Antibiotics have been a cornerstone of modern medicine since the 1940s, revolutionizing the treatment and prevention of infectious diseases. In animal production systems, the emergence of antimicrobial resistance is driven by multiple interrelated factors, including inappropriate and excessive antimicrobial use, improper dosing and incomplete treatment regimens, routine prophylactic and metaphylactic practices, limited veterinary oversight, suboptimal husbandry conditions, inadequate hygiene and biosecurity measures, high animal stocking densities, and continuous exposure to antimicrobial residues through contaminated feed, water, or manure. Collectively, these practices impose sustained selective pressure that facilitates the emergence and persistence of antimicrobial-resistant microorganisms in animal production systems.

Antibiotics have been widely used in animal husbandry, often at sub-therapeutic doses, to enhance growth and improve feed efficiency, which has a positive impact on the overall value of animal products. Additionally, it has been demonstrated that adding antibiotics to animal feeds is a significant method of increasing feed efficiency, encouraging animal growth and raising the value of the animal products.¹ However, the widespread misuse has fuelled a global public health crisis: antimicrobial resistance (AMR).

The World Health Organization (WHO) has identified AMR as one of the top ten global health threats.² A 2024 study in The Lancet estimated that antibiotic resistance directly caused 1.27 million deaths worldwide in 2019 and was associated with nearly 5 million deaths. Projections indicate that if current trends continue, there could be 1.91 million direct deaths annually by 2050, and it could play a role in 8.22 million deaths per year by then.³ As a result, worldwide efforts have been made to slow the spread of AMR. As a result, in 2015, the Global Action Plan on Antimicrobial Resistance (GAP) was developed with the goal of putting national action plans into action to slow the spread of AMR. This crisis, often termed a “Silent Pandemic”, necessitates a search for novel and effective alternatives to conventional antibiotics, particularly those that cause nosocomial infections and have a propensity to develop multidrug-resistance.

To combat AMR, researchers have called for more controlled and judicious use of antibiotics, including restricting prescriptions to specialists and mandating thorough antibiogram testing prior to drug delivery. The hunt for novel, potent molecules against bacteria that are already resistant are all necessary to combat antibiotic resistance, according to a number of researchers.^4,5 The scale and impact of this crisis are illustrated by the emergence of major resistant pathogens and their global spread, as summarized in Table. This review will explore various strategies from natural compounds to cutting-edge technologies that can be used to combat drug-resistant pathogens and address this urgent global challenge (Figure).

Table:
Major Antimicrobial-Resistant Pathogens and Their Global Impact

Abbreviation: Methicillin-Resistant Staphylococcus aureus (MRSA), Healthcare Associated- Methicillin-Resistant Staphylococcus aureus) (HA-MRSA), Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), Oxacillinase (OXA), Multidrug-Resistant Tuberculosis (MDR-TB), Extensively Drug-Resistant TB (XDR-TB), Trimethoprim/sulfamethoxazole (TMP-SMX), Vancomycin-Resistant Enterococci (VRE), Carbapenem-Resistant Enterobacteriaceae (CRE), Pan-Drug-Resistant (PDR), Pneumococcal Conjugate Vaccines (PCVs).

Alternative antimicrobial strategies
Antimicrobial peptides (AMPs)
Also known as host defence peptides, are a diverse class of naturally occurring peptides (12-50 amino acid residues long), that are part of the innate immune system. They possess a net positive charge (due to Arg and Lys residues) and a high percentage of hydrophobic residues (usually 50%), enabling them to form structures that target the negatively charged surfaces of bacterial cell membranes.

Mechanism of action
The primary mechanism of action for AMPs is their ability to disrupt bacterial cell membranes. Most AMPs are positively charged and are attracted to the negatively charged components of bacterial cell membranes. Once they bind to the cell membrane, they can form pores that destabilize the lipid bilayer, leading to rapid cell death. This membrane-targeting mechanism makes it difficult for bacteria to develop resistance compared to antibiotics that target specific enzymatic pathways.⁶ AMPs can also have non-membrane-mediated effects, such as inhibiting intracellular processes like protein or DNA synthesis.

 Advantages and applications
AMPs exhibit broad-spectrum activity against a wide range of microorganisms, including Gram-positive and Gram-negative bacteria, fungi, and viruses.⁷ Plants and animals naturally produce amphipathic cationic peptides known as antimicrobial peptides as a component of their innate defense system.⁷ The Antimicrobial Peptide Database lists over 3,257 AMPs.⁸ viz. bacteriocins, defensins, tachyplesins, β-defensins, protegrins, and insect defensins.^9,10 In combination with conventional antibiotics, AMPs can have a synergistic effect, lowering the minimal inhibitory concentration required to combat multidrug-resistant bacteria.¹¹ Studies have shown their effectiveness in poultry as immune-boosters and growth enhancers,¹² and insect defensins have demonstrated potential against antibiotic-resistant Staphylococcus aureus.¹³ In both in vitro and in vivo investigations, bacteriocins derived from a variety of microorganisms have demonstrated encouraging outcomes in preventing the growth of Clostridium perfringens in broiler chickens.¹⁴ However, the main hurdles for AMPs are their cost of production, potential toxicity at higher concentrations, and susceptibility to degradation by host proteases. Efforts are ongoing to engineer more stable and effective synthetic AMPs.

Bacteriophage therapy
This therapy uses lytic bacteriophages (phages) viruses that exclusively infect and kill bacteria to treat infections. A lytic phage hijacks the bacterial host’s machinery to replicate its own DNA, producing new phages until the host cell bursts, or lyses, releasing the new viruses to infect more bacteria.¹⁵

Mechanism of action
The primary advantage of phage therapy is its high specificity, allowing phages to target a narrow range of bacterial species while leaving beneficial microbiota unharmed.¹⁵

Advantages and applications
This approach has been used to treat infections in both humans and animals.¹⁶ Phage cocktails have shown success against pathogens like Salmonella, Campylobacter, and E. coli O157:H7.¹⁷ In 2006, the U.S. Food and Drug Administration (US-FDA) approved a phage cocktail (LMP-102TM) as a food additive to control Listeria contamination in meat. Studies in poultry and pigs have also demonstrated the effectiveness of phages in preventing colibacillosis and Clostridium infections and also reducing Salmonella colonization by up to 99.9% in the tonsils, ileum, and cecum.^18,19

Immunomodulators
Immunomodulatory agents enhance the host’s immune system to more effectively combat infections, shifting the focus from directly killing the pathogen to empowering the host’s natural defenses.

Antibacterial vaccines
Immunotherapy involves stimulating the host’s immune system to fight off infections.

Mode of action
Antibacterial vaccines, or bacterins, are a key component of this approach. They are preparations made from weakened or killed bacteria that train the immune system to recognize and neutralize specific pathogens.²⁰

Types and challenges
Vaccines can be live attenuated or killed. While live attenuated vaccines can provide a strong immune response, they carry a risk of reverting to full virulence.^21,22 Killed vaccines, which are safer, produced by destroying bacterial colonies cultured in vitro and then adding adjuvants to boost the immune response.²³ They are currently used in many poultry vaccines against pathogens like Pasteurella multocida and Salmonella, Mycoplasma, Ornithobacterium, Haemophilus, Staphylococcus, E. coli and Bordatella.¹ Vaccines offer a preventative strategy that can significantly reduce the need for antibiotics.²⁴ The success of pneumococcal conjugate vaccines in reducing resistant strains is a notable example.²⁵

Antibacterial vaccines are still uncommon on the market, in contrast to the antiviral vaccine business, which is quite developed. Although immunizations against C. jejuni and E. coli O157 have been demonstrated to be efficacious in cattle and chicken, respectively.²³ S. aureus vaccines are made to prevent bovine mastitis, however according to a systematic review that included 24 in vivo research, methodological variations and a lack of stricter scientific standards might occasionally make it difficult to determine how effective these vaccinations are.²⁶ One major issue remains the development of a vaccination that is both affordable and useful enough to be used in developing nations.²⁷ Despite the challenges this approach may pose, it can serve as a powerful defense against the bacterial strains for which vaccinations are available, hence reducing the need for antibiotics.²⁸ However, their development and commercialization remain challenging due to high costs, a lack of standardized efficacy evaluation, and the potential for bacteria to develop resistance to non-vaccine serotypes.^23,25

Monoclonal antibodies
These lab-produced antibodies are designed to bind to specific bacterial components, such as toxins or surface proteins, to either neutralize the pathogen directly or mark it for destruction by the host’s immune cells.²⁹

Cytokines and immunostimulants
These molecules, such as interferons or colony-stimulating factors, can be administered to enhance the activity of various immune cells, including phagocytes and lymphocytes, improving the body’s ability to clear infections.²⁵

CRISPR-Cas systems
The CRISPR-Cas system is an adaptive immune mechanism in bacteria that can be repurposed to fight antimicrobial resistance. This gene-editing tool offers a highly specific and targeted approach to eliminating pathogenic bacteria or disabling their resistance genes.

Mechanisms of action
The core mechanism of CRISPR-Cas involves a guide RNA (gRNA) that directs the Cas protein to a specific DNA sequence, which it then cleaves.

“Cure” bacteria of resistance: CRISPR-Cas can be programmed to target and destroy plasmids-small, circular DNA molecules that often carry antibiotic resistance genes within a bacterium. This makes the bacterium susceptible to existing antibiotics again.³⁰

Kill the pathogen: By targeting essential genes on the bacterial chromosome, the CRISPR-Cas system can induce irreversible DNA damage, leading to the death of the cell.³¹

Challenges
Delivering the CRISPR-Cas system effectively into bacterial cells is a significant technical hurdle.³² Viral vectors, such as phages, are being explored as a delivery method. The potential for off-target effects and the possibility of bacteria developing anti-CRISPR mechanisms are also active areas of investigation.^33,34

Prebiotics, probiotics and synbiotics
These dietary supplements have been used in animal husbandry to promote growth and enhance health, offering a safe alternative to antibiotic growth promoters.³⁵

Prebiotics
Indigestible food components (e.g., fructooligosaccharides and man-nanoligosaccharides) that selectively promote the growth of beneficial gut bacteria.³⁶ They possess immune-stimulating and growth-promoting qualities, but their high cost and potential for gastrointestinal side effects are drawbacks.³⁷ At the moment, acidifiers and multifunctional oligosaccharides are the most promising prebiotics.¹

Probiotics
Live microbial feed supplements (e.g. Bacillus, Lactobacillus, Lactococcus, Streptococcus, Enterococcus, Pediococcus, Bifidobacterium, Bacteroides, Pseudomonas, yeast, Aspergillus, and Trichoderma) that improve gut microbial balance and inhibit the growth of pathogens through competitive exclusion.^38,39 Administering Bacillus sp. has been shown to reduce Salmonella and Clostridium growth in poultry.⁴⁰

Synbiotics
Products that combine probiotics and prebiotics to maximize their synergistic benefits.⁴¹ Studies have shown that synbiotics can significantly enhance weight gain, improve immune function, and reduce diarrheal morbidity in animals. For example, chicken weight gain was considerably enhanced when diets supplemented with Biomin®IMBO (a mixture of Enterococcus fecium, cell wall fragments, fructooligosaccharides and phycophytic compounds).⁴² According to certain reports, piglets that were given synbiotics have improved immune function, increased average daily gain and digestibility, decreased diarrheal morbidity and mortality, made weaning stress response easier, and significantly improved performance.⁴³ The high cost of production is one potential obstacle to the adoption of synbiotics.⁴⁴

Other promising approaches
Phytobiotics
Plant extracts, or phytobiotics, with antibacterial, anti-inflammatory, and anti-parasitic properties.⁴⁵ They can be used alone or in combination with antibiotics to combat resistant bacteria.⁴⁶ Numerous studies have demonstrated their antibacterial activity against a range of microorganisms both in vitro and in vivo.⁴⁷ For example, a number of edible Asian plants showed antibacterial action against Bacillus cereus, L. monocytogenes, S. aureus and E. coli.⁴⁸ It is evident from the use of specific plant extracts in traditional medicine to treat diarrheal and urinary tract infections,⁴⁹ among other conditions, that plant extracts can significantly lower the need for antibiotics.⁴⁶

Anti-virulence strategies
Anti-virulence strategies have emerged as a promising alternative to traditional antibiotics by targeting the factors that make bacteria harmful, rather than killing them outright. This approach reduces the selective pressure that drives the evolution of antibiotic resistance.

Quorum-sensing and quorum quenching
Quorum sensing is a bacterial communication system that is essential for coordinating collective behaviours like biofilm formation, toxin production, and resistance gene expression.^50-52 In this method cell interact by generating and detecting extracellular signalling molecules called autoinducers and changing their gene expression in response to the density of the cell population is called as quorum sensing.⁵³ Gram-positive bacteria emit autoinducing peptides (AIPs), Gram-negative bacteria release N-acyl homoserine lactones (AHLs), autoinducer-2 (AI-2), and other signalling molecules such fatty acids, esters, and quinolones are the examples of autoinducers.¹

Quorum quenching
Involves interfering with these signals to disarm the bacteria without killing them. This approach may reduce the selective pressure for resistance development.⁵² This unique approach may reduce the selective pressure for resistance development, making it an intriguing alternative.

Biofilm dispersal agents
Biofilms are complex bacterial communities encased in a protective matrix, making them highly resistant to antibiotics. Agents that can disrupt or prevent biofilm formation are effective anti-virulence tools.⁵⁴

Toxin inhibitors
These strategies target and neutralize the toxins produced by bacteria, thereby preventing disease symptoms without affecting bacterial viability.⁵⁵

Nanoparticles
Nanoparticles (NPs) provide a platform for alternative antimicrobial strategies. They can kill bacteria and prevent biofilm formation through three potential mechanisms like oxidative stress, the release of metal ions and non-oxidative mechanisms. Conjugating small-molecule drugs onto NPs such as silver nanoparticles, can also create a synergistic effect against resistant strains.⁵⁶ Compared to traditional antibiotics, they may have longer-lasting antibacterial activity, less toxicity, and a lesser chance of resistance.^57,58

Role of Artificial Intelligence (AI)
AI is transforming antimicrobial discovery. Machine learning algorithms are used to predict resistance patterns, optimize treatment plans, and accelerate the de novo design of new antimicrobial agents, providing potential solutions to the current AMR dilemma.⁵⁹

One health approach
The One Health concept is a holistic framework that recognizes the interconnectedness of human, animal, and environmental health, and it is critical for managing AMR on a global scale.⁶⁰ This approach acknowledges that the overuse of antibiotics in human medicine and veterinary care. The transmission of multidrug-resistant organisms (MDROs) and resistance genes is a key focus.⁶¹ For example, resistant bacteria from animal farms can spread to the environment through farm runoff and to humans through contaminated food. Similarly, hospitals are hotbeds for resistance, with MDROs spreading to the environment via wastewater and to other countries through international travel. By promoting collaboration among stakeholders in healthcare, agriculture, and environmental management, the One Health approach aims to track and contain this flow of resistance.⁶⁰ More than just a strategy for reducing antibiotic use, the One Health approach emphasizes improving sanitation, biosecurity, and vaccination programs in all sectors. By preventing infections in the first place, we can significantly reduce the need for antibiotics. This comprehensive strategy, adopted by international organizations like the Food and Agriculture Organisation (FAO), World Health Organisation (WHO), and World Organisation for Animal Health (WOAH), addresses the root causes of resistance to safeguard public health and the sustainability of global food systems.⁶²