الفهرس 
INTRODUCTION AND AIM OF THE STUDYOnly 14 pages are availabe for public view
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Abstract
The global crisis of antimicrobial resistance has been threatening our ability to treat and prevent serious bacterial infections. It is responsible for hundreds of thousands of deaths every year, and the mortality rates are expected to rise to millions in a few decades if no timely action is taken. The WHO has considered it as one of the top ten threats facing global health.
High rates of antimicrobial-resistant bacteria have been reported from animal farms worldwide that could also spread to humans and the environment. This threat is majorly driven by the extensive unregulated use of antimicrobials in animal husbandry. The rates of antimicrobial use have been widely studied in human medicine. However, much less attention was paid to studying them in animal husbandry.
The present study aimed to determine the prevalence of ”serious antimicrobial resistance threats” in conventional vs. organic livestock farms in Egypt. In addition, it aimed at shedding light on antimicrobial use in animal farming and the drivers behind it.
The study included a total of one hundred samples collected from eight cattle and poultry farms. The samples were examined for the presence of ESBL-producing and fluoroquinolone-resistant E. coli, fluoroquinolone-resistant Salmonella, and VRE. The resistant isolates were studied for their antimicrobial susceptibility and the presence of ARGs. The resistance rates in conventional farms were compared to those in an organic farm. Additionally, a total of 111 questionnaires were filled out for 111 livestock farms in Egypt. They included the types of antimicrobials used in farms, the rates of their use, the use indications, and their effect on production efficiency.
The present study’s results can be summarized as follows:
1. The studied conventional farms had a significantly higher rate of antimicrobial-resistant bacteria than the organic farm (73.81% vs. 18.75%).
2. In conventional farms, all the studied antimicrobial-resistant bacterial types were detected, with the following rates: ESBL-producing E. coli (27.38%), fluoroquinolone-resistant
E. coli (25%), E. coli with both resistance traits (35.71%), VRE (7.14%), and fluoroquinolone-resistant Salmonella (1.19%).
3. Almost one-third (32.05%) of the resistant E. coli isolates were also colistin-resistant. The rate increased to 50% in isolates that were both ESBL-producing and fluoroquinolone-resistant.
4. In the organic farm, only single isolates of ESBL-producing E. coli were detected, and none of them was colistin-resistant.
5. The E. coli isolates were most resistant against ampicillin (96.09%-100%), cefazolin (88.24%-100%), tetracycline (87.5%-90.38%), ciprofloxacin (53.57%-100%), and gentamicin (33.93%-60.00%). None of the isolates was imipenem-resistant.
6. The isolated fluoroquinolone-resistant Salmonella was also MDR.
7. All vancomycin-resistant E. faecium isolates were also resistant to ciprofloxacin, tetracycline, penicillin, erythromycin, and quinupristin-dalfopristin. On the other hand, all non-faecalis/faecium VRE were susceptible to all the tested antimicrobials, except for one isolate that was tetracycline-resistant. None of the VRE isolates were resistant to linezolid nor teicoplanin.
8. Feces samples contained the highest prevalence of antimicrobial-resistant bacteria (83.33%), followed by litter samples (68.75%), wastewater (56.25%), and soil samples (37.5%).
9. Poultry farms had a significantly higher prevalence of ESBL-producing E. coli that
co-resisted fluoroquinolones (58.33%) and colistin-resistant E. coli (44.44%) than cattle farms (5.56% and 16.67%, respectively). Also, all E. faecium were found only in a poultry farm, while all non-faecalis/faecium VRE were found only in cattle farms.
10. The most prevalent ESBL-production gene was bla-TEM (82.14%), followed by bla-CTX-M (48.22%), and the least was bla-SHV (19.64%), either alone or in combination with another gene.
11. The most prevalent fluoroquinolone-resistance genes were qnrS (82.69%) and qnrB (42.31%), either alone or in combination with another gene(s).
12. Five VRE isolates harbored vanA gene (83.33%), none carried vanB gene, and one isolate was negative for both genes.
13. With a 74% response rate, all the surveyed farms reported using antimicrobials, and almost two-thirds (64.86%) used them for non-therapeutic purposes.
14. The most common infection control measures were: vaccination (100%), insect and rodent control (80.18%), isolating sick animals (77.48%), and regular cleaning (72.97%).
15. The most commonly used antimicrobials were penicillins (81.08%), macrolides (78.38%), and tetracyclines (72.07%). Almost half of the studied farms (49.55%) used colistin, of which 54.55% used it for disease prevention and growth promotion.
16. More than one-third of farms (35.14%), always or most of the time, did not leave a withdrawal period between using antimicrobials and slaughtering or using animal products.
17. Poultry farms had significantly higher rates of non-therapeutic antimicrobial use (87.27%), total colistin use (80%), and non-therapeutic colistin use (52.27%) than cattle farms (41.86%, 9.30%, and 25.00%, respectively).
18. Non-therapeutic use of antimicrobials did not decrease the FCR in any of the farm types.
19. The majority of participants (75.67%) thought that non-therapeutic antimicrobial use in livestock can be partially (54.05%) or completely replaced (21.62%).
20. Most of the participants (80.18%) were willing to receive training related to antimicrobial use in livestock, namely on: proper use of antimicrobials in farm animals (59.62%), prophylaxis against infections in farm animals (30.77%), and antimicrobial resistance (28.85%).
It can be concluded from the study that:
1. A significantly higher level of antimicrobial resistance was found in the conventional livestock farms than the organic farm.
2. Fluoroquinolone-resistant, colistin-resistant E. coli, MDR Salmonella, and VRE were found only in the conventional farms.
3. Poultry farms had significantly higher rates of ESBL-producing and fluoroquinolone-resistant E. coli and colistin-resistant E. coli than cattle farms.
4. Most of the livestock farms in Egypt (64.86%) use antimicrobials for non-therapeutic purposes (i.e., for disease prevention and growth promotion), including those that are highly important, critically important, and last-resort options for human medicine.
5. The use of antimicrobials for non-therapeutic purposes did not increase the feed efficiency.
6. Thinking that antimicrobials are useful, even slightly, and that most of the other farms are using antimicrobials for non-therapeutic purposes were associated with increased levels of non-therapeutic antimicrobial use in livestock farms in Egypt.
7. Most of the surveyed farm personnel (80.18%) are willing to receive training about the proper use of antimicrobials in livestock.
from the present study’s results, the following recommendations are advised:
1. There is a need for Egyptian guidelines for the use of antimicrobials in livestock that consider both human and veterinary medical needs.
2. The use of antimicrobials that are last-resort options for human medicine should be banned in livestock.
3. There is a high demand for campaigns to raise farm personnel’s awareness. They should include essential biosafety measures, consequences of injudicious antimicrobial use, and successful interventions worldwide.
4. A national surveillance system is needed to assess the trends in antimicrobial resistance and antimicrobial use in livestock in Egypt.
5. There is a need for studies to investigate the spread of antimicrobial resistance threats found in livestock farms to humans.