Intrinsic resistance refers to resistance resulting from the inherent characteristics of microorganisms (Melander et al., 2023). Changes in glycopeptide in the bacterial cell envelope is one of the examples of intrinsic resistance in Gram-negative bacteria by altering the impermeability of the outer membrane of the bacteria (Christaki et al., 2020). The restriction entry of antibiotics, cause by the prorins proteins, contributing to its resistance (Bellido et al., 1992). Additionally, in Proteus mirabilis, Serratia marcescens, Burkholderia spp., Yersinia spp., the pmrCAB operons, encodes the PmrC, mediates polymyxin and modification the lipid increases bacterial resistance to the polymyxin B (Marceau et al., 2004; Poirel et al., 2017).

The acquired drug resistance is achieved through the transfer of genetic material by multiple mechanisms. It emerges via spontaneous mutations of microorganism or the obtain of new genetic material conferring drug resistance to the microorganism (Durao et al., 2018; Gonzalez-Villarreal et al., 2022). Three primary mechanisms for such gene transfer horizontally: transformation, transduction, and conjugation. Transformation is a process of DNA recombination where heterogeneous DNA fragments from a donor enter a microorganism and become and integrated part of its inheritance properties (Winter et al., 2021). Yet this natural transformability is limited to only a few bacterial species. Transduction also involves the transfer of genetic material. Unlike transformation, transduction occur between a bacteriophage and an infected bacterium through the action of a bacteriophage (a virus that infects bacteria) (Reygaert, 2018). Conjugation is one of the most significant mechanisms of gene transfer horizontally. This process requires direct physical contact between bacterial cells, during which genetic material is transferred. This transfer occurs through the formation of a sex pilus, a plasmid is transferred in the recipient bacterium. In a single conjugation event, multiple there can be a few drug resistance genes located at the plasmid passing through the recipient bacterium, as a result, the recipient bacterium obtains the multidrug resistance (Graf et al., 2019; Wang et al., 2019; Gonzalez-Villarreal et al., 2022).

Adaptive drug resistance is characterized as the capacity of microorganisms to adapt reversibility and become resistant to one or more antibiotics in response to specific environmental signals. The drug resistance response to some environmental conditions, such as stress, growth state, pH, concentrations of ions, nutrient conditions, or exposure to sub-inhibitory levels of antibiotics. Adaptive drug resistance is temporary in nature, which is different from other types of drug resistance. (Sandoval-Motta and Aldana, 2016; D'Aquila et al., 2023). It enables bacteria to respond swiftly to antibiotic challenges, but once the inducing signal is no longer present, the bacteria typically revert to their original susceptibility to the antibiotics (Lazar et al., 2023).

There exists an inherent variation in the capacity of bacteria to restrict the entry of antimicrobial agents. The structures and functions of the lipopolysaccharide (LPS) layer in Gram-negative bacteria create a barrier against specific types of molecules. Consequently, these bacteria possess natural drug resistance to certain classes of prominent antimicrobial agents (Blair et al., 2014; Salam et al., 2023). Mycobacteria, on the other hand, have an outer membrane with a significant lipid content, making it easier for hydrophobic drugs like rifampicin and fluoroquinolones to penetrate the cell. However, the access to hydrophilic drugs is limited due to this hydrophobic barrier (Kumar and Schweizer, 2005; Baran et al., 2023).

The outer membrane of bacteria serves as a robust defense against undesirable substances. However, this protective barrier also hinders the entry of nutrient substances. To address this limitation, bacteria employ porins that enable the movement of hydrophilic molecules of certain sizes (Fernandez and Hancock, 2012).

Porins are beta barrel proteins that cross a cellular membrane and act as a pore, through which molecules can diffuse.

The porins are composed of a beta barrel structure that crosses cell membrane. The porins act as a pore with hydrophilic amino acids (AA) inside and hydrophobic AA locating at the position facing the outer membrane through which the molecule can pass and diffuse. This configuration creates a pore that facilitates the attraction and transportation of hydrophilic molecules entering the cell. While porins can exist as monomers, they are often found in stable trimers, and each unit is believed to function independently (Vergalli et al., 2020). Porins causing antibiotic resistance are associated with the decreased amount of porins or reduced porin protein expression.

In a clinical strain of Klebsiella pneumoniae, for example, a nonsense mutation in the OmpK36 porin cause the protein cannot translated correctly (Wozniak et al., 2012). However, the bacterium the development of compensated for this defect by up-regulating other selective porins, ensuring the maintenance of significance transportation of nutrient molecules. Such adaptation might lead to developing resistance to carbapenem antibiotics (Garcia-Fernandez et al., 2010). As a result, the penetration of antibiotics into the cell is limited, contributing to the bacterium’s innate resistance to antimicrobial agents.

The development of biofilms by certain microorganisms contribute to another mechanisms of resistance. Such biofilms are found in Escherichia coli, Staphylococcus epidermidis, and Pseudomonas aeruginosa. The feature of biofilm in organisms which are of great variety is the attachment to the surface via production of extracellular polymers. Biofilms can provide defense and attachment to bacterial cells with increased tolerance and resistance to antibiotics through various processes, including obstructing the penetration of antibiotics. The growth of biofilm-forming organisms is slower, this can be explained that limited by nutrient and oxygen can be utilized. Additionally, biofilms can reduce the of antibiotics across the biofilms, making it harder for antimicrobial agents to eliminate the bacteria within the biofilm effectively. As a result, bacteria in biofilms can evade the effects of antibiotics, leading to persistent infections that are challenging to the treatment (Van Acker et al., 2014; Hall and Mah, 2017; Dutt et al., 2022).

Bacteria can alter in the target sites of antibiotics is a mechanism of resistance, making it difficult or even ineffective for drugs to bind to the altered target. This alteration is caused by gene mutations for the expression of protein that composes the drug target site.

For example, in DNA gyrase if there are mutation in quinolone-resistance-determining region (QRDR), it will contribute to resistant to fluoroquinolone in microorganism (Ashley et al., 2017). Methylation of genes can be another strategy for the development of AMR. By utilizing erm methylases against macrolides, lincosamides, and streptogramin B antibiotics in both Gram-positive and Gram-negative bacteria (Saha and Sarkar, 2021). Additionally, methylation of the cfr gene has been associated with drug resistance development in various bacteria. Staphylococcus spp. demonstrate a decreased affinity to β-lactam antibiotics because the change of in the penicillin-binding protein sites (Foster, 2017). These modifications in drug targets are crucial factors contributing to bacterial resistance against specific classes of antibiotics (Darby et al., 2023).

Alteration in the ribosome results in AMR that impacts protein expression, including macrolides, tetracycline, chloramphenicol, aminoglycosides (AGs), etc. Aminoglycosides are bound to the 30S subunit of ribosome, while chloramphenicol, macrolides, lincosamides, and streptogramin B antibiotics bind to the 50S subunit of ribosome, causing the inhibition of protein expression (Lambert, 2002; Kapoor et al., 2017; Tarin-Pello et al., 2022).

Three primary enzymes are responsible for inactivating antibiotics, namely, β-lactamases, aminoglycoside-modifying enzymes, and chloramphenicol acetyltransferases (AACs) (Kapoor et al., 2017; Reygaert, 2018).

Specific enzymes neutralize aminoglycoside modifying enzymes (AGEs) by carrying out phosphoryl-transferases, nucleotidyl transferases, adenylyl-transferases, and AACs reactions (Costa et al., 2020; Jannat et al., 2022). These aminoglycoside-modifying enzymes (AMEs) alter the structure of aminoglycoside molecules, reducing their affinity and hindering their binding to the 30S ribosomal subunit. Consequently, AMEs provide extended spectrum resistance to aminoglycosides (AGs) and fluoroquinolones (FQs) (Strateva and Yordanov, 2009). AMEs have been identified in strains of S. aureus, Enterococcus faecalis, and Streptococcus pneumonia (Kapoor et al., 2017; Ahmadian et al., 2021).

Resistance to chloramphenicol is found in certain Gram-positive and Gram-negative bacteria, as well as some Haemophilus influenzae strains. These resistant bacteria produce an enzyme called chloramphenicol acetyltransferase, which acetylates hydroxyl groups of chloramphenicol (Tolmasky, 2000). This modified form of chloramphenicol loses its ability to bind to the 50S ribosomal subunit properly (Schwarz et al., 2004).

β-lactamases, for instance, can hydrolyze a wide range of β-lactam antibiotics containing ester and amide bonds, such as penicillin, cephalosporins, monobactams, and carbapenems (Diene et al., 2023). To date, approximately 300 different β-lactamases have been identified. These enzymes are broadly distributed and can be classified using two central systems: Ambler (structural classification) and Bush-Jacoby-Medeiros (functional classification). Here, we discuss the widely used Ambler classification of β-lactamases.

In the beginning, Ambler categorized β-lactamases into two primary groups (Salahuddin et al., 2018; Tooke et al., 2019): class A, which encompasses serine β-lactamases with active sites, and class B, which consists of metallo-β-lactamases reliant on a divalent metal ion, usually Zn²⁺, for their function (Hall and Barlow, 2005). Subsequently, a novel form of serine β-lactamases was uncovered, displaying modest sequence similarity to the pre-existing class A enzymes. This newly identified group was labeled as class C or AmpC β-lactamases. Furthermore, another set of serine β-lactamases, known as OXA β-lactamases, emerged. These enzymes are unlike the other types β-lactamases, prompting their classification as class D.

Drug modification is a frequently utilized strategy to render antibiotics ineffective, particularly in the case of aminoglycosides (e.g., kanamycin, gentamicin, and streptomycin), chloramphenicol, and β-lactams. Several AMEs have been identified in producer bacteria, including N-acetyl transferases (AAC), O-phosphotransferases (APH), and O-adenyltransferases (ANT) (Peterson and Kaur, 2018). These enzymes modify aminoglycoside antibiotics by acetylating, phosphorylating, or adenylylating them. The Streptomyces species produce these enzymes that show similar biological activities to the antibiotic-resistant clinical strains. But the connection between modification enzymes and the biosynthesis of aminoglycoside in the host is not clear (Benveniste and Davies, 1973). Certain species may harbor enzymes responsible for modification despite not producing antibiotics, and vice versa.

Streptomycin resistance is an exception as both antibiotic biosynthesis pathway and related enzyme responsible for modification in self-resistance are understood. For example, self-resistance of streptomycin in Streptomyces griseus is achieved by the 6-phosphotransferase that can transfer the active product to an inactive form streptomycin-6-phosphate (Christaki et al., 2020). The 6-phosphotransferase is involved in the last step in the streptomycin synthesis, and its production is affected by genes involved in synthesis pathway.

However, biological activities of the AMEs in the host bacteria are controversial (Munir et al., 2023). Some believe that AMEs are not involve contribute to resistance in host bacteria while might serve other metabolic functions (Martinez, 2018; Lu et al., 2023). The sequence analysis of AMEs demonstrated the diversity of these enzymes and are encoded by different genes. Since they have similar biological functions, they may experience different convergent paths for similarity. Indeed, these enzymes have certain sequence and structural similarity between AMEs and other cell metabolic proteins (Saleh et al., 2023).

Efflux pumps, responsible for extrusion of drugs and toxins from bacterial cells, are bacterial transport proteins that care classified into two types, primary and secondary transporters (Blair et al., 2014; Alenazy, 2022; Salam et al., 2023). The primary transporters belong to the ATP-binding cassette (ABC) family and activated via ATP binding and hydrolysis to facilitate efflux. On the other hand, the secondary transporters include various families, including the major facilitator superfamily (MFS), resistance nodulation division (RND) family, small multidrug resistance (SMR) family, and multidrug and toxic compound extrusion (MATE) family (Reygaert, 2018; Hajiagha and Kafil, 2023; Palazzotti et al., 2023).

These secondary transporters rely on the energy generated by the electrochemical potential of the membrane to drive the efflux process. For example, a recent study indicated that GI-M202a, in conjunction with the MFS transporter in Pseudomonas pnomenusa, played a crucial role in facilitating the transmission of polymyxin B resistance (Gao et al., 2023). The regulatory mutations result in the increased expression of efflux pumps and can cause MDR in the bacteria (Huang et al., 2022; Lorusso et al., 2022). This phenomenon has been predominantly observed in efflux systems belonging to the RND efflux family (Colclough et al., 2020). These regulatory mutations can enhance the efflux activity of these pumps, allowing the bacteria to expel multiple types of drugs and thereby develop resistance to various antibiotics. In cancer cells, MDR-related drug transporters, such as ABC transporters, are active in the efflux of drugs, conferring MDR to cancer cells (Banerjee et al., 2023; Bo et al., 2023; Fan et al., 2023).

Acinetobacter baumannii is an MDR pathogen commonly found in healthcare settings, where choices for treatment are frequently restricted. The overexpression of AdeABC, one of the multidrug RND efflux pump is responsible for the drug resistance of A. baumannii (Colclough et al., 2020). The increased number of RND efflux pumps causes the A. baumannii resistant to an extensive variety of antibiotics, such as aminoglycosides. It reduces susceptibility to fluoroquinolones, tetracycline, tigecycline, chloramphenicol, erythromycin, trimethoprim, netilmicin, meropenem, and even the dye ethidium bromide. Studies of clinical MDR strains of A. baumannii have demonstrated that the primary contributor to drug resistance is often the AdeABC efflux pump. This significantly constrains the potential treatment choices against this microorganism (Ragueh et al., 2023). Consequently, tigecycline is regarded as the last-resort antibiotics for addressing infections brought about by MDR Gram-negative bacteria (Hornsey et al., 2011).

Drug resistance/tolerance can be assessed using killing assays like time-kill curves, which display a bimodal killing pattern in cases of drug persistence (Foerster et al., 2016). However, these assays are labor-intensive and show significant variability, necessitating numerous repetitions and making them less feasible for routine clinical microbiology. Moreover, the levels of antibiotic persistence observed in vitro in laboratories might not accurately reflect the persistence levels in patients from whom the bacterial strains were isolated, considering the complex factors contributing to this unstable phenomenon. Consequently, measurements of antibiotic persistence in laboratory conditions only offer approximations of bacterial behaviors during in vivo infections. Nonetheless, they still provide essential supplementary information to aid physicians in making therapeutic decisions (Huemer et al., 2020).

An alternative method for testing drug tolerance is the “Replica Plating Tolerance Isolation System” (REPTIS), developed by Hiramatsu and colleagues, which has proven successful in identifying and selecting ciprofloxacin (CIP)-tolerant mutants in S. aureus (Matsuo et al., 2019). REPTIS does not require adjusting antibiotic concentrations, addressing this limitation. In this method, a sterile silk cloth transfers colony-forming units (CFUs) onto a fresh plate (replica plate) where surviving bacteria can grow. The level of drug tolerance is determined by counting the number of growing bacteria within the former inhibition zone. While REPTIS cannot detect induced antibiotic persistence, it holds the potential for adaptation in automated use within diagnostic microbiology laboratories.

The MALDI-TOF MS-based approaches are utilized for the efficient antimicrobial resistance identification (Florio et al., 2020). This technology has been investigated for detecting antimicrobial resistance in pathogenic fungi (Florio et al., 2018). The aim is to address the urgent need for identifying drug resistance patterns quickly and accurately, allowing clinicians to make informed treatment decisions for better patient outcomes. A detection protocol using MALDI-TOF MS was explicitly studied for Carbapenemase-Producing Organism (CPO), Bacteroides fragilis, a Gram-negative strain carrying the drug resistant gene cfiA that can encode the carbapenemase enzyme (Johansson et al., 2014).

Antimicrobial resistance is a crucial global health challenge, and unfortunately, there is no straightforward remedy (Morrison and Zembower, 2020; Kaur et al., 2022; Talaat et al., 2022). Current endeavors revolve around enhancing diagnosis, antibiotic-prescribing methods, and infection prevention strategies to combat this issue. Nevertheless, the development of new antimicrobial compounds has been limited, and those under consideration often do not belong to new antibiotic classes (Spizek, 2018). Additionally, the effectiveness of new antimicrobials is compromised by the rapid adaptability of microorganisms, leading to their potential short lifespan. Consequently, innovative treatment approaches are indispensable in the battle against both existing and evolving antimicrobial resistance (Blair et al., 2014; McEwen and Collignon, 2018). Figure 2 shows the contemporary strategies employed to combat microbial resistance.