium spp. for soybean (Glycine max L. Merrill.) and Azospirillum brasilense for corn (Zea mays L.) or co-inoculation in soybean. The objective was to assess the microbiological quality of such inoculants concerning the target microorganisms and contaminants. In the laboratory, 18 samples taken in five states were serial diluted and spread on culture media for obtaining pure and morphologically distinct colonies of bacteria, totaling 85 isolates. Molecular analysis based on partial sequencing of the 16S rRNA gene revealed 25 genera of which 44% harbor species potentially pathogenic to humans; only one of the isolates was identified as Azospirillum brasilense, whereas no isolate was identified as Bradyrhizobium. Among 34 isolates belonging to genera harboring species potentially pathogenic to humans, 12 had no resistance to antibiotics, six presented intrinsic resistance, and 18 presented non-intrinsic resistance to at least one antibiotic. One of the samples analyzed with a shotgun-based metagenomics approach to check for the microbial diversity showed several genera of microorganisms, mainly Acetobacter (~ 32% of sequences) but not the target microorganism. The samples of inoculants produced on farm were highly contaminated with non-target microorganisms, some of them carrying multiple resistances to antibiotics.

Antimicrobial resistance and genetic diversity of Enterococcus faecalis from yolk sac infections in broiler chicks

Despite restrictions on the use of antibiotics in poultry, the percentage of multidrug resistant bacteria, isolated from both adult birds and chicks, remains high. These bacteria can spread between countries via hatching eggs or chicks. Antibiotic resistant bacteria can also pose a threat to hatchery and farm workers or to consumers of poultry. The aim of the study was to perform a phenotypic and genotypic analysis of the drug resistance of E. faecalis isolates from yolk sac infections in broiler chicks from Poland and the Netherlands and to determine their genetic diversity. The tests revealed resistance to antibiotics from category D, that is, tetracycline (69.7%); category C – lincomycin (98.7%), erythromycin (51.3%), aminoglycosides (high-level streptomycin and kanamycin resistance – 10.5% and 3.95%, respectively), and chloramphenicol (7.9%); and category B – ciprofloxacin (25% with resistance or intermediate resistance). No resistance to penicillin, ampicillin, high-level gentamicin, tigecycline, or linezolid was noted. Various combinations of the erm(B), tet(M), tet(L), tet(O), ant(6)-Ia, aph(3′)-IIIa, ant(4′)-Ia, cat, and msr(A/B) genes were detected in all isolates (irrespective of the drug-resistance phenotype). Among isolates that carried the tet(M) and/or the tet(L) gene, 28% also had the Int-Tn gene, in contrast with isolates possessing tet(O). There were 28 sequence types and 43 PFGE restriction patterns. About 60% of isolates were of sequences types ST59, ST16, ST116, ST282, ST36, and ST82. Nine new sequence types were shown (ST836-ST844). In conclusion, broiler chicks can be a source of drug-resistant sequence types of E. faecalis that are potentially hazardous for people and animals. Restrictive programs for antibiotic use in broiler breeding flocks should be developed to decrease drug resistance in day-old chicks and reduce economic losses during rearing.

Effects of dicopper oxide and copper sulfate on growth performance and gut microbiota in broilers

An experiment was conducted to determine the effects of two sources of copper (Cu) from copper sulfate (CuSO4) and dicopper oxide (Cu2O, CoRouge) at three levels of inclusion (15, 75, and 150 mg/kg) on growth performance and gut microbiota of broilers. A total of 840 one-d-old male chickens (Ross 308) were weighed and randomly allocated to seven dietary treatments: negative control (NC, a basal diet without Cu addition), and the NC supplemented with 15, 75, or 150 mg Cu/kg from CuSO4 or Cu2O (12 replicate pens/treatment, 10 chicks per pen). Broilers were challenged by reusing an old litter with high concentrations in Clostridium perfringens to promote necrotic enteritis. Broiler performance was registered at d 21, 35, and 42. Excreta samples were collected at d 14, 28, and 42 for antimicrobial resistance (AMR) analyses. At d 43, one broiler per pen was euthanized to obtain ileal content for microbial characterization. Body weight d 35 and daily gain d 42 improved (P < 0.05) in Cu2O as Cu dose inclusion increased from 15 mg/kg to 150 mg/kg. Supplementation of 150 mg/kg of Cu from Cu2O decreased the abundance (P < 0.01) of some families such as Streptococcaceae and Corynebacteriaceae and increased the abundance (P < 0.05) of some commensal bacteria like Clostridiaceae and Peptostreptococcaceae. Phenotypic AMR was not different among treatments on d 14 and 28. Isolated Enterococcus spp. from broilers fed the NC diet on d 42 showed higher (P < 0.05) resistance to enrofloxacin, gentamicin, and chloramphenicol compared with Cu treatments. By contrast, the isolated Escherichia coli from broilers fed 150 mg/kg of Cu, either from CuSO4 or Cu2O, showed higher (P < 0.05) resistance to streptomycin and chloramphenicol compared to the NC. This study suggests that supplementing 150 mg/kg of Cu from Cu2O establishes changes in the gut microbiota by regulating the bacterial population in the ileum, which may explain the positive impact on broilers' growth performance.

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.

Impact of application of heat-activated persulfate oxidation treated erythromycin fermentation residue as a soil amendment: Soil chemical properties and antibiotic resistance

Erythromycin fermentation residue (EFR) is the precipitation of fermentative biowaste used for extracting erythromycin (ERY) and may be disposed via land application after heat-activated persulfate (PS) oxidation treatment. However, the effects of the treated EFR as a soil amendment on soil chemical properties and the potential resistance risks caused by introduced ERY remain unclear. Here, a laboratory soil incubation experiment was performed to investigate the soil pH, salinity, introduced antibiotics, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), as well as bacterial community structure in the treated EFR-amended soil. The results indicated that pH in treated EFR-amended soil decreased firstly and then increased. The salinity of soil increased but soil was still non-saline soil. In addition, the introduced ERY in the treated EFR-amended soil decreased with the half-life of 12.3 d. Moreover, the relative abundances of ERY resistance genes and MGEs in the treated EFR-amended soil were much lower than those in the control at the end of incubation. Bacterial community structure in the treated EFR-amended soil converged to similar structure in control soil after 49 d incubation. Our results showed that heat-activated PS oxidation treatment of EFR prior to application to soil might be in favor of limiting the spread of ERY resistance genes and MGEs.

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.

A critical review of antibiotic resistance in probiotic bacteria

Probiotics are defined as live microorganisms that, when administered in adequate amounts, confer a health benefit upon the host. At present, probiotics are gaining popularity worldwide and are widely used in food and medicine. Consumption of probiotics is increasing with further in-depth research on the relationship between intestinal flora and host health. Most people pay more attention to the function of probiotics but ignore their potential risks, such as infection and antibiotic resistance transfer to pathogenic microbes. Physiological functions, effects and mechanisms of action of probiotics were covered in this review, as well as the antibiotic resistance phenotypes, mechanisms and genes found in probiotics. Typical cases of antibiotic resistance of probiotics were also highlighted, as well as the potential risks (including pathogenicity, infectivity and excessive immune response) and corresponding strategies (dosage, formulation, and administration route). This timely study provides an avenue for further research, development and application of probiotics.

Characteristics of methicillin-resistant Staphylococcus aureus from broiler farms in Germany are rather lineage- than source-specific

Methicillin-resistant Staphylococcus aureus (MRSA) are a major concern for public health, and broiler farms are a potential source of MRSA isolates. In this study, a total of 56 MRSA isolates from 15 broiler farms from 4 different counties in Germany were characterised phenotypically and genotypically. Spa types, dru types, SCCmec types, and virulence genes as well as resistance genes were determined by using a DNA microarray or specific PCR assays. In addition, PFGE profiles of isolates were used for analysis of their epidemiological relatedness. While half of the isolates belonged to spa type t011, the other half was of spa types t1430 and t034. On 3 farms, more than 1 spa type was found. The most common dru type was dt10a (n = 19), followed by dt11a (n = 17). Susceptibility testing of all isolates by broth microdilution revealed 21 different resistance phenotypes and a wide range of resistance genes was present among the isolates. Up to 10 different resistance phenotypes were found on individual farms. Resistance to tetracyclines (n = 53), MLS_B antibiotics (n = 49), trimethoprim (n = 38), and elevated MICs of tiamulin (n = 29) were most commonly observed. Microarray analysis detected genes for leucocidin (lukF/S), haemolysin gamma (hlgA), and other haemolysines in all isolates. In all t1430 isolates, the egc cluster comprising of genes encoding enterotoxin G, I, M, N, O, U, and/or Y was found. The splitstree analysis based on microarray and PCR gene profiles revealed that all CC9/SCCmec IV/t1430/dt10a isolates clustered apart from the other isolates. These findings confirm that genotypic patterns were specific for clonal lineages rather than for the origin of isolates from individual farms.

Antimicrobial resistance monitoring of commensal Enterococcus faecalis in broiler breeders

Enterococcus faecalis (E. faecalis) has rapidly acquired resistance to multiple antimicrobials, and the antimicrobial resistance of E. faecalis from broiler breeders has been implicated in its vertical transmission to their offspring. The objective of this study was to investigate the antimicrobial resistance and genetic diversity of commensal E. faecalis isolated from the broiler breeder farms. Among a total of 229 E. faecalis isolates from 9 broiler breeder farms, the highest resistance rate was observed in tetracycline (78.2%), followed by doxycycline (58.1%) and erythromycin (43.7%), and the prevalence of antimicrobial resistance showed significant differences among the 9 broiler breeder farms (P < 0.05). The tetM gene (77.1%) and ermB gene (85.0%) were detected at the highest levels in 179 TE-and 100 E-resistant isolates, respectively. Twenty-four high-level gentamicin-resistant isolates carried aac(6″)Ie-aph(2″)-la gene, and 9 high-level ciprofloxacin-resistant isolates showed point mutations in both gyrA and parC genes. All high-level gentamicin-resistant or high-level ciprofloxacin-resistant isolates showed one of the two different virulence gene patterns, ace-asa1-efaA-gelE complex or ace-efaA-gelE complex. These results indicate that constant epidemiological monitoring at the breeder level is required to prevent the pyramidal transmission of antimicrobial-resistant E. faecalis.

Impact of added copper, alone or in combination with chlortetracycline, on growth performance and antimicrobial resistance of fecal enterococci of weaned piglets

Studies suggest a link between added copper (Cu) and co-selection of antimicrobial resistance (AMR) in Enterococcus spp., but data are inconsistent. This study aimed to assess the impact of added Cu, alone or with a feed-grade antimicrobial, on growth performance, transferable Cu resistance gene (tcrB) prevalence, abundance of tcrB in fecal community DNA, and AMR in fecal enterococci in weaned piglets. A total of 320 barrows (DNA 200 × 400, DNA Genetics) weaned at approximately 21 d of age with 7.4 kg (7.4 ± 0.06 kg) BW were used in a 28-d study. Piglets were fed a common non-medicated diet for 7 d of acclimation. Treatments were arranged in a 2 × 2 factorial design with main effects of added Cu (0 vs. 200 mg/kg Cu from Cu sulfate) and chlortetracycline (0 vs. 440 mg/kg CTC). Growth performance and fecal samples were obtained on days 0, 14, and 28. There was no evidence (P > 0.05) for Cu and CTC interaction in growth performance. Pigs fed diets with added Cu had increased (P < 0.05) ADG and ADFI from days 0 to 14, with no evidence for differences (P > 0.05) from days 15 to 28 and 0 to 28. Pigs fed diets with CTC had improved (P < 0.01) ADG, ADFI, and G:F from days 0 to 28. Prevalence of tcrB-positive enterococci was not affected by the addition of Cu and/or CTC (P > 0.05). Prevalence of tcrB-positive enterococci was higher on day 14 than other sampling days (P = 0.002). Prevalence of tetracycline resistance gene [tet(M)]-positive enterococci was not affected by treatments or day (P > 0.05). Prevalence of macrolide resistance gene [erm(B)]-positive enterococci had a significant treatment and sampling day interaction (P = 0.021). The abundance of the tcrB gene in feces, quantified by PCR, was not affected by Cu treatment. The median Cu minimum inhibitory concentrations (MIC) of tcrB-negative and -positive isolates were 3 and 20 mM, respectively (P < 0.001). For day 0 and day 28, all Enterococcus isolates were susceptible to gentamicin, kanamycin, streptomycin, daptomycin, and tigecycline, with a majority of isolates resistant to chloramphenicol, erythromycin, lincomycin, linezolid, tetracycline, tylosin tartrate, and Synercid. In conclusion, 200 mg/kg added Cu or 440 mg/kg CTC in nursery diets improved growth performance of nursery pigs. Added Cu, with or without a selection pressure of CTC, did not increase Cu-resistant enterococci and did not co-select resistance to antibiotics.

Genetic characterization of high-level aminoglycoside-resistant Enterococcus faecalis and Enterococcus faecium isolated from retail chicken meat

Retail chicken meat can play a role in the transfer of drug resistance to humans through the handling or ingestion of improperly cooked meat contaminated with resistant enterococci. In fact, high-level aminoglycoside-resistance (HLAR) in enterococci identified in human cases. Therefore, the prevalence and genetic characterization of HLAR in enterococci in retail chicken meat were investigated in this study. Of the 345 enterococci strains, 29 (8.7%) showed HLAR. All HLAR in enterococci carried at least 1 of 2 aminoglycoside-modifying enzyme genes, aac(6')Ie-aph(2″)-Ia and ant(6)-Ia. Among the 13 isolates that carried aac(6')Ie-aph(2″)-Ia, 3 had pattern A, with IS256 at both ends, and the other 10 had pattern D, without IS256 at both ends. All HLAR in enterococci also showed multidrug resistance. Among the 24 erythromycin-resistant enterococci, 19 (79.2%) harbored the ermB gene, and one (4.2%) harbored both the ermB and ermA genes. A total of 21 enterococci were tetracycline-resistant and harbored one or more of the following tetracycline resistance genes tet(M), tet(L), and tet(O). The Int-Tn gene was detected in one isolate (3.4%) carrying the tet(M) and ermB genes. All 4 chloramphenicol-resistant isolates carried either the phenicol resistance gene cfr alone (one isolate), both cfr and fexA (one isolate), or both fexA and optrA (2 isolates). Four efflux pump genes, efr(A), efr(B), emeA, and lsa, were detected in all HLAR in Enterococcus faecalis isolates. These results improve our understanding of the transmission dynamics of HLAR in enterococci from non-hospital sources to humans.

Vancomycin and florfenicol resistant Enterococcus faecalis and Enterococcus faecium isolated from human urine in an Egyptian urban-rural community

Multidrug resistance is one of the top three threats to global public health. Understanding resistance of bacteria is important to help decrease resistance and improve the development of novel antimicrobial agents or other alternative tools to combat public health challenges. Thus, the goal of this study was to investigate the vancomycin and florfenicol resistance genes of five E. faecalis and 15 E. faecium isolated from patients with urinary tract infections. There were 20 Enterococcus obtained from the library collection of randomly selected private hospitals located in the city of El Qanater El Khayreya; these samples were isolated during 2017. Samples were evaluated for their phenotypic characterization of virulence factors, antimicrobial resistance and PCR was conducted to detect the prescence of the vancomycin vanABC and florfenicol resistance genes encoding the catAB, fexAB and cfu. There were six different antibiotic resistance profiles observed. The 20 isolates showed resistance to clindamycin, oxytetracycline and gentamycin. Resistance was evident to ciprofloxacin, norfloxacin and florfenicol in the absence of the cfr gene in all of the 20 Enterococcus isolates. In addition, all isolates produced biofilms and were classified as extensive drug resistant. MAR_indices of the isolates were >0.6. The MAR_index of human isolates of enterococci suggest these pathogens originate from a high-risk source of contamination where antibiotics are often used. This information highlights a possible public health concern to the Egyptian community. The results also suggest the emergence of a linezolid sensitive-vancomycin resistant E. faecium and E. faecalis in the absence of the cfr gene.

Occurrence of antibiotics and their associations with antibiotic resistance genes and bacterial communities in Guangdong coastal areas

The concentration of 8 antibiotics and 21 antibiotic resistance genes were investigated in the coastal areas of Guangdong, China. Total concentrations of antibiotics ranged from 0.43 ng/L to 1040.31 ng/L. The concentrations of tetracyclines were much higher than that of sulfonamides in most sampling sites. The abundance of target antibiotic resistance genes ranged from 1.82 × 10⁵ to 5.9 × 10⁹ copies/mL and tetM accounted for the highest percentages of detected antibiotic resistance genes in most sampling sites. Furthermore, the dominant phyla in water samples were Proteobacteria, Bacteroidetes and Actinobacteria. The relationship between antibiotics, antibiotic resistance genes, and bacterial communities was also investigated. As a result, the abundance of sul1 was positively correlated with the concentration of sulfadiazine, sulfamethoxazole and sulfonamide p-methyl oxypyrimidine. Besides, sulfonamide p-methyl oxypyrimidine, sulfadiazine and p-aminobenzenesulfonamide were significantly correlated with the bacterial communities. These findings suggested that the residues of antibiotics in coastal areas of Guangdong affect the distribution of antibiotic resistance genes and alter the microbial communities.

Hysterical tetracycline in intensive poultry farms accountable for substantial gene resistance, health and ecological risk in Egypt- manure and fish

Although the poultry production sector plays a key role in sustaining the majority of animal protein demand in Egypt, the deleterious effects of widespread antibiotic resistance on health and environment are currently not well recognized. Litter and dropping samples from broiler and layer poultry farms as well as, tilapia samples from the Nile River and aquaculture farms were collected from Upper Egypt. Samples were extracted and examined for tetracycline residues [tetracycline (TC), chlortetracycline (CTC), oxytetracycline (OTC) and doxycycline (DC)] using HPLC. In addition, tetracycline resistance genes [tet (M), tet (W), tet (Q) and tet (G)] were screened from pooled intestinal contents collected from twelve broiler farms in Upper Egypt. The antibiotic resistance genes results revealed that tet (W) was confirmed to be expressed in all intestinal samples. In contrast, tet (Q) and tet (M) were detected only in 42% and 17% of the samples, respectively. CTC and OTC were the antimicrobial compounds with the highest concentrations in poultry litter and droppings, with concentrations of 6.05 and 2.47 μg g^-1 (CTC) and 5.9 and 1.33 μg g^-1 (OTC), respectively. However, the concentrations of DC were significantly higher than those of the other compounds in both aquaculture and Nile River tilapia. The tetracycline residue levels in aquaculture tilapia were significantly higher than those in Nile River tilapia. The hazard quotients (HQs) exceeded 1 for OTC, CTC and DC, which highlights the great risk of using broiler litter to fertilize agricultural land. Moreover, the presence of DC and CTC indicates that consumption of aquaculture tilapia poses a considerable health risk. Therefore, poultry litter or droppings containing tetracycline residues and tet resistance determinants used for aquaculture or as farmland fertilizers could be major sources of antibiotic resistance in fish, humans and environment.

Molecular epidemiology of antibiotic-resistant Enterococcus spp. from the farm-to-fork continuum in intensive poultry production in KwaZulu-Natal, South Africa

The poultry industry is among the main protein suppliers worldwide. Thus, this study determined the antibiotic resistance and virulence profiles of Enterococcus spp. along the farm-to-fork production chain of an intensive poultry system in the uMgungundlovu District, Kwazulu-Natal, South Africa. Overall, 162 samples along the continuum (growth phase, transport and post-slaughter) were evaluated for the presence of Enterococcus spp. using selective media, biochemical tests and polymerase chain reaction (PCR). Resistance profiles were assessed by Kirby-Bauer disk diffusion method following the WHO-AGISAR recommended antibiotics panel for Enterococcus spp. Antibiotic resistance and virulence genes were detected using real-time PCR. Clonal relatedness was evaluated by REP-PCR. Overall, 131 isolates were recovered across the continuum, (34% E. faecalis, 32% E. faecium, 2% E. gallinarum and 32% other Enterococcus spp.). Resistance to tetracycline (79%), erythromycin (70%), nitrofurantoin (18%), ampicillin (15%), streptomycin (15%), chloramphenicol (10%), ciprofloxacin (4%), tigecycline (4%), gentamicin (4%), teicoplanin (3%) was observed among all Enterococcus spp.; no vancomycin resistance (0%) was recorded. Also, 24% of E. faecium were resistant to quinupristin-dalfopristin. Twenty-four multidrug resistance (MDR) antibiograms were observed across all species; E. faecium (43%) showed the highest frequency of MDR. The most frequently observed antibiotic resistomes were tetM (76%) and ermB (66%) while smaller percentages were noted for aph(3')-IIIa (12%) and vanC1 (1%). Virulence genes efaAFs (100%), cpd (96%) and gelE (80%) were more prevalent in E. faecalis. Clonality revealed that isolates along the continuum were highly diverse with major REP-types consisting of isolates from the same sampling point. This study highlights the diversity of MDR Enterococcus in the food chain with isolates harbouring resistance and virulence genes. These could be reservoirs for the potential transfer of pathogenic enterococci carrying these genes from poultry to humans through the food chain continuum, thus, underscoring the need for routine antibiotic resistance surveillance in food animals.

Clonal Structure and Antibiotic Resistance of Enterococcus spp. from Wild Birds in Poland

The purpose of this study was to analyze the antibiotic resistance and genetic diversity of 27 enterococci (Enterococcus faecium, Enterococcus hirae, Enterococcus durans, and Enterococcus casseliflavus) isolated from wild bird species. Resistance to lincomycin was most common, followed by erythromycin, ciprofloxacin, tetracyclines, high level of aminoglycoside, and β-lactam antibiotics. No vancomycin- and chloramphenicol-resistant isolates were identified. The antibiotic resistance was linked to the tet(M), tet(L), erm(A), erm(B), msr(A/B), pbp5, ant(6)-Ia, and aph(3')-IIIa genes. Tn916/Tn1545-like transposons were detected. The high-level resistance to gentamicin was associated with the presence of gene aph(2″)-Id. All 18 E. faecium isolates were divided into 16 pulsotypes and 17 sequence types (STs), among which 7 STs were newly assigned (ST1266-ST1272). A majority of E. faecium isolates possess multilocus sequence typing profiles belonging to clonal complex 17 (CC17), the major epidemic lineage responsible for nosocomial infections. Two ST17 and newly described ST1267 and ST1271 (an SLV and DLV of ST17, respectively) of E. faecium isolates carried the type 1 allele of the housekeeping gene purK detected in hospital-related strains. Our results indicated that wild birds could be a source of resistant E. faecium isolates, belonging to CC17 and may represent a hazard to human health by transmission of these isolates.

Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance

Use of antibiotics in human and animal medicine has applied selective pressure for the global dissemination of antibiotic-resistant bacteria. Therefore, it is of interest to develop strategies to mitigate the continued amplification and transmission of resistance genes in environmental reservoirs such as farms, hospitals and watersheds. However, the efficacy of mitigation strategies is difficult to evaluate because it is unclear which resistance genes are important to monitor, and which primers to use to detect those genes. Here, we evaluated the diversity of one type of macrolide antibiotic resistance gene (erm) in one type of environment (manure) to determine which primers would be most informative to use in a mitigation study of that environment. We analyzed all known erm genes and assessed the ability of previously published erm primers to detect the diversity. The results showed that all known erm resistance genes group into 66 clusters, and 25 of these clusters (40%) can be targeted with primers found in the literature. These primers can target 74%–85% of the erm gene diversity in the manures analyzed.

IS26-Flanked Composite Transposon Tn6539 Carrying the tet(M) Gene in IncHI2-Type Conjugative Plasmids From Escherichia coli Isolated From Ducks in China

Tet(M)-type proteins confer resistance to tetracycline and related antibiotics by interacting with the ribosome. Genes encoding Tet(M) have been found in a range of bacteria, including Escherichia coli. In the current study, conjugation experiments were performed between seven different tetracycline-resistant, azide-susceptible E. coli strains isolated from ducks and tetracycline-sensitive, azide-resistant E.coli J53. Transconjugants were obtained from two of the strains at a frequency of 1.2 × 10^-8. PCR, southern blotting and sequencing demonstrated that tet(M) in the transconjugants was located on a ~50 kb IncHI2-type plasmid and was part of a composite transposon, designated Tn6539. This transposon is flanked by two IS26 elements in opposite orientation and contains the Tn3ΔtnpA+Δorf13-lp-tet(M)+gamma delta+tnpX+ΔtnpR sequences. The Δorf13-lp-tet(M) sequence was a highly conserved genetic fragment in E. coli harboring tet(M) and mainly located in the composite transposons flanked by IS6-family elements. In summary, Tn6539 is a new composite transposon capable of horizontal transfer of tet(M) among E. coli isolates.

Characteristics of High-Level Ciprofloxacin-Resistant Enterococcus faecalis and Enterococcus faecium from Retail Chicken Meat in Korea

Genes encoding ciprofloxacin resistance in enterococci in animals may be transferred to bacteria in the animal gut and to zoonotic bacteria where they could pose a human health hazard. The objective of this study was to characterize antimicrobial resistance in high-level ciprofloxacin-resistant (HLCR) Enterococcus faecalis and Enterococcus faecium isolated from retail chicken meat. A total of 345 enterococci (335 E. faecalis and 10 E. faecium) were isolated from 200 chicken meat samples. Of these, 85 E. faecalis isolates and 1 E. faecium isolate were confirmed as HLCR enterococci. All 86 HLCR enterococci displayed gyrA- parC point mutations consisting of S83I-S80I (94.2%, 81 isolates), S83F-S80I (2.3%, 2 isolates), S83Y-S80I (2.3%, 2 isolates), and S83Y-S80F (1.2%, 1 isolate). Sixty-one (72.9%) of the 86 HLCR enterococci showed multidrug resistance to three to six classes of antimicrobial agents. Multilocus sequence typing revealed that E. faecalis had 17 different sequence types (ST) and E. faecium had 1 different ST, with ST256 observed most often (44 isolates, 51.8%). Although these results cannot exclude the possibility that pathotypes of enterococci isolated from chicken might represent transmission to or from humans, the foodborne HLCR E. faecalis indicated that the food chain is a potential route of enterococcal infection in humans.

WILD BIRDS AS A POTENTIAL SOURCE OF KNOWN AND NOVEL MULTILOCUS SEQUENCE TYPES OF ANTIBIOTIC-RESISTANT ENTEROCOCCUS FAECALIS

We assessed the antibiotic resistance and genetic diversity of 27 Enterococcus faecalis isolates from 25 wild bird species in Poland. Resistance to lincomycin (100%) was most common followed by tetracycline (48%), erythromycin (44%), and ciprofloxacin (22%). High-level resistance to streptomycin and kanamycin was observed in 19% and 15% of isolates, respectively. One isolate (4%) exhibited low-level resistance to penicillin and vancomycin, and all isolates were susceptible to gentamicin and chloramphenicol. Antibiotic resistance was linked to the tet(M), tet(L), erm(A), erm(B), msr(A/B), ant(6)-Ia, and aph(3')-IIIa genes. None of the tested van ( vanA, vanB, vanC1, vanC2/C3, vanD, vanE, vanG) genes were found in the vancomycin-resistant isolate. Based on pulsed-field gel electrophoresis and multilocus sequence typing analysis, the E. faecalis population from wild birds revealed high genetic diversity. All isolates were divided into 22 pulsotypes and 18 sequence types (STs), among which seven STs were newly assigned (ST748-ST753 and ST764). The most-prevalent STs were ST290 and ST374 followed by ST287 and ST34. The coexistence of strains assigned to the same STs in wild birds and in nonwildlife populations strongly indicated that many wild bird species could constitute a source of E. faecalis for infections in humans, pets, and farm animals.

Detection of Antibiotic Resistance and Resistance Genes in Enterococci Isolated from Sucuk, a Traditional Turkish Dry-Fermented Sausage

The aim of this study was to isolate enterococci in Sucuk, a traditional Turkish dry-fermented sausage and to analyze isolates for their biodiversity, antibiotic resistance patterns and the presence of some antibiotic resistance genes. A total of 60 enterococci strains were isolated from 20 sucuk samples manufactured without using a starter culture and they were identified as E. faecium (73.3%), E. faecalis (11.7%), E. hirae (8.3%), E. durans (3.3%), E. mundtii (1.7%) and E. thailandicus (1.7%). Most of the strains were found resistant to rifampin (51.67%) followed by ciprofloxacin (38.33%), nitrofurantoin (33.33%) and erythromycin (21.67%). All strains were found susceptible to ampicillin. Only E. faecium FYE4 and FYE60 strains displayed susceptibility to all antibiotics. Other strains showed different resistance patterns to antibiotics. E. faecalis was found more resistant to antibiotics than other species. Most of the strains (61.7%) displayed resistance from between two and eight antibiotics. The ermB, ermC, gyrA, tetM, tetL and vanA genes were detected in some strains. A lack of correlation between genotypic and phenotypic analysis for some strains was detected. The results of this study indicated that Sucuk manufactured without using a starter culture is a reservoir of multiple antibiotic resistant enterococci. Consequently, Sucuk is a potential reservoir for the transmission of antibiotic resistance genes from animals to humans.

Genetic diversity and antimicrobial resistance profile of Enterococcus faecalis isolated from broilers with vertebral osteomyelitis in Southeast Brazil

Vertebral osteomyelitis (VO) is a worldwide emerging disease that affects broilers. Recently, the isolation of Enterococcus faecalis in cases of the disease has been described. This study aimed at determining the genetic diversity and antimicrobial resistance profile of 12 E. faecalis strains isolated from broilers with VO. Strains were isolated from nine flocks from six farms in a high-density poultry production area in Southeast Brazil and were evaluated using multilocus sequence typing and phylogenetic analysis. Antimicrobial susceptibility tests and PCR were performed to detect antimicrobial resistance genes. E. faecalis isolates belonged to different sequence types (ST), six of which (ST49, ST100, ST116, ST202, ST249, and ST300) have been previously described. Strains ST708 and ST709 were newly identified in this study. Strain ST49 was most frequently isolated (50% of the flocks) from the analysed VO cases. No phylogenetic or phylogeographic relationship was found among the strains. The VO isolated E. faecalis strains showed highest resistance to aminoglycosides, mainly gentamicin (40%), but were highly susceptible to vancomycin (10%). Aminoglycoside resistance genes were detected in seven E. faecalis strains, and AAC6'-APH2″ genes were most frequently detected. The results showed that E. faecalis strains isolated from recently reported VO cases were highly diverse genetically. The diversity of genotypes in circulation in the analysed flocks, without apparent relationship among them, raises questions on aetiopathogenesis of the disease in broilers and evolutionary aspects of E. faecalis.

Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale

Genetic information about Enterococcus hirae is limited, a feature that has compromised our understanding of these clinically challenging bacteria. In this study, comparative analysis was performed of E. hirae R17, a daptomycin‐resistant strain isolated from pork purchased from a retail market in Beijing, China, and three other enterococcal genomes (Enterococcus faecium DO, Enterococcus faecalis V583, and E. hirae ATCC^™9790). Some 1,412 genes were identified that represented the core genome together with an additional 139 genes that were specific to E. hirae R17. The functions of these R17 strain‐specific coding sequences relate to the COGs categories of carbohydrate transport and metabolism and transcription, a finding that suggests the carbohydrate utilization capacity of E. hirae R17 may be more extensive when compared with the other three bacterial species (spp.). Analysis of genomic islands and virulence genes highlighted the potential that horizontal gene transfer played as a contributor of variations in pathogenicity in this isolate. Drug‐resistance gene prediction and antibiotic susceptibility testing indicated E. hirae R17 was resistant to several antimicrobial compounds, including bacitracin, ciprofloxacin, daptomycin, erythromycin, and tetracycline, thereby limiting chemotherapeutic treatment options. Further, tolerance to biocides and metals may confer a phenotype that facilitates the survival and adaptation of this isolate against food preservatives, disinfectants, and antibacterial coatings. The genomic plasticity, mediated by IS elements, transposases, and tandem repeats, identified in the E. hirae R17 genome may support adaptation to new environmental niches, such as those that are found in hospitalized patients. A predicted transmissible plasmid, pRZ1, was found to carry several antimicrobial determinants, along with some predicted pathogenic genes. These data supported the previously determined phenotype confirming that the foodborne E. hirae R17 is a multidrug‐resistant pathogenic bacterium with evident genome plasticity and environmental adaptability.

Antibiotic resistance in lactococci and enterococci: phenotypic and molecular-genetic aspects

Extensive use of antibiotics in medicine, veterinary practice and animal husbandry has promoted the development and dissemination of bacterial drug resistance. The number of resistant pathogens causing common infectious diseases increases rapidly and creates worldwide public health problem. Commensal bacteria, including lactic acid bacteria of genera Enterococcus and Lactococcus colonizing gastrointestinal and urogenital tracts of humans and animals may act as vehicles of antibiotic resistance genes similar to those found in pathogens. Lactococci and enterococci are widely used in manufacturing of fermented products and as probiotics, therefore monitoring and control of transmissible antibiotic resistance determinants in industrial strains of these microorganisms is necessary to approve their Qualified Presumption of Safety status. Understanding the nature and molecular mechanisms of antibiotic resistance in enterococci and lactococci is essential, as intrinsic resistant bacteria pose no threat to environment and human health in contrast to bacteria with resistance acquired through horizontal transfer of resistance genes. The review summarizes current knowledge concerning intrinsic and acquired antibiotic resistance in Lactococcus and Enterococcus genera, and discusses role of enterococci and lactococci in distribution of this feature.

Effect of the selective pressure of sub-lethal level of heavy metals on the fate and distribution of ARGs in the catchment scale

Our previous study demonstrated that high levels of antibiotic resistance genes (ARGs) in the Haihe River were directly attributed to the excessive use of antibiotics in animal agriculture. The antibiotic residues of the Xiangjiang River determined in this study were much lower than those of the Haihe River, but the relative abundance of 16 detected ARGs (sul1, sul2 and sul3, qepA, qnrA, qnrB, qnrD and qnrS, tetA, tetB, tetW, tetM, tetQ and tetO, ermB and ermC), were as high as the Haihe River particularly in the downstream of the Xiangjiang River which is close to the extensive metal mining. The ARGs discharged from the pharmaceutical wastewater treatment plant (PWWTP) are a major source of ARGs in the upstream of the Xiangjiang River. In the downstream, selective stress of heavy metals rather than source release had a significant influence on the distinct distribution pattern of ARGs. Some heavy metals showed a positive correlation with certain ARG subtypes. Additionally, there is a positive correlation between individual ARG subtypes and heavy metal resistance genes, suggesting that heavy metals may co select the ARGs on the same plasmid of antibiotic resistant bacteria. The co-selection mechanism between specific metal and antibiotic resistance was further confirmed by these isolations encoding the resistance genotypes to antibiotics and metals. To our knowledge, this is the first study on the fate and distribution of ARGs under the selective pressure exerted by heavy metals in the catchment scale. These results are beneficial to understand the fate, and to discern the contributors of ARGs from either the source release or the selective pressure by sub-lethal levels of environmental stressors during their transport on a river catchment scale.

Characterization of fecal vancomycin-resistant enterococci with acquired and intrinsic resistance mechanisms in wild animals, Spain

The objectives were to evaluate the presence of vancomycin-resistant enterococci with acquired (VRE-a) and intrinsic (VRE-i) resistance mechanisms in fecal samples from different wild animals, and analyze their phenotypes and genotypes of antimicrobial resistance. A total of 348 cloacal/rectal samples from red-legged partridges (127), white storks (81), red kites (59), and wild boars (81) (June 2014/February 2015) were inoculated in Slanetz-Bartley agar supplemented with vancomycin (4 μg/mL). We investigated the susceptibility to 12 antimicrobials and the presence of 19 antimicrobial resistance and five virulence genes. In addition, we performed multilocus sequence typing, detection of IS16 and studied Tn1546 structure. One VRE-a isolate was identified in one wild boar. This isolate was identified as Enterococcus faecium, harbored vanA gene included into Tn1546 (truncated with IS1542/IS1216), and belonged to the new ST993. This isolate contained the erm(A), erm(B), tet(M), dfrG, and dfrK genes. Neither element IS16 nor the studied virulence genes were detected. Ninety-six VRE-i isolates were identified (89 Enterococcus gallinarum and seven Enterococcus casseliflavus), with the following prevalence: red kites (71.2 %), white storks (46.9 %), red-legged partridges (7.9 %), and wild boars (4.9 %). Most E. gallinarum isolates showed resistance to tetracycline (66.3 %) and/or erythromycin (46.1 %). High-level resistance to aminoglycosides was present among our VRE-i isolates: kanamycin (22.9 %), streptomycin (11.5 %), and gentamicin (9.4 %). In general, VRE-i isolates of red kites showed higher rates of resistance for non-glycopeptide agents than those of other animal species. The dissemination of acquired resistance mechanisms in natural environments could have implications in the global spread of resistance with public health implications.

Phenotypic and genotypic characterization of Enterococcus cecorum strains associated with infections in poultry

Background

From the beginning of the 21^st century Enterococcus cecorum has emerged as a significant health problem for poultry raised under intensive production systems. To obtain new insights into this bacterial species, we investigated 82 clinical isolates originating from different poultry flocks in Poland between 2011 and 2014.

Results

Phenotypically, isolates from clinical cases showed ability to growth at low temperatures (4 °C, 10 °C), and differences in growth at 45 °C (74.4 %). Survival at high temperatures (60 °C, 70 °C) was observed for 15, 30 min. More than half of strains survived at 60 °C even after prolonged incubation (1 h), but none survived after 1 h at 70 °C. Total growth inhibition was observed on agar supplemented with tergitol or potassium tellurite. Relatively high number of isolates gave positive reactions for β-galactosidase (βGAL 80 %), Voges Proskauer test (60 %), less for β-mannosidase (17 %), glycogen and mannitol (12 %). The metabolic fingerprinting for E. cecorum obtained in Biolog system revealed ability to metabolise 22 carbon sources. Only 27/82 strains contained ≥ 1 virulence genes of tested 7, however 2.4 % isolates carried 6. Increased antimicrobial resistance was observed to enrofloxacin (87 %), teicoplanin (85 %), doxycycline (83 %), erythromycin (46 %). Most strains (75/82) showed multidrug resistance. The single isolate was resistant to vancomycin (VRE) and high level gentamicin (HLGR). Linezolid resistance among clinical isolates was not found. PFGE revealed diversity of E. cecorum from cases. It could be assumed that transmission of pathogenic strains between flocks regardless of type of production or geographical region may be possible.

Conclusions

Clinical infections in poultry caused by E. cecorum may indicated on new properties of this bacterial species, previously known as a commensal. Despite many common phenotypic features, differences were found among clinical isolates. Several, widely distributed pathogenic E. cecorum strains seemed to be responsible for infection cases found in different poultry types.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-016-0761-1) contains supplementary material, which is available to authorized users.

Occurrence and distribution of antibiotics, antibiotic resistance genes in the urban rivers in Beijing, China

The occurrence and distribution of sulfonamide and tetracycline, corresponding bacterial resistant rate and resistance genes (ARGs) and two integrase genes were investigated in seven urban rivers in Beijing, China. The total concentration of sulfonamide and tetracycline ranged from 1.3 × 10(1)-1.5 × 10(3) ng/L and 3.9 × 10(1)-5.4 × 10(4) ng/L for water, and 1.0 × 10(0)-2.7 × 10(2) and 3.1 × 10(1)-1.6 × 10(2) ng/g for sediment, respectively. The sul resistant rate was 2-3 times higher than tet resistant rate in both surface water and sediment. The average rate of sul resistance and tet resistance were up to 81.3% and 38.6% in surface water, 89.1% and 69.4% in the sediment, respectively. The sul1, tetA and tetE genes were predominant in term of the absolute abundance. The absolute abundance of ARGs in Wenyu River and Qinghe River, which were close to the direct discharging sites, were 5-50 times higher than those in the other investigated urban rivers, suggesting that the source release played an important role in the distribution of ARGs. The sul1 and sul2 genes had positive correlation (p < 0.05) with sulfonamides, and the tet resistance genes was significantly correlated with tetracyclines (p < 0.05), indicating that some ARGs and antibiotics in the urban rivers had identical sources of pollution. Considering principal component analysis, sampling sites (QH5, QH6, B1, B2, B3 and BX2) intimated that a complex interplay of processes govern fate and transport of ARGs in the junction of rivers. These results are significant to understand the fate, and the contribution of ARGs from the source release. In view of the large-scale investigation of urban rivers system in Beijing, it reflected the bacterial resistance in sewage drainage system. Such investigation highlights the management on controlling the pollutant release which was seemed as a major driving force for the maintenance and propagation of many ARGs during the development of urbanization in the future.

Variability of Bacterial Communities in the Moth Heliothis virescens Indicates Transient Association with the Host

Microbes associated with insects can confer a wide range of ecologically relevant benefits to their hosts. Since insect-associated bacteria often increase the nutritive value of their hosts' diets, the study of bacterial communities is especially interesting in species that are important agricultural pests. We investigated the composition of bacterial communities in the noctuid moth Heliothis virescens and its variability in relation to developmental stage, diet and population (field and laboratory), using bacterial tag-encoded FLX pyrosequencing of 16S rRNA amplicons. In larvae, bacterial communities differed depending on the food plant on which they had been reared, although the within-group variation between biological replicates was high as well. Moreover, larvae originating from a field or laboratory population did not share any OTUs. Interestingly, Enterococcus sp. was found to be the dominant taxon in laboratory-reared larvae, but was completely absent from field larvae, indicating dramatic shifts in microbial community profiles upon cultivation of the moths in the laboratory. Furthermore, microbiota composition varied strongly across developmental stages in individuals of the field population, and we found no evidence for vertical transmission of bacteria from mothers to offspring. Since sample sizes in our study were small due to pooling of samples for sequencing, we cautiously conclude that the high variability in bacterial communities suggests a loose and temporary association of the identified bacteria with H. virescens.

Identification and prevalence of tetracycline resistance in enterococci isolated from poultry in Ilishan, Ogun State, Nigeria

Background:

Tetracycline is one of the most frequently used antibiotics in Nigeria both for human and animal infections because of its cheapness and ready availability. The use of tetracycline in animal husbandry could lead to horizontal transfer of tet genes from poultry to human through the gut microbiota, especially enterococci. Therefore, this study is designed to identify different enterococcal species from poultry feces in selected farms in Ilishan, Ogun State, Nigeria, determine the prevalence of tetracycline resistance/genes and presence of IS256 in enterococcal strains.

Materials and Methods:

Enterococci strains were isolated from 100 fresh chicken fecal samples collected from seven local poultry farms in Ilishan, Ogun State, Nigeria. The strains were identified by partial sequencing of 16S rRNA genes. Antibiotic susceptibility of the isolates to vancomycin, erythromycin, tetracycline, gentamicin, amoxycillin/claulanate, and of loxacin were performed by disc diffusion method. Detection of tet, erm, and van genes and IS256 insertion element were done by polymerase chain reaction amplification.

Results:

Sixty enterococci spp. were identified comprising of Enterococcus faecalis 33 (55%), Enterococcus casseliflavus 21 (35%), and Enterococcus gallinarium 6 (10%). All the isolates were resistant to erythromycin (100%), followed by tetracycline (81.67%), amoxicillin/clavulanic acid (73.33%), ofloxacin (68.33%), vancomycin (65%), and gentamicin (20%). None of the enterococcal spp. harbored the van and erm genes while tet(M) was detected among 23% isolates and is distributed mostly among E. casseliflavus. IS256 elements were detected only in 33% of E. casseliflavus that were also positive for tet(M) gene.

Conclusion:

This study provides evidence that tetracycline resistance gene is present in the studied poultry farms in Ilishan, Ogun State, Nigeria and underscores the need for strict regulation on tetracycline usage in poultry farming in the studied location and consequently Nigeria.

Clinical Approach of High Technology Techniques for Control and Elimination of Endodontic Microbiota

The main goal in endodontic treatment is to eradicate or at least reduce intraradicular microbial population to levels that are more compatible with periapical lesions healing process. Since endodontic infections are polymicrobial in nature, intraradicular survival of endodontic microbiota and their pathogenic properties are influenced by a combination of their virulence factors. The purpose of this article is to review the endodontic microbiota and their respective virulence attributes, as well as perform a literature review of the effects of disinfection procedures in the treatment of endodontic infections to gain best practices. Conventional technique for root canal preparation includes mechanical debridement and application of antimicrobial irrigants. Recently, laser irradiation has been used to enhance the results of root canal treatment through its thermal effect. To reduce thermal side effects, laser activated irrigation (LAI) and photon induced photoacoustic streaming (PIPS) were introduced. Antimicrobial photodynamic therapy (aPDT) by photochemical reaction uses light at a specific wavelength to activate a nontoxic photosensitizer (PS) in the presence of oxygen to produce cytotoxic products. Different PSs are used in dentistry including methylene blue (MB), toluidine blue O (TBO), indocyanine green (ICG) and curcumin. Among different options, ICG could be the best choice due to its peak absorption at wavelength of 808 nm, which coincides with the commercial diode laser devices. Also, this wavelength has more penetration depth compared to other wavelengths used in aPDT.

In Vitro Adsorption and in Vivo Pharmacokinetic Interaction between Doxycycline and Frequently Used Mycotoxin Binders in Broiler Chickens

Mycotoxin binders are readily mixed in feeds to prevent uptake of mycotoxins by the animal. Concerns were raised for nonspecific binding with orally administered veterinary drugs by the European Food Safety Authority in 2010. This paper describes the screening for in vitro adsorption of doxycycline-a broad-spectrum tetracycline antibiotic-to six different binders that were able to bind >75% of the doxycycline. Next, an in vivo pharmacokinetic interaction study of doxycycline with two of the binders, which demonstrated significant in vitro binding, was performed in broiler chickens using an oral bolus model. It was shown that two montmorillonite-based binders were able to lower the area under the plasma concentration-time curve of doxycycline by >60% compared to the control group. These results may indicate a possible risk for reduced efficacy of doxycycline when used concomitantly with montmorillonite-based mycotoxin binders.