Mechanisms of Antimicrobial Resistance of E. coli

Abstract

Escherichia coli has become a major significant pathogen behind infections, many researches have been conducted on possible drugs that can successfully eradicate the pathogenic isolates. To ensure survival, E. coli strains improvised resistant mechanisms to allow them to maneuver through with life among bactericidal agents. The chapter gives an overview of the antimicrobial resistance mechanisms found in major groups of antimicrobial drugs. E. coli uses enzymes in defying drug susceptibility for example aminoglycoside modifying enzymes in modifying drug recognition sites, in cephalosporin, penicillin the pathogen indulged in the use of β-lactamases to break down the β-lactam ring on the structure of the drugs. In fluoroquinolones, the pathogen uses efflux pumps, DNA gyrase mutation as a mechanism of resistance. The continuous use of drugs induces resistance mechanisms to increase, there is a need for continuous researches on drugs effectivity and the discovery of new and better medication to fight against E. coli pathogens.

1. Introduction

Escherichia coli is one of the most primitive microorganisms that are affecting the normal body functionality, bringing sickness, attributed by infections that are becoming difficult to cure since the microorganisms are evolving with time they tend to mutate and produce different species which are resistant to drugs that were previously effective in fighting and eradicating the bacterial species. The aspect of antimicrobial resistance has become a non-healing wound in as much as health is concerned, with time the wound continues to deepen and expand bringing in more confusion, sickness as well as problems in medicinal drug references [1].

E. coli Resistant germs are emerging at an alarming rate, posing a growing threat to human society. Antibiotic misuse and overuse, as well as antibiotic buildup in the environment, have been blamed for the growth of antimicrobial resistance (AMR). With the pharmaceutical industry’s lack of new medication development, it is becoming very difficult to tackle diseases behind the infection [2].

It is believed the long-term use of drugs on E. coli has brought problems in curing the infections it causes because of many adaptive mechanisms the pathogen has developed to discard drug susceptibility over time thereby allowing its survival and perpetuation [3]. According to the World Health Organization (WHO) [4], the long-term use of drugs, misuse and abuse of drugs are the foundation of creating resistant mechanisms that may lead to difficulties in prevention as well as treatment.

2. Mechanisms of resistance

2.1 Mechanisms of resistance to cephalosporin drugs

Third-generation Cephalosporin has been used as a successor of penicillin which has been resisted by many drugs due to long-term use on the pathogens. Third-generation cephalosporin drugs are a much-improved version that has been useful in eradicating bacterial species such as E. coli [5]. However, with time, the bacteria tend to become resistant to the drugs due to the improvising of mechanisms to create barriers and different structures that are not recognized by the drugs for disruption of the bacterial cell. Since some drugs recognize specific polypeptide sequences where the chemical drugs cleave for destruction. Such actions involve acquired mechanisms of resistance which involve the passing down of resistant plasmids from cell to cell, another way includes the intrinsic mechanism of resistance whereby the cell creates ways of denouncing the drug susceptibility by adjusting or improving structures within the cell. They can change the polypeptide sequences also creating structures that limit the uptake of the drug from the environment, by modifying specific sites targeted by the drugs the cell automatically deprives recognition thus inducing resistance [6].

2.1.1 Penicillin and cephalosporin β-lactam mode of action

The gram-negative bacterial cell wall is made up of a complex structure which is made of a thinner peptidoglycan layer with a structure of crosslinking peptidoglycan precursors made by adjoining N-acetyl glucosamine and the N-acetyl muramic acid proteins which are then cross-linked to form several layers of peptidoglycan catalyzed by Transpeptidase and de-alanyl carboxypeptidase. The penicillin-binding proteins form the D-ala D-ala cross-linkages of the peptidoglycan wall in cell wall synthesis. The β-lactam ring in penicillin and cephalosporin will bind to the enzymes (Trans-peptidase and D-ala- carboxyl peptidase) thereby preventing bacterial cell synthesis leading to bacterial cell wall damage that will cause bursting after being subjected to the low osmotic pressure of the surrounding environment. The antibiotic penicillin-binding complex will stimulate the release of autolytic compounds that are capable of digesting the cell wall [7].

2.1.2 Resistance mechanisms

Quite several researches have outlined that multidrug-resistant species which include E. coli have been a long-term migraine problem with the drastic increase in resistance as of date, with special attention on the development of the extended-spectrum β-lactamase (ESBL). The genes which are encoded by the ESBLs are located in the plasmid of the bacterium cell and most cases, they are transferred through horizontal transfer to other cells. E. coli has acquired resistance to β-lactam antibiotics through the production of the β-lactamase enzyme which is used to break down the β-lactam ring of most penicillin derivatives [8]. β-lactamase enzymes are the biggest and greatest reason why penicillin drugs are failing to eradicate infections behind E. coli bacteria.

With this problem being pointed out by scientists, new-generation drugs of the cephalosporin class were invented which were believed to defy the stability of many bacterial β-lactamases on the drug, thereby allowing the drug to temper with the bacterial structure and eliminate them. With persistent use and exposure to the third-generation drugs which include; cedox, cefixime, cefotsxime and avycaz which have been successfully superior to older penicillin drugs in terms of effectiveness on treatment assays. In the early 1980s, in response to the increasing prevalence and spread of β-lactamase, third-generation cephalosporins or oxyimino groups were introduced into clinical practice. Resistance to these broad-spectrum cephalosporins quickly emerged. As early as 1983, Germany published the first report on the SHV2 enzyme that can hydrolyze these antibiotics [8]. The continuous use of these third-generation cephalosporins has brought along dynamic inducement on the production of many mutated lactamases in many bacteria, allowing survival and denying drug effects. The β-lactamase in ESBLs contains serine chemicals at their active site which hydrolyzes the spectrum of cephalosporins using an oxyminoside chain [9].

The TEM1, TEM2 are genes that aid in coding for the ESBLs through mutation to alter the amino acid configuration of the β-lactamases, thereby extending the degree of affinity and complementarity for the spectrum of the β-lactam antibiotics to be susceptible for hydrolysis. There are several groups of ESBLs with similar behaviors but different evolutionary histories. The largest population is TEM and sulfhydryl reagent variable (SHV) β-lactamase mutants, with members exceeding 150 [10]. Mutations affecting a small number of key amino acids expand the active site of the enzyme, allowing it to bypass the oxyimino substitution that normally protects the β-lactam ring. Therefore, although the classic TEM and SHV enzymes cannot significantly hydrolyze the oxyiminocephalosporin, the mutant can do so, thereby conferring resistance to its host strain [10].

The CTX-M enzyme is another type of ESBLs. Based on sequence homology, they are divided into five subgroups. Most of these subgroups have evolved due to the leak of the chromosomal β-lactamase gene of Kluvera spp., which is a less clinically significant Enterobacter spp.). After migrating to mobile DNA, CTX-M β-lactamase can further evolve. E. coli isolates that produces CTX-M enzyme have been identified as the cause of urinary tract infections. Some reports indicate that the CTX-M ESBL may now be the most common ESBL type in the world [10, 11].

Figure 1; Showing the mechanisms in which gram-negative bacteria can be resistant to penicillin and third-generation cephalosporin drugs. The penicillin-binding protein is being modified in such a way to prevent complementary pairing with the drug (C) that is the modification of the drug target. The B-lactamase enzyme (D) cleaving the B lactam structure of the drug defying its susceptibility and action. At (E) showing efflux pumping of the drugs from the cell [12].

Figure 1.

B1-Metallo-β-Lactamases: Where do we stand? Adapted from Mojica et al. [12].

3. Resistance on fluoroquinolones

Quinolones are the most frequently used drugs against E. coli infection because they are highly bioavailable meaning they have a good tissue distribution once administrated in the body orally [13]. This fact has caused several doctors to prefer referencing quinolones once an E. coli infection is detected. However, the major factor behind E. coli resistance in Fluoroquinolones is through mutations in the genome of the bacteria that is DNA gyrase [14].

3.1 Fluoroquinolone mode of action

The mode of action of fluoroquinolones is by making complexes with DNA Gyrase and topoisomerase IV on the DNA chromosome thereby allowing for the disruption of the DNA sequence of E.coli. Fluoroquinolone antibiotics have a chemical structure that allows them to interrupt E. coli activity through the alteration of the DNA Gyrase and the Topoisomerase IV protein structure, thereby preventing any form of replication and translation processes for protein synthesis bringing for the destruction of E. coli microorganisms. The interruption with DNA Gyrase affects the conversion of the relaxed double-stranded DNA into a negatively super twisted form that allows the replication to commence, this diminishes relegation through entrapping of the enzymes changing their protein arrangement in their active site preventing complementarity with the DNA strand. The replication fork is held steady by Topoisomerase IV and the interruption of its structure affects the replication fork formation, therefore, prohibiting replication to proceed [14].

3.2 Mechanisms of resistance

3.2.1 DNA Gyrase and Topoisomerase Base substitution

The mutation in the genome results in amino acid-base substitution in the Gyrase A Gene (GyrA) and topoisomerase IV proteins [14]. Changes on those two genomic structures have been termed the quinolone resistance determining regions. The research conducted by Friedman [15], outlined that the amino acid substitution happens between 67 and 106 bases specifically at bases 83 and 87, therefore altering the drug targets. Further researches proved that there are other sites found on the nalidixic acid-resistant mutant that was not thermo-tolerant had a 5′ base change of guanine to thiamine, in the codon 87 which is expected to reduce the susceptibility of quinolone to nalidixic acid due to the substitution of tyrosine for aspartic acid [15].

However, some investigations are taking place with the intention to defend and uplift the bactericidal status and this includes recent studies done on nybomycin, where investigations on the susceptibility of fluoroquinolone-sensitive and fluoroquinolone-resistant strains were conducted and discovered that nybomycin was successively efficient in destroying the bacterial species [16].

It is important to determine whether the E. coli mutants are thermotolerant or non-tolerant because this aids in determining how they can be susceptible to drugs and how temperatures can affect the genomic structures [17]. E. coli strains have adaptation characteristics such as physiological, metabolic and proton consuming acid-resistant mechanisms that allow their survival and perpetuation in acid environments below pH 2. They reduce the effects of acid damage by modifying the membrane, altering membrane porins to reduce proton influx and periplasmic chaperons [18].

3.2.2 Efflux pumping

Active efflux pumping is a mechanism by which a substance that is not needed in the cell is pumped out to prevent the damages that the substance or chemical may bring to the cell, they are used in moving a variety of different toxic compounds out of the cell and in bacteria they use it to pump out antibiotics. It is a major fundamental characteristic in antimicrobial resistance of gram-negative bacteria including E. coli [19]. The efflux pump family in enterobacteriaceae called the resistance nodulation division (RND), is the most significant factor behind multidrug resistance and one of the most characterized RND systems in enterobacteriaceae is the AcrAB-TolC efflux systems. Expression of the AcrAB and TolC genes are regulated by the MarA protein in E. coli [20].

In the E. coli operon, the expression of AcrAB is controlled or mediated by AcrR which is a repressor located at the upstream part of the acrAB operon where the expression can be transcribed or repressed [20, 21]. Studies have shown that mutations are taking place in the acrR which means there is no repression of expression for AcrAB which means the more the expression the higher the rate of pumping out of the drugs [22]. They also have a specific modification of the porin membrane channel proteins which have a specific mediated width that allows the in and outflow of the substance of the cell. The porins for example against vancomycin are modified in such a way that the vancomycin molecules cannot pass through into the cell [23]. The major porins in E. coli such as OmpF and OmpC protein were believed to be the drug binding sites, however recent studies show that there have been changes in their structural arrangements making the drugs unable to bind to the proteins. The presence of mutant porins can even cause resistance to carbapenems which are believed to be the most efficient and reliable drugs against E. coli and other bacterial species [23, 24].

Most enterobacteriaceae gram-negative bacteria have developed specialized genes which aid in resisting carbapernemdrugs which are called the ndm genes which are often found branch host range conjugative plasmids which work in conjunction with other resistance genes. The ndm genes have a transposon mechanism which means they are found on plasmids as well as the host chromosomes and can move between the two at a much higher frequency thereby enabling the resistance build-up in many cells in a much-minimized time range via transformation mechanisms [25].

4. Resistance on aminoglycosides

Aminoglycoside drugs have been part of the fight against E. coli pathogenic species, however with the changes in the phenotype of the E. coli isolates for example the ever-evolving changes in the ESBL structure as well as the genes that the aminoglycoside drugs encode for susceptibility [26].

4.1 Aminoglycoside mode of action

Aminoglycosides are bactericidal agents that inhibit the synthesis of bacterial proteins through the interruption of the ribosomes. They interfere by binding to the 30S and 50S ribosomal subunits, they inhibit the translocation process of moving the peptidyl-tRNA from the A site to the P site thereby causing mRNA misreading in that way denouncing the translation process forwarding zero protein synthesis, which entails no budding, multiplication and denouncing perpetuation and survival [26].

4.2 Mechanism of resistance on aminoglycoside drugs

There are more than 50 types of aminoglycosides modifying enzymes which include, acetyltransferases (aac), phosphotransferases (aph) and nucleotidyltransferases (ant), these enzymes are capable of modifying aminoglycosides at their respective drug recognition sites [27]. The main cause of resistance to the aminoglycoside drugs is that more than one aminoglycoside modifying enzymes may be found in a single isolate bringing in a high probability rate of resistance to the drugs [28].

Mancin [28], conducted a population analysis of genetic and enzymatic resistance of E. coli to aminoglycosides, they concluded that the genes aac(6′) and aac(3) can cause significant resistance to amikacin and kanamycin. Another study on genes was conducted by Bodendoerfer [29], where they concluded that in Switzerland the most prevalent resistance genes included the aph(3′)-la, aac(3)-lld and aac(6′)-lb-cr, they also alluded that the genes tend to change in their structural arrangement which is a mediated by the action of the transposon mechanisms of the resistant genes. The mechanisms of the jumping gene continues to be a threat to human health, because the transposon genes can be transferred to the next cell through transformation and conjugation processes which will cause the development of more resistant genes prior to transcription and translation, this information has caused migraine headaches to researchers and scientists who are working tirelessly in the attempt of denouncing resistance [29].

5. Conclusion

E. coli bacteria continues to be a nuisance in the medical field bringing endless prospects in resistance against the drugs that are used in an attempt of eradicating the bacteria. The bacterial species has so many different forms of isolates that differ from one another both structurally and genetically, hence the drug that is susceptible to one E. coli may be found ineffective to another E. coli variant species. The review showed that there are many different mechanisms in which E. coli strains are becoming more and more difficult to treat, some evolving to possess enzymes that work in a conjunctive manner to denounce the effect of the drug.

The evolution brings forth the production of many different isolates with different protein structures for drug resistance and allows perpetuation and survival. This alarms for continuous assessments to provide information on the drugs and the interference with the pathogenic microorganism, how the bacteria respond in susceptibility, which will act as a fortress in tracing the reason behind resistance tomorrow. Studies are of importance to help and provide practical proof on how to tackle pathogens which will aid in improving health, denouncing long hospital stays and even patients from succumbing to infections caused by the microorganism.

Conflict of interest

The authors declare no conflict of interest.