Antimicrobial Resistance and Clonal Lineages of Escherichia coli from Food-Producing Animals

Escherichia coli are one of the most important pathogenic bacteria readily found in the livestock and widely studied as an indicator that carries drug-resistant genes between humans, animals, and the environment. The use of antimicrobials in the food chain, particularly in food-producing animals, is recognized as a significant contributor to the development and spread of antimicrobial resistance (AMR) and resistance genes can be transferred from the farm through the food-chain. The objective of this review is to highlight the background of the antimicrobials use in food-producing animals, more specifically, to study clonal lineages and the resistance profiles observed in E. coli, as well as in extended spectrum beta-lactamases (ESBL) producing E. coli, in a set of food-production animals with greater relevance in food consumption, such as pigs, poultry, cattle, fish farming and rabbits. Regarding the prevalence of ESBL-producing E. coli among farm animals, high-to-moderate prevalence was observed, and the highest resistance rates to tetracycline and ampicillin was detected in different farms in all geographic regions. Worldwide pandemic clones and high-risk zoonotic E. coli clones have been identified in most food-producing animals, and some of these clones are already disseminated in different niches, such as the environment and humans. A better understanding of the epidemiology of E. coli and ESBL-producing E. coli in livestock is urgently needed. Animal production is one of the major causes of the antibiotic resistance problem worldwide and a One Health approach is needed.

Probiotics in Rabbit Farming: Growth Performance, Health Status, and Meat Quality

The rabbit's complex microbiota of the gastrointestinal tract (GIT) plays a critical role in feed digestion, in vitamin production, in fermentative activity with production of volatile fatty acids, and stimulation of immune response, as well as in the infection defence against pathogens and countering environmental stresses. To prevent digestive disorders of this fragile ecosystem, rabbit breeders adopt suitable diets supplemented with additives such as probiotics. Probiotics can interact with the host and with the other microflora leading to an increased health status. A review on the effects of probiotics on rabbit growth performance, health status, and meat quality was conducted to reduce the incidence of digestive diseases and enhance productive performance. Some authors observed that the supplementation of probiotics to the diet improved feed conversion ratio and growth and digestion coefficients, while other authors reported a lack of effect on the live performance. Benefits derived from the use of probiotics were observed on the mortality and the morbidity. The studies performed, to evaluate the effects of probiotic supplementation in diets on the immune response, showed variations in the results. Some authors reported no significant effect on haematological parameters, such as total protein, immunoglobulins, and IgG, while others observed a significant increase or decrease of the same parameters. Most of the research reported significant modifications of intestinal morphology and positive effects on the GIT microbiota, supporting the host's natural defences. Regarding the carcass and meat quality, the studies reported only partial and opposing results.

Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 12: Tetracyclines: tetracycline, chlortetracycline, oxytetracycline, and doxycycline

The specific concentrations of tetracycline, chlortetracycline, oxytetracycline and doxycycline in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for these four tetracyclines was estimated. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tetracycline, chlortetracycline, oxytetracycline, whilst for doxycycline no suitable data for the assessment were available. Uncertainties and data gaps associated with the levels reported were addressed. It was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC for these antimicrobials.

Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 9: Polymyxins: colistin

The specific concentrations of colistin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels of colistin in feed that showed to have an effect on growth promotion/increased yield were reported. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials.

Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 8: Pleuromutilins: tiamulin and valnemulin

The specific concentrations of tiamulin and valnemulin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tiamulin, while for valnemulin no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these two antimicrobials.

Characterization of bacteriocinogenic Enterococcus isolates from wild and laboratory rabbits for the selection of autochthonous probiotic strains in Tunisia

AIM

The objective of this study was to characterize lactic acid bacteria (LAB) from rabbits to be used as potential autochthonous probiotic.

METHODS AND RESULTS

Fifteen faecal samples were collected from wild and laboratory rabbits. One hundred and eight isolates were collected and tested for their inhibitory power against eight pathogenic bacteria. Among them, 43 Enterococcus isolates were able to inhibit at least one pathogen. Enterocine genes entA, entB and entP were detected in 14, 17 and 22 isolates, respectively. These isolates were tested for their antibiotic susceptibility and genes encoding virulence factors. Relevant phenotypes of antibiotic resistance were observed especially for ampicillin, vancomycin and linezolid. The following virulence genes were detected (number of positive isolates): hyl (5), esp (8), gelE (30), agg (2), ace (21), efa (6), CylL_L/s (5), cob (26), cpd (32) and ccf (33). Five isolates were considered as safe and showed tolerance to both acid and bile salt.

CONCLUSION

Bacteriocinogenic enterococci isolates from rabbits may show relevant resistance phenotypes and virulence factors. In addition, one Enterococcus durans isolate presents promising autochthonous probiotic candidate.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study reveals interesting properties for E. durans isolate and supports their utilization as autochthonous probiotic in rabbit husbandry.

Beneficial effects of Enterococcus faecium EF9a administration in rabbit diet

<p>Forty-eight rabbits aged five weeks (Hycole breed, both sexes) were divided into experimental (EG) and control (CG) groups, 24 animals in each, and fed a commercial diet with access to water <em>ad libitum</em>. Rabbits in EG had Enterococcus faecium EF9a probiotic strain added to their drinking water (1.0×10⁹ colony forming units/mL 500 μL/d/animal) for 28 d (between 35 and 63 d). The experiment lasted for 42 d. The animals remained in good health condition throughout the experiment, and no morbidity and mortality was noted. There was a higher live weight at 63 d of age (+34 g; <em>P</em>&lt;0.0001), final live weight at 77 d of age (+158 g; <em>P</em>=0.0483), and average daily weight gain between 63 and 77 d of age in the EG group rabbits than in CG group rabbits (+8 g/d; <em>P</em>&lt;0.0001). No significant changes in caecal lactic acid and total volatile fatty acid concentrations, jejunal morphological parameters and phagocytic activity were noted during the treatment. The tested serum parameters were within the range of the reference values. EF9a strain sufficiently established itself in the rabbit’s gastrointestinal tract. At 63 d of age, a significant decrease in coliforms (<em>P</em>&lt;0.05), coagulase-positive staphylococci (<em>P</em>&lt;0.01), pseudomonads (<em>P</em>&lt;0.01) and coagulasenegative staphylococci (CoNS, <em>P</em>&lt;0.001) was noted in the faeces of the EG group rabbits compared to the CG rabbits. Antimicrobial effects of EF9a strain in the caecum against coliforms (<em>P</em>&lt;0.001), CoNS (<em>P</em>=0.0002) and pseudomonads (<em>P</em>=0.0603) and in the appendix (coliforms, <em>P</em>&lt;0.05) were detected.</p>

Autochtonous Strain Enterococcus faecium EF2019(CCM7420), Its Bacteriocin and Their Beneficial Effects in Broiler Rabbits-A Review

The present review evaluates and compares the effects achieved after application of rabbit-derived bacteriocin-producing strain Enterococcus faecium CCM7420 with probiotic properties and its bacteriocin Ent7420. The experiments included varying duration of application (14 and 21 days), form of application (fresh culture and lyophilized form), combination with herbal extract and application of the partially purified enterocin-Ent7420, produced by this strain. Results from these studies showed that E. faecium CCM7420 strain was able to colonize the gastrointestinal tract (caecum) of rabbits (in the range < 1.0-6.7 log cycle, respectively 3.66 log cycle on average), to change the composition of intestinal microbiota (increased lactic acid bacteria, reduced counts of coliforms, clostridia and staphylococci), to modulate the immunity (significant increase of phagocytic activity), morphometry (enlargement absorption surface in jejunum, higher villi height:crypt depth (VH:CD) ratio), physiological (serum biochemistry; altered total proteins, glucose and triglycerides levels) and parasitological (Eimeria sp. oocysts) parameters and to improve weight gains (in the range 4.8-22.0%, respectively 11.2% on average), feed conversion ratio and meat quality (physicochemical traits and mineral content).

Can Enterocin M in Combination with Sage Extract Have Beneficial Effect on Microbiota, Blood Biochemistry, Phagocytic Activity and Jejunal Morphometry in Broiler Rabbits?

Simple Summary

The weaning period is one of the most critical phases in a rabbit’s life, when rabbits are most sensitive to various spoilage agents, often with fatal outcome. Preventing these post-weaning alimentary disturbances and improving gut health through the use of natural substances has become an area of research activity in rabbit nutrition. The possibilities of “in vivo” administration of bacteriocins in rabbits are often limited. Our study focused therefore on improving rabbits’ health using enterocin M and sage extract, alone and also in combination, mainly to determine their effect on the microbiota, phagocytic activity, serum biochemistry, and morphometry of rabbits. The antibacterial effect of both additives was observed in the gastrointestinal tract of rabbits. Several biochemical parameters (increased in total proteins (TPs) using enterocin (Ent) M, reduction of alanine aminotransferase (ALT) using sage and its hypocholesteremic effect alone and in combination with EntM, and improvement of mineral levels) were optimized. All additives, but mostly EntM, showed a tendency to improve the jejunal morphological parameters.

Abstract

The present study investigated the effects of enterocin (Ent) M and sage extract alone and also in combination on the gut microflora, phagocytic activity, blood biochemistry, and morphometry of rabbits. Sixty-four rabbits (aged five weeks, M91 meatline, both sexes) were divided into three experimental groups: E (EntM; 50 µL/animal/day), S (sage; 10 µL/animal/day), and E + S (EntM + sage) groups and control group (C). The additives were administered in drinking water for a period of 21 days. Dietary supplementation of EntM and sage significantly reduced the coliforms (E: p < 0.001; S: p < 0.001; E + S: p < 0.001) in feces, while simultaneous addition of EntM and sage decreased enterococci (E + S: p < 0.0001), lactic acid bacteria (E + S: p < 0.01), and coagulase-positive staphylococci (E + S: p < 0.0001) in the appendix. Sage addition reduced HDL (S: p < 0.001) and LDL cholesterol (S: p < 0.001; E + S: p < 0.001), LDL/HDL ratio (S: p < 0.001; E + S: p < 0.01), and increased urea (S: p < 0.01; E + S: p < 0.001) and creatinine (S: p < 0.001; E + S: p < 0.001) in serum. EntM and sage application, alone or in combination, improve the jejunal morphometry (p < 0.0001) in rabbits.

ESBL and AmpC β-Lactamases in Clinical Strains of Escherichia coli from Serra da Estrela, Portugal

Background and Objectives: Given the considerable spatial, temporal, and ecological factors, heterogeneity, which affects emergency response, persistence, and dissemination of genetic determinants that confer microorganisms their resistance to antibiotics, several authors claim that antibiotics' resistance must be perceived as an ecological problem. The aim of this study was to determine the prevalence of broad-spectrum bla genes, not only Extended-spectrum β-lactamases (ESBL) but also AmpC-types, in clinical strains of Escherichia coli isolated from Portugal (in the highest region of the country, Serra da Estrela) to disclose susceptibility profiles among different genotypes, and to compare the distribution of bla genes expressing broad-spectrum enzymes. Materials and Methods: Clinical strains of Escherichia coli presenting resistance to third generation (3G) cephalosporins and susceptibility to inhibition by clavulanic acid were studied by means of phenotypic and molecular profiling techniques for encoding β-lactamases genes. Results: Strains were mainly isolated from hospital populations (97%). Molecular analysis enabled the detection of 49 bla genes, in which 55% (27/49) were identified as blaOXA-1-like, 33% (16/49) as blaCTX-M-group-1, 10% (5/49) as blaTEM, and 2% (1/49) were identified as genes blaCIT (AmpC). Among all blaOXA-1-like detected, about 59% of strains expressed at least another bla gene. Co-production of β-lactamases was observed in 40% of strains, with the co-production of CTX-M group 1 and OXA-1-like occurring as the most frequent. Conclusions: This is the first study using microorganisms isolated from native people from the highest Portuguese mountain regions, showing an unprecedent high prevalence of genes blaOXA-1-like in this country.

Effect of a lytic bacteriophage on rabbits experimentally infected with pathogenic Escherichia coli

Pathogenic <em>Escherichia coli</em> (<em>E. coli</em>) is severely threatening the rabbit industry in China, and the concern over antibiotic-resistant bacteria has given rise to an urgent need for antibiotic alternatives. In this study, a member (ZRP1) of the <em>Myoviridae</em> family was isolated from rabbit faeces using a strain of rabbit atypical enteropathogenic <em>E. coli</em> (ZR1) as host. The one-step growth curve indicated that the latent period was around 25 to 30 min and the burst size was 144±31 plaque-forming unit/cell. The rate of phage-resistant mutation was 7×10^–5±4×10^–5. When the bacteriophage input at the multiplicity of infection (MOI) was 0.1, 1 or 10, the growth of host <em>E. coli</em> in broth was inhibited for 5 h. A single intravenous injection of ZRP1 at MOI 0.1, 1 or 10 significantly prolonged the survival time of rabbits which simultaneously received a lethal dose of ZR1.