Antibiotic Use and Resistance in Agriculture Sector

Antibiotic Use and Resistance in Agriculture Sector: Comparison

Please note this is a comparison between Version 1 by Zeinab Breijyeh and Version 2 by Peter Tang.

Possible new ways for the development of novel classes of antibiotics are discussed here, for which there is no pre-existing resistance in human bacterial pathogens. By utilizing research and technology such as nanotechnology and computational methods (such as in silico and Fragment-based drug design (FBDD)), there has been an improvement in antimicrobial actions and selectivity with target sites. Moreover, there are antibiotic alternatives, such as antimicrobial peptides, essential oils, anti-Quorum sensing agents, darobactins, vitamin B6, bacteriophages, odilorhabdins, 18β-glycyrrhetinic acid, and cannabinoids. Additionally, drug repurposing (such as with ticagrelor, mitomycin C, auranofin, pentamidine, and zidovudine) and synthesis of novel antibacterial agents (including lactones, piperidinol, sugar-based bactericides, isoxazole, carbazole, pyrimidine, and pyrazole derivatives) represent novel approaches to treating infectious diseases. Nonetheless, prodrugs (e.g., siderophores) have shown to be an excellent platform to design a new generation of antimicrobial agents with better efficacy against multidrug-resistant bacteria.

antibiotic
resistance
antimicrobial agents

1. Introduction

Prior to the turn of the 20th century, infectious diseases were the main contributor to high morbidity and mortality rates around the world [1]. The period of antibiotics, which saw the discovery and development of numerous antibacterial drugs, began with Fleming’s discovery of penicillin in 1929. Regrettably, the emergence of resistant strains was brought on by the overuse and careless use of antibiotics ^[2][3][2,3]. According to 2019 systemic analytic research, there were 4.95 million fatalities attributable to antimicrobial resistance (AMR). With 27.3 deaths per 100,000 people, western sub-Saharan Africa has the highest mortality rate, whereas Australasia has the lowest mortality rate with 6.5 deaths per 100,000 people [4]. Twelve families of bacteria have been identified by the World Health Organization (WHO) as the most dangerous to human health and have been divided into three priority groups: critical pathogens (Acinetobacter, Pseudomonas, and Enterobacteriaceae), high priority pathogens (Enterococcus faecium, Staphylococcus aureus, Helicobacter pylori, Campylobacter, Salmonella spp., Nisseria gonorrhoeae), and medium priority pathogens (Streptococcus pneumoniae, Shigella spp.) ^[5][6][7][8][5,6,7,8]. The presence of multidrug-resistant (MDR) ESKAPE pathogens (including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and extensively drug-resistant (XDR) bacteria has rendered even the most effective drugs ineffective. Therefore, its necessary to develop novel strategies and approaches to overcome the problem of increasing AMR ^[9][10][11][9,10,11].

2. Antibiotic Classification

New antibiotic use methods should be implemented on a local and global level to combat resistance, and the development of novel treatments requires a thorough understanding of how antibiotics function. Table 1 summarizes how antibiotics produce their effects through a variety of mechanism of action. Antibiotic-mediated cell death is a complicated process that begins with a physical interaction between the medication and its particular target in bacteria, altering the bacterium’s biochemical, molecular, or ultrastructural levels. The development of DNA double-stranded DNA breaks, the halting of DNA-dependent RNA synthesis, cell envelop damage, protein mistranslation, and stress induction are only a few of the methods through which antibiotics can cause cell death [12]. Antimicrobial agents are divided into two categories on the basis of how they affect bacteria in a test tube: (1) bactericidal (kill bacteria) antibiotics such as β-lactams, glycopeptides, lipopeptides, rifamycins, aminoglycosides, and fluoroquinolones, and (2) bacteriostatic (prevent bacterial growth) antibiotics such as sulfonamides–trimethoprim and macrolides. Bacteriostatic substances can also be described as having a minimum bactericidal concentration (MBC) to minimum inhibitory concentration (MIC) ratio higher than four, and bactericidal substances when the MBC to MIC ratio is lower than or equal to four [13].

Table 1.

List of antimicrobial agent and their mechanism of action.

Antibiotics Family	Mechanism of Action	Antibiotics
β-lactam	Binds to the serine active site of penicillin-binding proteins (PBPs) or the allosteric site in PBP2a to inhibit bacterial cell wall peptidoglycan transpeptidation ^[14]^[15][14,15].	Penicillins Cephalosporins Carbapenems Monocyclic β-lactams β-lactamase inhibitors (e.g., clavulanic acid) (Figure 1)
Glycopeptides	Interacts with the membrane-bound lipid II precursor of peptidogly and can prevent peptidoglycan from being incorporated into an essential structural cell wall component [16].	Vancomycin Teicoplanin Telavancin Dalbavancin Oritavancin (Figure 1)
Lipopeptide	Carries out their action by causing Gram-positive bacteria’s cell membrane integrity to be compromised, which results in cell death ^[17]^[18][17,18].	Polymyxins Daptomycin Amphomycin Friulimicin Ramoplanin Empedopeptin (Figure 2)
Rifamycins	RNA polymerase (RNAP) inhibitors are used to treat tuberculosis (TB) [19].	Rifampin Rifabutin Rifapentine (Figure 3)
Aminoglycoside	By attaching to the 30S ribosome’s A-site on the 16S ribosomal RNA, they inhibit protein synthesis [20].	Streptomycin Apramycin Tobramycin Gentamcin Amikacin Neomycin Arbekacin Plazomicin (Figure 3)
Fluoroquinolones	Target DNA gyrase, topoisomerase IV, and topoisomerase type II to prevent bacteria from synthesizing DNA [21].	Nalidixic acid Enoxacin Norfloxacin Ciprofloxacin Ofloxacin Lomefloxacin Sparfloxacin Grepafloxacin Clinafloxacin Gatifloxacin Moxifloxacin Gemifloxacin Trovafloxacin Garenoxacin (Figure 4)
Sulfonamides–Trimethoprim	Sulfonamides interfere with the activity of the dihydropteroate synthase enzyme by competing with p-aminobenzoic acid (PABA) in the process of dihydrofolate production.The dihydrofolate reductase enzyme is inhibited by trimethoprim because it competes directly with it [22].	Sulfamethoxazole Trimethoprim (Figure 4)
Macrolides	Target the nascent peptide exit tunnel (NPET) of the bacterial 50S ribosomal subunit, which is responsible for the release of newly synthesized protein from the ribosome, ultimately preventing protein synthesis ^[23]^[24][23,24].	Erythromycin Clarithromycin Azithromycin Fidaxomicin Telithromycin (Figure 4)
Tetracyclines	Bind to the small subunit’s decoding site and prevent bacterial protein synthesis ^[25]^[26][25,26].	Chlortetracycline Oxytetracycline Tetracycline Demeclocycline Doxycycline Minocycline Lymecycline Meclocycline Methacycline RolitetracyclineTigecycline Omadacycline Sarecycline Eravacycline (Figure 5)
Oxazolidinones	Block the translation sequence by interacting with the 50S subunit (A-site pocket) at the peptidyl transferase center (PTC) to inhibit protein synthesis [27].	Linezolid Sutezolid Eperezolid Delpazolid Tedizolid Tedizolid phosphate Radezolid TBI-223 (Figure 5)
Streptogramins	Inhibit protein synthesis during the elongation step by attaching to bacterial ribosomes [28]. The antibiotic has two unique structural groups (A and B) that cooperate to increase the affinity of group B in the nearby nascent peptide exit tunnel (NPET) when group A binds to the peptidyl transferase center (PTC) [29].	Quinupristin Pristinamycin Virginiamycin (Figure 6)
Phenicoles	Inhibit protein synthesis by binding to the 50S ribosomal subunit [30].	Chloramphenicol Thiamphenicol Florfenicol (Figure 6)
Lincosamides	Activate amino acid monomers by aminoacyl-tRNA, chain initiation, elongation, and termination of the formed polypeptides on the ribosome, which disrupts bacterial growth and death. These are only a few of the many processes that can be affected to prevent microbial protein synthesis [31].	Lincomycin Clindamycin (Figure 6)

Figure 1. Chemical structure of penicillins, cephalosporins, carbapenems, monocyclic β-lactams, clavulanic acid (β-lactamase inhibitors), vancomycin, teicoplanin, telavancin, dalbavancin, and oritavancin.

Figure 2.

Chemical structure of polymyxins, daptomycin, amphomycin, friulimicin, ramoplanin, and empedopeptin.

Figure 3.

Chemical structure of rifampin, rifabutin, rifapentine, streptomycin, apramycin, tobramycin, gentamycin, amikacin, neomycin, arbekacin, and plazomicin.

Figure 4. Chemical structure of nalidixic acid, enoxacin, norfloxacin, ciprofloxacin, ofloxacin, lomefloxacin, sparfloxacin, grepafloxacin, clinafloxacin, gatifloxacin, moxifloxacin, gemifloxacin, trovafloxacin, arenoxacin, sulfamethoxazole, trimethoprim, erythromycin, clarithromycin, azithromycin, fidaxomicin, and telithromycin.

Figure 5. Chemical structure of chlortetracycline, oxytetracycline, tetracycline, demeclocycline, doxycycline, minocycline, lymecycline, meclocycline, methacycline, rolitetracycline, tigecycline, omadacycline, sarecycline, eravacycline, linezolid, sutezolid, eperezolid, delpazolid, tedizolid, tedizolid phosphate, radezolid, and TBI-223.

Figure 6.

Chemical structure of quinupristin, pristinamycin, virginiamycin, chloramphenicol, thiamphenicol, florfenicol, lincomycin, and clindamycin.

3. Antimicrobial Resistance

The World Health Organization (WHO) describes antimicrobial resistance as a natural phenomenon that happens when germs cease responding to antibiotics that they were previously susceptible to before. Resistance makes treating infections more difficult or impossible ^[8][32][8,32]. In bacteria, there are two types of resistance: acquired and natural [33]. Natural resistance can either be produced or intrinsic (expressed in a species without connection to horizontal gene transfer) (the natural bacterial genes are only expressed to resistance levels after exposure to an antibiotic). Contrarily, acquired resistance can develop after acquiring genetic material that already exhibits it through horizontal gene transfer (HGT) (transformation, transposition, and conjugation) or by causing a mutation in the cell’s DNA during replication ^[8][33][34][8,33,34]. Antimicrobial resistance mechanisms include drug inactivation, decreased intracellular drug concentration, and altered drug targets (Figure 7) ^[35][36][35,36]. One of the most significant mechanisms of acquired resistance is the change or degradation of antibiotics. Bacterial enzymes have the ability to alter a number of antibiotics, including aminoglycoside, chloramphenicol, and β-lactam ^[37][38][37,38]. By increasing efflux or decreasing influx, one can lower drug concentration [39]. Bacteria can develop a high level of inherent resistance owing to this method. Porin mutations in resistant strains alter the permeability of bacterial membranes, which reduces medication uptake into the cell. For instance, OprD, a particular porin in strains of P. aeruginosa, can result in a mutation for carbapenem resistance [40]. The Proteobacterial Antimicrobial Compound Efflux (PACE) superfamily, the Resistance Nodulation Division (RND) family, the Small Multidrug Resistance (SMR) superfamily, the Multidrug and Toxic Compound Extrusion (MATE) superfamily, and the ATP (adenosine triphosphate)-Binding Cassette (ABC) superfamily are the six families that make up the transmembrane proteins that make up efflux pumps ^[41][42][41,42]. The most prevalent efflux pumps in both Gram-positive and Gram-negative bacteria are MFS and RND pumps [39]. The medication target changing is another method of resistance. Examples include the resistance to glycopeptide and polymyxin antibiotics caused by enzymes that chemically alter components of the cell membrane necessary for antibiotic binding. Methyltransferases are another example of target modifying enzymes since they change the rRNA elements on the ribosome and thus become resistant to antibiotics including aminoglycoside, lincosamide, macrolide, streptogramin, and oxazolidinone [43]. Another phenomenon known as “target protection” occurs when an antibiotic target’s resistance protein protects it from antibiotic-induced inhibition (target protection protein). Tetracycline ribosomal protection proteins (TRPPs) are an illustration of this mechanism [44].

Figure 7.

Mechanism of antimicrobial resistance which include reduce intracellular antibiotic concentration, antibiotic inactivation, and target site alteration.

4. Antibiotic Use and Resistance in Agriculture Sector

β-lactams, aminoglycosides, tetracyclines, macrolides, and other antibiotics with comparable modes of action to those used by humans are causing a lot of concern due to their possible side effects and risk management strategies [45]. Because medicines are available over the counter, their overuse, abuse, and misuse are linked to antibiotic resistance [46]. Antibiotic resistance is caused by the use of antibiotics in animals raised for food. Food safety and public health may suffer if antibiotic residues are found in products obtained from animals that are intended for human consumption ^[47][48][49][47,48,49]. Use of unnecessary antibiotics in animals for the purpose of promoting development, as well as waste products from veterinary care and livestock farming, human waste streams, and soil fertilization, can result in the release of antibiotics pollution into the environment. As a result, it is possible to think of the environment as a reservoir for antibiotics and bacteria that are resistant to antibiotics, and their resistance genes ^{[45][50][51][52]}[45,50,51,52]. Reports that some bacterial infections in humans are brought on by animal pathogens (zoonotic pathogens) such as Salmonella spp., Staphylococcus spp., Yersinia enterocolitica, Enterococcus spp., Listeria monocytogenes, Campylobacter jejuni and Escherichia coli ^[53][54][55][53,54,55] have demonstrated that antibiotic resistance can be transmitted directly or indirectly from animal to human. To prevent antibiotic resistance and maintain the potency of the available antibiotics, a number of practices should be regulated for the prudent use of antibiotics in the clinical and agricultural sectors ^[56][57][56,57]. The demand for antibiotics to cure illnesses can be decreased by improving animal feed, waste management, and animals’ natural immunity. Moreover, using antibiotic alternatives including prebiotics, probiotic vaccines, and bacteriophages can help reduce the need for antibiotics ^[58][59][60][58,59,60].