Escherichia coli is classified within the order Enterobacterales and family Enterobacteriaceae (1). E. coli exhibits notable versatility as a bacterial species, characterized by a comprehensive phylogenetic substructure. More than 160 E. coli serotypes have been categorized according to their major surface antigens, namely H (components of flagella), O (oligosaccharide polymer), and K (capsular polysaccharides) (Tuttle et al., 2021). E. coli can be classified into various groups based on its genetic substructures that are linked with different phylogenies. E. coli can be categorized using this method into the following groups: A, B1, B2, C, D, E, F, and clade. The pathogenic E. coli strains that cause infections outside the intestine often belong to groups B2 and D, while the non-pathogenic E. coli strains are typically classified as belonging to groups A or B1. Groups E and F are associated with the primary groups B2 and D. It is noteworthy that E. coli strains showing an identical phenotype but having different genetic makeup are categorized under the concealed clade I group. E. coli is a familiar commensal bacterium that colonizes the gut soon after birth. It competes successfully in the human gut and is the most prevalent facultative anaerobe in the human intestinal microbiota (Pais et al., 2022).

Even though E. coli is a widely recognized bacteria that lives in harmony with its host, numerous hazardous strains of E. coli exist. Certain strains of E. coli have adapted to their environment and have developed particular virulence factors that enhance their ability to adjust to new surroundings, thereby enabling them to cause a range of illnesses, including both intestinal and extraintestinal infections. The classification of pathogenic E. coli: E. coli that produce Shiga toxins (STEC), enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), and diffusely adherent E. coli (DAEC), Shigella/enteroinvasive E. coli (EIEC), enterotoxigenic E. coli (ETEC) and adherent-invasive E. coli (AIEC). Diarrhea due to E. coli is classified particularly as a leading cause of mortality and desolation in nations that are still developing associated with bacterial infections among other pathogens. Infectious diarrhea is associated with moderate mortality and is generally less severe in industrialized countries but affects many people and represents a significant disease burden ( Figure 1 ). These classifications are based on the acquisition of virulence factors and the characteristics of the resulting illness (Mafokwane et al., 2023; Mueller and Tainter, 2023).

The ailments comprise stomach flu, inflammation of the colon, bloody diarrhea, Hemolytic uremic syndrome (HUS), bladder infection, blood poisoning, lung inflammation, and brain membrane inflammation. Certain of these illnesses pose a considerable risk of death if not handled appropriately, hence it is crucial to combat them with highly potent antibiotics (Rahal et al., 2012). Nevertheless, in recent times, the primary worry has been the rising instances of foodborne epidemics in high income nations, brought about by harmful E. coli present in tainted meat, fruits, and vegetables (Mohamed and Habib, 2023). ExPEC is by far the leading cause of urinary tract infection (UTI) (hence the label uropathogenic E. coli [UPEC]) and bacteremia (Russo and Johnson, 2003). E. coli isolates are typically classified operationally as ExPEC based on their presumed intrinsic virulence potential as inferred from the presence/absence of specific putative or proven virulence genes irrespective of their immediate source of isolation. Thus, a molecular typing tool is needed for determination of whether an anonymous isolate is likely ExPEC or non-ExPEC. In contrast with ExPEC, the E. coli strains that cause diarrhea are referred to collectively as diarrheagenic E. coli (DEC) or intestinal pathogenic E. coli (IPEC). Additionally, in contrast with both ExPEC and DEC, nonpathogenic commensal E. coli strains colonize the human intestine without causing disease and may even be beneficial to the host by harvesting energy, protecting against other pathogens, or regulating host immunity. There is, however, a thin line between the definition of virulence and fitness factors in ExPEC and commensals. It has been suggested that ExPEC virulence might be a by-product of the commensal lifestyle (Malberg Tetzschner et al., 2020).

Simple UTIs, the most frequent bacterial infections worldwide, are caused by UPEC in between 50% and 90% of cases. Both genders can have UTIs, but women are more vulnerable due to their physiological and anatomical differences (i.e. the urethra is shorter and more proximal to the rectum). According to earlier studies, 50% of women and 15% of men, respectively, would get at least one UTI in their live s (Minardi et al., 2011; Whelan et al., 2023).

Managing UTIs is becoming increasingly difficult due to the growing resistance of UPEC to commonly prescribed antimicrobial drugs. Several recent guidelines have repositioned nitrofurantoin as a first-line antibiotic for the treatment of lower UTI. While the prevalence of nitrofurantoin resistance remained low (Giske, 2015). Besides nitrofurantoin, fosfomycin is another important oral antibiotic for the treatment of uncomplicated UTI. In several Asian countries, fosA3 currently is the main mechanism of fosfomycin resistance in E. coli (Ho et al., 2013a, b). The commonly used antimicrobial agents for UTIs include β-lactams such as penicillin, cephalosporins, monobactams, and carbapenems (Raunak et al., 2022). In addition to the increasing frequency of E. coli infections, their persistent drug resistance is a serious issue. Enterobacteriaceae strains that are multidrug-resistant (MDR) extremely drug-resistant (XDR) and resistant to nearly all current antibiotics have emerged as a result of recent evolution (Kot, 2019). MDR are labelled as such because of their in vitro resistance to more than one antimicrobial agent. Infections with MDR can lead to inadequate or delayed antimicrobial therapy, and are associated with poorer patient outcomes. XDR means resistance to multiple antimicrobial agents, but also to their ominous likelihood of being resistant to all, or almost all, approved antimicrobial agents. From the Greek prefix ‘pan’, meaning ‘all’, pandrug resistant (PDR) means ‘resistant to all antimicrobial agents (Magiorakos et al., 2012). According to several studies, 4 of 19 low- and middle-income countries (LMICs) in Genes 2022 have high rates of MDR UPEC isolates, ranging from 42% in China to 49.8% in Iran and alarming 68% in Pakistan or even 98% in Mexico ( Table 1 ). Age, recurrent UTIs, catheterization, previous use of antibiotics, hospitalization, nursing home stays, urinary tract abnormalities, and nursing home residence have all been identified as risk factors for the emergence of MDR strains (Genao and Buhr, 2012).

ESBL stands for Extended Spectrum β-Lactamase. β-lactamase enzymes break down and destroy some commonly used antibiotics, including penicillins and cephalosporins, and make these drugs ineffective for treating infections. ESBL production is associated with a bacterium usually found in the bowel. This resistance means that there are fewer antibiotic options available to treat ESBL-producing Enterobacterales infections. The primary curative antibiotics for ESBL-producing E. coli were cephalosporin and carbapenem; nevertheless, following the emergence of carbapenem-resistant E. coli isolates (CREC) and the global spread of these variants, polymyxin, tigecycline, fosfomycin, and aminoglycosides, either alone or in conjunction with other antibiotics, are the antibiotics that continue to be efficacious against CREC (Terbtothakun et al., 2021). Nevertheless, research has indicated that infections triggered by E. coli strains that are resistant to carbapenem are linked to elevated mortality rates as they are resistant to numerous categories of antibiotics, such as fluoroquinolones, trimethoprim-sulfamethoxazole, and broad-spectrum cephalosporins (Kot, 2019).

Various mechanisms of resistance are exhibited by E. coli strains, including the production of different β-lactamase enzymes, lowered permeability of the membrane, formation of capsule and biofilm, employment of efflux pumps, and enzymatic modification. E. coli strains that are MDR or XDR employ various means of dissemination, such as the transfer of high-risk mobile genetic elements – including plasmids and transposons – containing multiple antibiotic resistance genes (ARGs). Antibiotic resistance results in restricted options for therapy, extended hospitalization durations, elevated expenses for treatment, and increased mortality rates. The rise in resistance to antibiotics and the lack of effectiveness of antibiotic treatments highlight the pressing necessity for the creation of alternative methods for treating UTIs. Most studies indicate that antimicrobial therapy for UTI requires regular antibiotic susceptibility testing to minimize the spread of MDR isolates. However, in LMIC antibiotics can be purchased over the counter, many people will just go to a pharmacy rather than get a prescription. Additionally, ongoing analysis of the antimicrobial susceptibility profiles of isolates from the UPEC in various regions would be highly beneficial in preventing the establishment of MDR or XDR clones (Perez and Van Duin, 2013; Kot, 2019; Sarshar et al., 2020).

Furthermore, exploring the processes behind the origin and dissemination of novel instances of antibiotic resistance is crucial for refining the recommendations for empirical antibiotic therapy for UTIs. Therefore, the goal of this review is to assess recent research and updates on AMR and the mechanisms that underlie changes in antibiotic resistant UPEC strains. We will also look at the many strategies used by E. coli to build resistance to numerous antibiotics.

To find relevant documents describing the mechanisms for resistance in pathotypes of E. coli, we searched PubMed (https://pubmed.ncbi.nlm.nih.gov/), Scopus and Google Scholar using the following search terms: (“Escherichia coli” OR “uropathogenic Escherichia coli” OR “UPEC”) AND “ antibiotic resistance mechanisms “. We also searched the resulting reference lists to identify additional articles.

Microorganisms use the formation of biofilms as a crucial survival strategy. Biofilm formation occurs in three main stages of biofilm formation have been identified: bacterial adhesion, quorum sensing (QS), and biofilm biomass formation (Li et al., 2023). Biofilms enable bacteria to withstand unfavorable conditions, including antibiotics. As a virulence factor, the biofilm enables the organism to adhere to both living and non-living surfaces and form tiny colonies that can multiply and protect themselves from the effects of antimicrobial treatments (Sharma et al., 2019; Nasrollahian et al., 2022). Apart from protecting pathogens against opsonization by antibodies, antimicrobial peptides, and phagocytosis, biofilms also prevent bacteria from being expelled by epithelial cells through the action of their cilia. Antibacterial chemicals are substantially less likely to harm bacterial populations in biofilms than they are to harm free-living bacteria. Because of this, biofilms can cause persistent infections that are difficult to treat, which is a serious public health concern (Nasrollahian et al., 2022). A self-made extracellular matrix that frequently consists of exopolysaccharides, amyloid fibers, secreted proteins, and extracellular DNA holds biofilms together and serves as their protective covering (Erskine et al., 2018). One process that facilitates the development of E. coli and helps it survive in the gastrointestinal, respiratory, and urinary tracts, ultimately leading to invasive infections (especially in individuals with weakened immune systems) and impeding its elimination is the creation of biofilms. Several genes, including rpoS, sdiA, and rcsA (biofilm-associated gene), play a significant role in biofilm formation and the acquisition of antibiotic resistance. Research has shown that the presence of adhesins such as FimH and MrkD is associated with the development of biofilms (Zhao et al., 2020) ( Figure 2 ). Different chemical gradients being established throughout the biofilm community, in combination with limited diffusion and the metabolic activity of resident bacteria, leads to the emergence of distinct subpopulations that often cooperate metabolically but respond differently to the microenvironment depending on their location along the gradient (Penesyan et al., 2020). QS is a regulatory system that controls cell density which regulates gene expression by sensing the concentration of small-signal molecules called autoinducers (AIs) that are synthesized and released by bacterial cells. Specifically, inhibition of biofilm formation can be achieved by either interference with the QS mechanism, adhesion mechanism, or disruption of EPS. Genetically, each stage of biofilm formation of E. coli is associated with activating a different set of genes such as luxS, fimH csgD, and bolA that regulates the expression of its virulence factors. Particularly in E. coli, the luxS gene is required to produce AI-2, which mediates the QS mechanism, stimulates biofilm formation, and regulates the biofilm architecture (Alshammari et al., 2023).

In addition, the link between the development of biofilms and antibiotic resistance has drawn the interest of numerous researchers. Prior investigations conducted on Pseudomonas aeruginosa and E. coli have highlighted the significance of oxygen gradients in regulating the varied gene expression related to metabolic specialization and biofilm formation (Beebout et al., 2019). It has been observed in earlier studies that biofilm development can be stimulated by certain antibiotics when administered in low concentrations, implying that the control of biofilms may be a part of the overall reaction to external stressors, such as antibiotics (Penesyan et al., 2020).

E. coli is protected by biofilms from the immune system and antibiotic therapy. Compared to planktonic bacteria, bacteria in biofilms are up to 1000 times more resistant to drugs. The following processes are the primary causes of antibiotic tolerance among bacteria in biofilms: reduced growth rates and stress responses, limited antimicrobial penetration, persister cells, efflux pumps, and horizontal gene transfer (Ballén et al., 2022).

Currently, there are multiple records regarding the links between the resistance to antibiotics and the creation of biofilms by E. coli strains. E. coli employs various strategies to guard against different antimicrobial agents. The effects of various antibiotics on E. coli biofilm have been studied, including amikacin (AN), cephalosporins (CE), ceftazidime (CAZ), cefoperazone (CFP), cefepime (FEP), piperacillin (PEF), piperacillin-tazobactam (PTZ), ciprofloxacin (CP), gentamicin (GM), meropenem (MEM), and netilmicin (INN). These findings show that bacterial populations do not survive in their free-living state but do survive in biofilm. According to studies by Fei Zhao et al., E. coli exposed to ampicillin showed the highest rates of antibiotic resistance, followed by tetracycline, with resistance rates of 74.6% and 64.9%, respectively (Fuzi et al., 2017). As a result, some studies have shown that there is a significant association between the formation of biofilm and antibiotic resistance and virulence genes. Another study by Davari Abad et al. found a substantial relationship between the expression of the sfa (S fimbriae) gene and the development of robust biofilms (Davari Abad et al., 2019).

A study by Qian et al. explored the relationship between antibiotic resistance, biofilm formation, and biofilm-specific resistance in E. coli strains collected from children in China. According to the research, isolates that were susceptible to or had intermediate resistance to cefoxitin (CFX), ceftriaxone (CTX), cefazolin (CFZ), and GM were unable to produce as robust of biofilms as their resistant counterparts. This suggests that there is a correlation between the ability of a bacterium to form a biofilm and its resistance profile. Additionally, the results revealed that non-susceptible isolates exhibited higher levels of biofilm formation compared to susceptible isolates in six categories, namely quinolones, fluoroquinolones, cephalosporins, aminoglycosides, macrolides, tetracyclines, and nitrofurans. The formation of biofilm was found to be similar in E. coli strains that were susceptible and those that were not susceptible to β-lactams and lipopeptides (Qian et al., 2022). A systematic review and meta-analysis found that UPEC isolates that cause UTI frequently develop biofilms. The findings showed that out of 37 studies, 17 have looked into the relationship between the production of biofilms and antibiotic resistance. Of them, 14/17 (82.4%) showed a direct link between the development of biofilms and antibiotic resistance. Interestingly, ESBL producers and MDR isolates exhibited a significantly higher ability to produce biofilms (Garousi et al., 2022). According to recent research from Iran, 58% of the 107 UPECs that produced biofilm were ESBL producers, with 50% of them testing positive for the AmpC gene and 40% for the carbapenemase gene (Qasemi et al., 2022).

CRISPR/Cas systems in E. coli act as a defense mechanism against mobile genetic elements, such as plasmids and phages, which are involved in the horizontal spread of resistance genes. When E. coli encounters foreign genetic material, the CRISPR/Cas system can capture and integrate fragments of this material into its own genome. These captured sequences, known as spacers, serve as a memory of past infections. During subsequent encounters with the same genetic material, the CRISPR/Cas system uses these spacers to recognize and target the invading DNA for destruction. This defense mechanism helps E. coli combat the horizontal transfer of resistance genes carried by mobile genetic elements. By targeting and cleaving the DNA of these elements, CRISPR/Cas systems can prevent the spread of antibiotic resistance within bacterial populations. Studies have shown that CRISPR/Cas systems play a crucial role in limiting the acquisition of antibiotic resistance genes by bacteria like E. coli, thereby aiding in the control of antibiotic resistance development and spread (Mayorga-Ramos et al., 2023 and Dziuba et al., 2023).

Mobile genetic elements, such as plasmids and transposons, play a significant role in the horizontal transfer of resistance genes in E. coli. These elements can carry genes that confer resistance to antibiotics, heavy metals, and other environmental stresses. When these mobile genetic elements are transferred between bacteria, they can spread resistance traits rapidly within bacterial populations. In E. coli, the transfer of resistance genes via mobile genetic elements contributes to the development and dissemination of antibiotic resistance. This horizontal gene transfer allows bacteria to acquire new resistance mechanisms, leading to the emergence of multidrug-resistant strains that pose a serious threat to public health. The ability of mobile genetic elements to transfer resistance genes between bacteria highlights the importance of understanding and monitoring the spread of these elements in combating antibiotic resistance in E. coli and other pathogenic bacteria (Liu et al., 2023 and Jeon et al., 2023).

The administration of four primary groups of β-lactam antibiotics, which comprise carbapenems, cephalosporins, penicillin, and monobactams, as novel therapeutic agents, has been associated with the proliferation of β-lactamases. The following section will examine ESBLs, carbapenemases, β-lactam/β-lactamase inhibitors, and AmpC β-lactamase.

Particularly in Enterobacteriaceae, genes that produce ESBL and carbapenemase frequently have a high rate of transmission through plasmids that also carry other resistance genes. When both resistances are present in the same strain, they are often on different plasmids since ESBL and carbapenemases are connected with different plasmids (Tilahun et al., 2021).

Current research endeavors to elucidate the reasons behind certain lineages exhibiting greater adaptability in acquiring and retaining these plasmids while avoiding any negative impact on their fitness. It is suggested that these clones may be able to outcompete commensal strains of the same species and establish protracted intestine colonization through the appearance of adaptive mutations in intergenic areas and selective pressure on genes linked to anaerobic metabolism (Dunn et al., 2019).

As a result, it has been suggested that ESBL-producing bacteria may be resistant to antibiotics other than carbapenems, such as fluoroquinolones, tetracyclines, and sulfonamides. They were found to be either CTX-M enzyme variations or TEM and SHV variants. It is more common in environmental isolates, indicating that the environment contains ESBL-producing organisms. This has a significant impact on the use of antibiotics, the price of treatment, patient outcomes, and the range of available treatments (Rawat and Nair, 2010).

The use of carbapenem antibiotics is generally reserved for the treatment of MDR infections; nevertheless, the emergence of carbapenemases diminishes their therapeutic potency. Carbapenemases are β-lactamases that hydrolyze carbapenems and monobactams to variable degrees as well as penicillins, often cephalosporins, and other β-lactams (Kattan et al., 2008).

CRE has grown significantly in importance as a global public health issue since the initial report in the early 1990s. The extensive usage of ESBLs is believed to have increased the use of carbapenems and contributed to the emergence of carbapenem resistance. More than 13,000 hospitalized cases due to CPE occurred in 2017 alone, according to a study from the Centers for Disease Control and Prevention (CDC) (Goodman et al., 2019). Additionally, according to the Turkish Ministry of Health, in hospitalized patients in 2020, carbapenem resistance was found to be 20.1% in E. coli strains and 75.2% in K. pneumoniae strains (Uyanik et al., 2022).

According to recent investigations, CREs are found in water and cattle in addition to hospitalized people. Five important carbapenems are regarded as KPC, NDM, OXA-48-like, VIM, and IMP-type. ESBL-producing bacteria derived from clinical samples may be carbapenem-resistant and possess the genes bla _OXA-48 , bla _{NDM -1}, bla _KPC , bla _IMP, and bla _VIM (Uyanik et al., 2022).

Individual antibiotic resistance genes are associated with particular pathogenic clones that are molecularly categorized by their sequence type (ST) at the strain level. For instance, CREC is frequently linked to the ST167, ST617, ST410, and ST38 lineages of E. coli, while E. coli ST131 frequently expresses ESBL enzymes (Palomino et al., 2023).

Multiple plasmids carrying are associated with higher fitness costs for the host bacterium. The availability of carbapenemase-producing Enterobacteriaceae has limited the range of antibiotics that can be used to treat ESBL infections. As an alternative, a combination of β-lactam/β-lactamase inhibitors like PIP-TZM may be used to treat these infections. New studies indicate that the use of β-lactam/β-lactamase inhibitor antibiotics as an alternative to carbapenem antibiotics is a significant and advantageous strategy for empirical therapy. However, the increasing prevalence of E. coli strains resistant to β-lactam/β-lactamase inhibitors present a hurdle to this therapeutic approach (Wilson and Török, 2018).

Some molecular tactics for antibiotic resistance are used by bacteria, including mutation, post-translational modification, and avoidance of antibiotic binding. Antibiotics may also be broken down inside the cell if they are unable to alter the bacterial metabolism. In this process, the participation of enzymes is crucial (Munita and Arias, 2016).

All bacteria possess efflux pumps, which are the main mechanism for MDR and drug resistance. Bacterial genomes often encode a number of efflux pumps, which are in charge of removing a wide range of substances from inside the cell. When overexpressed, efflux pumps have a significant impact on both the intrinsic drug sensitivity of a bacterial species as well as the development of clinically significant antibiotic resistance. The increased expression of efflux pump genes could be due to mutations in regulators or the insertion of IS elements that act as powerful promoters upstream of these genes. Mobile genetic elements can also be used to acquire new pump genes (Li and Nikaido, 2009; Soto, 2013).

Efflux pumps, which facilitate bacterial pathogenicity and medication resistance, are attracting medical professionals seeking treatments for MDR, with drug efflux pump inhibition potentially treating various health issues. Tetracycline-specific efflux pumps, or Tet pumps, provide strong resistance to tetracyclines, whereas multidrug efflux systems export a broad spectrum of substrates, frequently including several drugs (Li and Nikaido, 2009; Grossman, 2016).

The seven unique efflux pump superfamilies that are present in bacteria have been rigorously described and characterized by microbiological, biochemical, and structural studies. Specific criteria, such as membrane topology, membrane-spanning properties, energy sources, substrate specialization, primary sequence similarity, and the stoichiometry of multi-subunit complexes, are used to categorize members of these families. Efflux pumps are classified into seven main categories: ATP-binding cassette (ABC), major facilitator (MFS), multidrug and toxic compound extrusion (MATE), small multidrug resistance (SMR), resistance-nodulation-cell division (RND), proteobacterial antimicrobial compound efflux (PACE), and p-aminobenzoyl-glutamate transporter (AbgT) ( Figure 4 ) (Chetri et al., 2019; Nishino et al., 2021). It is worth mentioning that ABC transporters require ATP to function, while other efflux systems generate energy from the potential gradient of protons.

Phospholipids, LPS, lipoproteins, and β-barrel porins make up the distinctive architecture of the OM of GNB. Toxic substances like bile acid and antibiotics are prevented from being transported by the OM, which acts as an extra barrier. As a result, substances with molecular weights more than 600 Da typically cannot pass through the GNB’s outer membrane. As a result, antibiotics like vancomycin and daptomycin, which have molecular weights more than 1400 Da, cannot cross the OM of GNB. Invasion, adherence, serum resistance, and antibiotic resistance all depend heavily on OMs. Some OMs in ESBL-producing bacteria have been removed, making it easier for resistance elements to transfer. The porins, which come in a variety of forms, are the OM proteins found in GNB in the highest abundance. Based on their action, they can be categorized as non-specific or specific porins (Choi and Lee, 2019).

In accordance with their functional structure, they are further divided into mono-, dimeric- or trimeric OM-spanning β-barrels porins. Porins play a pivotal role, not only in preserving the structural integrity of the GNB envelope, but also in facilitating the passive diffusion of various compounds. For example, the non-specific porin, known as outer membrane protein A (OmpA), enables the passive transport of a wide range of small molecules. This is a peptidoglycan-linked protein that engages with peptidoglycan through non-covalent interactions and possesses a flexible periplasmic domain. Porins are tightly linked to antibiotic resistance in GNB because they promote the passive diffusion of drugs across the OM (Choi and Lee, 2019). For instance, the non-specific porin OmpF has been shown to allow β-lactams and fluoroquinolones to enter the OM. As a result, some GNB, such as E. coli, K. pneumoniae, Serratia marcescens, P. aeruginosa, and Enterobacter aerogenes, were resistant to a number of β-lactam antibiotics. On the other hand, deletion of OmpA raised A. baumannii’s resistance to a number of antibiotics, including β-lactams. The complexity of porin-mediated antibiotic resistance, according to Choi et al., was demonstrated by their findings. Rather than transporting antibiotics, OmpA is critical for maintaining the integrity of the membrane. These OmpA functions require the C-terminal domain. OmpF is linked to membrane permeability and antibiotic transport, yet the ompF mutant displays antibiotic resistance characteristics. Increased susceptibility to antibiotic was not found. These effects of OmpF on membrane integrity could be the cause of these outcomes. A significant porin for the OM permeability for β-lactams is known to be OmpF. Multiple β-lactam antibiotics were much more resistant to the ompF mutant. A novel porin, YddB, which appears to be involved in the passive transport of novobiocin across the OM, was also discovered by them through their thorough analysis of porins peculiar to E. coli. The purpose of YddB, an outer membrane protein with a projected β-barrel shape, is unknown. Compared to the wild-type strain, the yddB mutant exhibits a markedly lower susceptibility to novobiocin. The deletion of any porin gene did not change the MIC of novobiocin, hence YddB appears to be a significant porin that is in charge of novobiocin’s OM penetration. The function of particular porins for antibiotic transport is only marginally significant, save from specific examples like YddB and LamB. Most non β-lactam antibiotics appear to penetrate the OM in a porin-independent manner, but the majority of β-lactam antibiotics are transported with non-specific porins, particularly OmpF and OmpC (Choi and Lee, 2019; Rodrigues et al., 2022).

The alteration of LPS by phosphoethanolamine (pEtN), galactosamine, hydroxylation, palmitoylation, and 4-amino-4-deoxy-L-arabinose (L-Ara4N) is linked to resistance to polymixins and cationic antimicrobial peptides. Among Enterobacteriaceae family species, the pmrHFIJKLM or pbgPE operon adds a 4-amino-4-deoxy-l-arabinose residue to lipid-A in the LPS structure. Due to this change, colistin’s affinity for LPS is reduced. Moreover, the pmrHFIJKLM operon is upregulated and the expression of the transmembrane protein (Mgr B) is downregulated by the PhoQ/PhoP and PmrAB signaling systems in response to acidic pH, cation concentration, and antimicrobial peptides. Clinical isolates of E. coli have been reported to show increased expression of the PhoQ/PhoP and PmrAB signaling systems due to point mutations or the insertion of sequences like IS5-like, IS1F-like, and ISKpn14 in the mgrB B gene. By using mcr-1-8 plasmids, another method of LPS modification is carried out. pEtN Transferase, which is encoded by Mcr-1 plasmids, changes the lipid in LPS molecules by including pEtN. Additionally, pEtN transfer is connected to the pmrC gene in Pmr signaling circuits. The CrrA/CrrB 2CS element and crrC appear to regulate PmrAB signaling circuits. There have been reports that the deletion or dysfunctional mutation of the crrC gene causes colistin resistance (Azam et al., 2021; Karami-Zarandi et al., 2023).

Currently, antibiotics such as cefiderocol, colistin, fosfomycin, nitrofurantoin, and tigecycline can successfully treat UPEC strains that are resistant to carbapenem. Different nations have different levels of antimicrobial agent resistance ( Figure 5 ) (Walker et al., 2022).

The FDA approved cefiderocol, a new type of cephalosporin antibiotic that acts as a siderophore, on November 14, 2019 for treating complicated UTIs in adults. Studies have demonstrated its effectiveness against carbapenem-resistant UPEC strains that belong to all Ambler classes, including those that produce ESBL, AmpC, KPC, and NDM-1 (El-Lababidi and Rizk, 2020; Walker et al., 2022).

Cefiderocol interacts with iron transport channels, allowing it to penetrate the bacterial outer membrane and infiltrate the periplasmic space, akin to a ‘Trojan horse’ strategy. Within this space, it achieves elevated concentrations, surpassing the resilience of most bacterial defense mechanisms, including efflux pumps, porins, and beta-lactamases. Subsequently, once inside, Cefiderocol binds to specific PBPs - PBP-3 and PBP-2, which are essential for cell wall synthesis. This binding inhibits the synthesis of peptidoglycan in the bacterial cell wall, ultimately resulting in cell lysis and bacterial death (Syed, 2021; Soriano et al., 2022). Cefiderocol can also circumvent other common β-lactam resistance pathways in GNB, like efflux pump up-regulation and porin deficiency (Bavaro et al., 2021).

Bassetti et al. conducted a phase 3 study involving patients with nosocomial pneumonia, bloodstream infections, or complicated UTIs caused by carbapenem-resistant GNB. The study found that cefiderocol was able to achieve microbiological eradication in 53% of patients with UTI, while only 20% of patients in the BAT group with UTI were able to achieve the same result (Bassetti et al., 2021). In a separate phase 2 trial involving patients with UTI caused by various carbapenem-resistant pathogens, including E. coli, cefiderocol was found to be more effective than imipenem-cilastatin, with a cure rate of 73% compared to 55% (p = 0.0004) (Portsmouth et al., 2018).Wang et al. reported A total of 26 E. coli isolates harboring NDM-5 showed high levels of cefiderocol resistance. They found 4 amino-acid insertions (YRIN/YRIK) at position 333 of PBP3 in the 26 E. coli isolates is associated with high levels of cefiderocol. According to Wang et al, 26 E. coli isolates that carried NDM-5 were found to be highly resistant to cefiderocol. The researchers identified four amino acid insertions (YRIN/YRIK) at position 333 of PBP3 in these isolates, which were linked to the high levels of cefiderocol resistance observed (Portsmouth et al., 2018).

Due to the limited rates of documented resistance, nitrofurantoin is still an effective first-line therapy and prevention for less severe UTIs (Tutone et al., 2022). The distinct and poorly known method of action of nitrofurantoin may explain why resistance to it develops more slowly than to other antimicrobials. The nfsA and nfsB genes produce enzymes called nitroreductases that are used by carbapenem-resistant GNB to break down nitrofurantoin into different antibacterial metabolites. These enzymes are not affected by the absence of oxygen ( Table 3 ) (McOsker and Fitzpatrick, 1994). The lowering of NF and the consequent formation of hazardous chemicals are prevented by this mutation. To exert a bacteriostatic effect, the metabolites bind to bacterial ribosomes and stop protein synthesis in addition to inhibiting enzymes involved in the citric acid cycle and those in charge of DNA and RNA synthesis. For the first time, nitrofurantoin resistance in E. coli has been documented, and it has been determined that this resistance is caused by a mutation in the gene that codes for the oxygen-insensitive enzyme nfsA. The lowering of NF and the consequent formation of hazardous chemicals are prevented by this mutation (Mahdizade Ari et al., 2023). The nfsA and nfsB genes’ deletion and insertion mutations are the primary cause of nitrofurantoin resistance. Furthermore, resistance may result from mutations in the ribE gene, which codes for the enzyme lumazine synthase, which is necessary for the synthesis of the nfsA and nfsB cofactor flavin mononucleotide (Wan et al., 2021).

High levels of NF resistance (median MIC of 96 mg/ml) are mostly caused by mutations in the oxygen-insensitive nitroreductases nfsA and/or nfsB (Mahdizade Ari et al., 2023). Plasmid-mediated resistance to nitrofurantoin is another possibility. First off, a number of plasmid types carry the multidrug-resistant flux gene oqxAB, which is frequently flanked by IS26, which contains the transposon Tn6010 (Ho et al., 2016). High-level nitrofurantoin resistance is caused by nfsA inactivation together with expression of the oqxAB gene; however, it is not known if high level resistance can also be caused by oqxAB gene isolation. Unlike other types of resistant bacteria, those that are resistant to nitrofurantoin have been found to have a higher occurrence of efflux genes that also make them resistant to β-lactams, cephalosporins, aminoglycosides, carbapenems, and tetracyclines. Additionally, 51% of them have been shown to have XDR. According to reports, 1.1% and 1.8%, respectively, of E. coli bacteria identified from UTI patients in the United States and France are NF resistant (Whelan et al., 2023).

According to clinical studies, nitrofurantoin usage increased antibiotic resistance in comparison to trimethoprim and cotrimoxazole in the control group of patients who received this antibiotic as prophylaxis. The research by Fisher et al., in which patients had been on nitrofurantoin for 9–12 months before surgery, cited this as its most significant finding (Fisher et al., 2018). Additionally, these results support research by Pickard et al. that discovered higher antibiotic resistance in bacteria isolated from individuals who had taken oral nitrofurantoin as a preventative measure (Pickard et al., 2018). It is therefore advised that nitrofurantoin only be used to treat UTI cases where other antibiotic resistance is present (Mahdizade Ari et al., 2023).

A broad-spectrum phosphonic antibiotic with bactericidal action against both Gram-positive and Gram-negative pathogens, fosfomycin was initially developed in Spain in 1969 (Findlay et al., 2023). Both oral and intravenous preparations of fosfomycin are offered for usage. Fosfomycin can be taken orally as fosfomycin trometamol and fosfomycin calcium, whereas fosfomycin for intravenous use comes in a formulation that contains succinic acid as an excipient and disodium in a ratio of 1 g to 8 g. Although oral formulations have been demonstrated to help treat male UTIs and acute bacterial prostatitis, they are not indicated as a first-line treatment for uncomplicated UTIs in women with infections caused by E. coli (Whelan et al., 2023). This is because after injection, higher intraprostatic concentrations are also attained in addition to the urine. Similar to nitrofurantoin, fosfomycin’s resistance rates among UPEC are still low, maintaining its therapeutic efficacy in the treatment of UTIs. Chromosome- or plasmid-mediated mechanisms give fosfomycin resistance to bacteria. The majority of resistance is chromosomally mediated and prevents the antibiotic from reaching the bacterium (Gardiner et al., 2019). Additionally, the mechanism of action is distinct, making the emergence of co-resistance improbable. Nevertheless, opposition is growing, particularly among ESBL manufacturers (Shaikh et al., 2015). By binding to the cysteine 115 residue of the enzyme N-acetyl glucosamine transferase (MurA), which catalyzes peptidoglycan synthesis in E. coli, fosfomycin inhibits the first stage of peptidoglycan production (Borisova et al., 2014). Glycerol phosphate (GlpT) and hexose phosphate (UhpT), two transport mechanisms, are used by fosfomycin to penetrate the bacterial cell wall. Glycerol phosphate (GlpT) and hexose phosphate (UhpT), two transport mechanisms, are used by fosfomycin to penetrate the bacterial cell wall. Fosfomycin resistance can be brought on by amino acid changes in the active site of the MurA target or mutations in the chromosomal glpT and uhpT genes (Abdelraheem et al., 2023) ( Table 3 ).

Another significant route for fosfomycin resistance is the generation of fosfomycin-inactivating enzymes (fos genes). Different fosfomycin-modifying enzymes, including FosA, FosB, FosC, and FosX, have been identified. These enzymes are encoded by the fos gene, which cleaves the oxirane ring to render fosfomycin inactive. FosA enzymes are the fosfomycin-modifying enzymes that are most commonly reported and are widespread in Enterobacteriaceae. The most often seen FosA determinant in E. coli is the FosA3 enzyme. Less often seen in E. coli are other fos genes including fosA4, fosA5, and fosA6 (Arca et al., 1997; Loras et al., 2020). A significant level of resistance was recently conferred by an E. coli strain isolated from urine that encodes fosA8, a protein that shares 80% of its amino acid sequence with fosA. This gene was linked to the genome of the species Leclercia decarboxylata, which naturally resists fosfomycin and has a gene pool for transferrable resistance (Whelan et al., 2023). According to a study conducted in Mexico on 350 ESBL-producing E. coli, 60.5% of the fosfomycin-resistant strains were fos-producing, with the majority of these strains carrying fosA3. In 28.9% of the cases, resistance in the strains resulted from mutations within the antibiotic transport system (Galindo-Méndez et al., 2022).

Another plasmid-mediated resistance gene known as fosL1 was discovered in Swiss isolates and is thought to have been acquired by Tn7-related transposition. Other fosA genes and this gene had 57% to 63% amino acid similarity (Kieffer et al., 2020).

According to an agar dilution technique used in a recent investigation in Egypt, 37 (38.5%) of the 96 E. coli isolates were found to be fosfomycin resistant (MIC 256 g/ml). Four isolates carry two of the 21 Fos genes that were found in the isolates. In this investigation, the fosfomycin-resistant gene FosA3 predominated, appearing in 11 isolates (47.8%), followed by the FosA, FosC2, FosA4, and FosA5 genes, which were discovered in 8 (34.8%), 4, 17, 4, and 1 (4.3%) of the 23 isolates with positive phosphonoformate test results, respectively. None of the isolates had the FosA6 or FosB genes (Abdelraheem et al., 2023).

A high incidence of antibacterial resistance was seen in the majority of the fosfomycin-resistant strains tested in this investigation, and 85.7% of these isolates were MDR. When compared to fosfomycin-susceptible isolates, cefazolin, cefoxitin, and ceftazidime resistance rates were considerably higher in fosfomycin-resistant isolates (P value 0.05) (Cheah et al., 2015; Loras et al., 2020).

Most frequently found on conjugative plasmids that also carry genes for ESBLs of the CTX-M subtype, FosA3 is the most prevalent plasmid-mediated fosfomycin-resistant gene in E. coli isolates (Wachino et al., 2010; Sato et al., 2013; Cao et al., 2017). When solely ESBL-producing E. coli were taken into account, specific studies in Spain found that the rates of fosfomycin resistance among E. coli isolated from urine samples of adult patients were 2.7% and 3.8%, respectively (Loras et al., 2020). As a result of our findings, Abu El-Wafa and Abouwarda in Egypt discovered 24.1% fosfomycin resistance in UPEC isolated from patients of various ages (Mohamed Abu El-Wafa and Abouwarda, 2022). Out of 199 UPEC isolates tested in the UK, nitrofurantoin, the current first-line treatment for uncomplicated UTIs, has the lowest resistance rate both hospital and community settings (Carter et al., 2023).

Trimethoprim is frequently used with the sulphonamide medication sulfamethoxazole, which inhibits the production of dihydrofolic acid, a cofactor necessary for the efficient synthesis of bacterial DNA (Masters et al., 2003). Mobile genetic elements, plasmids, and integrons are strongly related to resistance to trimethoprim and sulfamethoxazole (Stephens et al., 2020; Mahmood and Ibrahim, 2023). The chromosomal folA and folP of a species that naturally resists trimethoprim and sulphonamides are the origin of the genes that encode these resistance proteins (Sánchez-Osuna et al., 2020). Several genes in the Dfr (di-hydrofolate reductase) family give resistance to trimethoprim. There are more than 30 dhfr genes; dfrA1 and dfrA17 are the two most prevalent in UPEC (Al-Assil et al., 2013). These dfrA genes are frequently located within integrons and on plasmids near sul genes, which provide resistance to sulfamethoxazole. They are also frequently discovered in bigger resistance islands, which frequently include the virulence genes fimH, fyuA, irp2, and sitA as well as the chromate-resistance gene chrA, the aminoglycoside genes aac(3)-IIa, aac(6)-Ib-cr, and aadA2, and the gene bla_CTX-M . Trimethoprim-sulfamethoxazole resistance has expanded widely among UPEC due to the intrinsic mobility linked with these resistance determinants (Zeng et al., 2021; Rahman et al., 2022; Mahmood and Ibrahim, 2023). Prior prescriptions of nitrofurantoin were discovered to be related with a decreased frequency of trimethoprim resistance. Selective pressure offered by earlier antibiotic therapy, notably the use of extended-spectrum penicillin, has been proven to cause trimethoprim resistance (Mulder et al., 2019).

Even though these mobile determinants have been proven to have the most impact on resistance to these medications, chromosomal mutations and efflux have also been shown to contribute to resistance to trimethoprim-sulfamethoxazole. In terms of efflux, research indicates that loss-of-function mutations in the GSH content-regulating genes gshA, grxA, and cydD lead to decreased periplasmic glutathione concentration, which in turn enhances the AcrAB-TolC efflux pathway (Song et al., 2021). This raises the possibility that changes in these genes might be the cause of chromosomal resistance to trimethoprim. Additionally, research that examined an E. coli knockout library discovered that the deletion of mgrB led to trimethoprim resistance. Significantly elevated genes in mgrB-deleted strains included phoP, phoQ, and folA. This is due to the fact that mgrB controls the expression of folA, demonstrating the possibility of trimethoprim resistance in several genes related to folate metabolism (Shi et al., 2021) ( Table 3 ).

According to recent data, a significant percentage of infections caused by CRE in the USA required the use of colistin and polymyxin B, which are considered last-resort drugs. This is often due to the fact that the bacteria have developed resistance to more commonly used antibiotics. Colistin is particularly effective against GNB, including Enterobacteriaceae and other types such as P. aeruginosa and A. baumannii. It was first found in 1947 (Karami-Zarandi et al., 2023b). The medicine was initially prescribed frequently, but as a result of its ineffectiveness and numerous side effects, including nephrotoxicity and neurotoxicity, its use gradually decreased. Despite these drawbacks, the WHO regards colistin as a “highest priority critically important antimicrobial for human medicine” due to its capacity to treat infections brought on by bacteria that are ordinarily resistant to antibiotic treatment. In Enterobacteriaceae, chromosome point mutations and changes, particularly in genes encoding two-component regulatory systems, such as PhoPQ and PmrAB/BasRS, can result in the acquisition of colistin resistance in E. coli and other MDR pathogens like K. pneumoniae or E. cloacae (Bialvaei and Samadi Kafil, 2015) ( Table 3 ).

Because of these mutations, eptA and the arnBCADTEF operon are expressed constitutively, which in turn causes lipid A to acquire 4-amino-4-deoxy-l-arabinose (l-Ara4n) and/or pEtN groups, modifying LPS. In 2016 saw the discovery of plasmid-encoded colistin resistance in a number of isolates from both humans and livestock in addition to chromosomal alterations. A single gene called mobilized colistin resistance-1 (mcr-1) produces a transferase enzyme that alters the bacterial lipid-A lipopolysaccharide. Additionally, this gene makes E. coli resistant to polymyxin drugs. The fact that mcr is a transposable genetic element and has been identified on a variety of bacterial plasmids, including the IncX4 and IncHI2, makes it possible for horizontal gene transfer. Since then, research on enterobacteria with mcr genes has been reported from all over the world, and as of now, variations with numbers ranging from mcr-1 to mcr-10 have been described (Bastidas-Caldes et al., 2022). There have been reports of 10 different classes of mcr, all of which encode pEtN transferases. Subsequent research showed that mcr-1 is distributed globally in a variety of different Enterobacteriaceae, but mainly E. coli (Anyanwu et al., 2023).

As a result, LPS changed with pEtN is responsible for MCR-mediated colistin resistance, whereas LPS modified with l-Ara4n and/or pEtN alterations is responsible for resistance conferred by chromosomal mutations. LPS modification takes place in the outer leaflet of the CM in both colistin resistance caused by chromosomal mutations and MCR (Humphrey et al., 2021).

Although not all LPS molecules are transformed in either membrane, this causes modified LPS to be present in both the CM and OM. Both l-Ara4n and pEtN have positive charges, which lowers lipid A’s anionic charge and is hypothesized to lower the lipid’s affinity for colistin’s cationic peptide ring. The presence of unaltered LPS molecules, which the polymyxin antibiotic can bind to, there is evidence that colistin can still harm the OM of MCR-1-producing E. coli. The fact that colistin did not permeabilize the CM of an MCR-1-producing strain, despite harming the outer membrane of resistant bacteria, explains why the bacteria are resistant to death or lysis and can withstand exposure to polymyxin. The MCR-1 strain is protected against colistin but not the outer membrane due to the high concentration of modified LPS and low total abundance of LPS in the cell membrane. This is because there are fewer unmodified LPS molecules in the cell membrane that colistin may target (El-Sayed Ahmed et al., 2020; Humphrey et al., 2021).

According to Humphery and colleagues, they found out that MCR-1-mediated resistance to colistin can shield E. coli from damage caused by CM through the modification of LPS with pEtN. However, this resistance does not prevent OM permeabilization. Although all MCRs are pEtN transferases, the researchers also noticed that the different mcr gene families have varying abilities to support E. coli’s survival and growth when exposed to colistin. Nonetheless, MCR-1 has consistently been found to be the most effective in protecting colistin due to the limited extent of CM permeabilization (Humphrey et al., 2021).

Colistin works by attaching itself to lipids through a binding process. a fraction of LPS found in GNB’s outer membrane, like that of E. coli. In particular, colistin binds to LPS molecules in the cytoplasmic membrane’s outer leaflet, rupturing it and killing the bacteria. The phosphate groups on the lipid A subset of LPS that are negatively charged enhance this interaction (El-Sayed Ahmed et al., 2020).

It is suggested that the primary cause of cell death is the ensuing breakdown of the inner membrane. Previous research in E. coli has shown that mutations in the sensor histidine kinase PmrB are a significant cause of colistin resistance. These mutations result in the constitutive production of the enzymes ArnT and EptA, which add positive charges to the phosphate groups of lipid A (4-amino-4-deoxy-L-arabinose and pEtN, respectively), reducing the affinity of colistin for lipid A. The acquisition of mobile genetic elements carrying mcr genes, which also results in the decorating of lipid A with pEtN, offers a different route toward colistin resistance (Janssen and van Schaik, 2021). According to Knopp et al., novel auxiliary peptides can also result in colistin resistance by interacting directly with PmrB and activating the two-component system. MCR stands for mobilized colistin resistance; LPS for lipopolysaccharide, and the first mcr gene was discovered in 2016 (Knopp et al., 2021). The distribution of mcr genes in E. coli differs significantly globally, according to a systematic review by Bastidas-Caldes et al. The overall crude prevalence was 6.52% (n = 11,583/177,720), with a non-clinical isolate prevalence of 8.71% (n = 15,001/172,140) and a clinical isolate prevalence of 1.76% (n = 1020/58,033) (Bastidas-Caldes et al., 2022).

After decades of antibiotic use, E. coli went from being a harmless bacterium to once again posing a hazard to human health. MDR strains of E. coli were created by this bacteria’s innate capacity to absorb genetic material from other bacterial species at the dawn of the antibiotic era. As more antibiotics were used, the primary resistant strains continued to be under selective pressure, and new resistant strains were chosen that had acquired antibiotic resistance by horizontal gene transfer or spontaneous mutation. This bacteria’s metabolism was modified in special clones to promote efficient energy use and better replication. Clones with a wide range of antibiotic resistance and an effective metabolism spread around the globe. Even though these clones are extremely resistant to practically all antibiotics, recent research suggests that adequate stewardship programs could improve the efficacy of the antibiotics now in use. For instance, the prevalence of ESBL-producing bacteria will decline if third-generation cephalosporins are in some cases replaced with PIP/TZM. Additionally, colistin can be used as part of a therapy against pathogenic germs when combined with other medications. A significant factor in the creation and spread of colistin resistance among GNB is the drug’s unprecedented use in human medicine, animal husbandry, aquaculture, and agriculture. Understanding the complexity of antibiotic resistance mechanisms in E. coli is crucial for the development of effective strategies to combat this growing public health crisis. By reviewing these mechanisms, we hope this will increase opportunities for the design of innovative therapeutic approaches and the implementation of prudent antibiotic stewardship practices to preserve the efficacy of current antibiotics and ensure a sustainable future for healthcare. However, there is an urgent need for more research into the resistance mechanisms in E. coli.

SN: Investigation, Validation, Writing – original draft, Writing – review & editing. JG: Investigation, Validation, Writing – original draft, Writing – review & editing. MH: Conceptualization, Investigation, Validation, Writing – original draft, Writing – review & editing.