Antibiotic Resistance Genes Database (ARDB)

Antimicrobial Drugs in general

Due to the fact that bacteria differ with eukaryotics with respect to morphology ,  and metabolism, many antibacterial drugs have been found which can inhibit processes in bacteria without disrupting them in the host. Such drugs are typically antibiotics which target bacterial enzymes that are distinct from their eukaryotic counterparts or which are involved in pathways like cell wall biosynthesis that is absent in eukaryotic cells.

Inhibitors of Peptidoglycan Synthesis:

Beta-Lactams: Inhibitors of peptidoglycan synthesis include the beta-lactams. Beta-lactams include the following:

1) penicillins: Penicillin was discovered by Alexander Fleming in 1928 and in 1940, several years before the introduction of penicillin as a therapeutic, a bacterial penicillinase was identifed by two members of the penicillin discvoery team. Maybe the most famous fungi species that produces penicillin is Penicillium chrysogenum.

Once the antibotic was used widely, resistant strains capable of inactivating the drug became prevalent, and synthetic studies were undertaken to modify peniccilin chemically to prevent cleavage by penicillinase (Beta-lactamases). Interestingly, the identification of a bacterail penicillinase before the use of the antibotic can now be appreicated in the light of recent findings that a large number of antibiotic r genes were componetns of natural microbial populations. This raises the question as to which came first, the antibiotic or resistance? (Davies, “origins and Evolution of Antibiotic Resistance” Microbiology and Molecualr Biology Reviews, 2010, p. 417-433)

–Ampillin:

2) cephalosporins.

Bacteria have evolved a host of strategies to resist beta-lactams such as beta-lactamases which hydrolyze beta-lactams. For example, CDC recommends a single dose of 500 mg of intramuscular ceftriaxone. Ceftriaxone belongs to the class of medicines cephalosporin antibiotics. Alternative regimens are available when ceftriaxone cannot be used to treat urogenital or rectal gonorrhea. See CDC

Inhibitors of folic acid Synthesis :

Sulfanilamides inhibit steps of folic acid biosynthesis in bacteria. Examples include sulfamethoxazole

Inhibitors of replication and transcription:

Quinolones which act on  (enzymes involved in super coiling). Examples include ciprofloxacin

Inhibitors of RNA polymerase:

Rifamycins: such as Rifampin.

Inhibitors of  protein synthesis:

Inhibitors of protein synthesis include 4 classes of drugs:

A) tetracyclines prevents binding of f-met (which is the 1st residue in almost all polypeptide chains of bacteria)  tRNA to the 30S subunit (bacteria have 30S and 50S subunits)

B) aminoglycosides which inhibit peptide elongation,

C) chloramphenicol which binds to the 50S subunit and also blocks peptide extension and

4) macrolides which also binds the 50S subnunit of the ribosome and prevents peptide bond formation.

–Azithromycin is a broad-spectrum macrolide antimicrobial among the most prescribed antimicrobial drugs in the United States. It is a erythromycin derivative with greatly enhanced activity against gram-negative bacteria (including Enterobacteriaceae) and provides coverage of many gram-positive organisms. Like other macrolide antimicrobials, azithromycin binds to the 23S portion of the 50S bacterial ribosomal subunit. It inhibits bacterial protein synthesis by preventing the transit of aminoacyl-tRNA and the growing protein through the ribosome. Azithromycin is less prone to disassociation from the gram-negative ribosome than erythromycin, conferring its greater efficacy against gram-negative pathogens. Pharmacokinetically, azithromycin rapidly moves from the bloodstream into tissues and, once there, readily crosses cellular membranes, allowing efficacy against intracellular pathogens. The usual dose is 250 mg or 500 mg, given once daily for 3 to 5 days, and in severe infections, a higher dose is used. A single dose is occasionally used at 30 mg/kg for otitis media and at 1 g for adults with Chlamydia. See Sandman, Azithroycin

Antibiotics (See Outline)

Biomarkers for determining Treatment:

Procalcitonin (PCT): is a blood marker for bacterial infections and has emerged as a promising tool to improve decisions about antibiotic therapy. Several randomised trails ahve demonstrated the feasibility of using procalcitonin for starting and stopping antiboiotics. Procalcitonin increases in bacterial infections and deccreased when pateints recover from the infection. Procolcitonin can be measured in the bood of patients by different commercially available assays with a turnaround time of about 1-2 hours and support clinical decision making about initiation and discontinuation of antibiotic therapy. (Shuetz, “Procalcitonin to initiate or discontinue antibiotics in acute respiratory tract infections” University o fGroningen (2017?

Administration of Antibodies as a Potential Treatment Strategy

Recent development in a number of areas are converging to make the medium-term future permissive for antibacterial mAb development. The majority of problematic infections with respect to failing antibiotic treatment is caused by ESCAPE pathogens (Enteroccocus faecium, S. arueeus, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacteriaceae including E coli and Kelbsiella pneumoniae. The widespead antibiotic resistance of these pathogens is most alarming in the hospital setting (noscoomial infections). For ccertain bacterial infections, soluble toxins are major contributors to pathogenesis. Oleksiewicz, Archives of Biochemistry and Biophysics, 526: 124-131 (2012).

IgA: Traditionally, immunoglobulin preparation for the prophylaxis and treatment of infection were largely compirsed of IgG. However, the successful use of breast milk for the prophylaxis and treatment of infant diarrhaea highlighted the potential benefits of plasma (monomeric) and mucosal (secretory) IgA for immunotherapeutic use. A clinical trial conducted by Eibl indciates that oral feeding with a plasma derived IgA rich immunoglobulin preparation may present the development of necrotizing enterocolitis. Oral feeding with IgAbulin also displays a therapeutic effect in immunodeficinet patients suffering from Clostridium difficile or Campylobacter jejuni induced diarrhaea. Hemmingsson and Hammarstrom (1993) also prophylactically adminsitered IgA rich immunoglobulin preparation in a nasal spray and reducts the incidence of respiratory tract infections in elite skiers and elite rowers.  (WO00/41721).

SIgA (secretory IgA): is one of the immune components of colostrum and plays a role in protecting against infection. An immunogloublin preparation dervied form bovine colostrum reacts against toxins associated with E. coli and Shigella infections in cell cultures in vitor. S-IgA from human colostrum also inhibits adherence of Vibrio cholera to intestinal tissue in vitro. Results form three separate bovine colostrum are anti-diarrheal in adult AIDS?HIV patients suffering from infection by C. parvum. (US 2002/0119928).

Simon (US 8,021,645) discloses a composition that incldues dimeric secretory IgA and pentameric IgM for treatment of C. difficile. The IgA or IgM therapeutic is optionally enterically coated or microencapsulated to withstand gastrointestinal exposure associated with oral delivery.

Administration of Antimicrobial Peptides

Antimicrobial peptides are produced by higher organisms as part of their immune defenses. They disrupt cell membranes and once inside bacterial can disrupt DNA, RNA and various proteins. Scientisits are developing peptides as alternative to antibiotics. Antimicrobial peptides have a positively charged region that pokes through the bacterial cell membranes and a hydrophobic stretch that enables interaction with and translocation accross these membranes. Another advantage of antimicrobial peptides is that as they recruit immune cells to combat infection, they also suppress overactice inflammatory responses which can cause sepsis.

Clavanin-A: is a naturally occurring antimicrobial peptide, originally isolated from the tunicate, a marine animal. The original form of the peptide kills many types of acteria but has been engineered to improve its effectiveness. The resulting molecules, called clavanin-MO is very potetent against a number of bacterail strains such as E coli and S. aureus that are resistant to most antibiotics.

Bacterialphages to treat Drug Resistant Bacteria

Bacterial infections that can’t be treated successfully with known antibiotics are a serious threat to health. Researchers have been searching for new ways to kill these resistant bacteria. Viruses called bacteriophages, or phages, are one method under study. Phages prey on bacteria. They infect certain bacteria, replicate inside them, and burst out, killing the bacteria. Dr. Graham F. Hatfull’s research laboratory at the University of Pittsburgh for example has been building a collection of phages. Over many years, college students in a global science program have isolated more than 10,000 phages from nature and has shown page treatment success against the Mycobacterium abscessus isolated from the patient’s infection, dubbed GD01, which was resistant to all nine antibiotics tested. See NIH

In a new study, MIT biological engineers showed that they could rapidly program bacteriophages to kill different strains of E. coli by making mutations in a viral protein that binds to host cells. These engineered bacteriophages are also less likely to provoke resistance in bacteria, the researchers found. See Science Daily

Bacteriophages (phages) have demonstrated inhibitory effects against ciprofloxacin-resistance bacteria. (Chegini, “Bacteriophages: The promising therapeutic approach for enhancing ciprofloxacin efficacy against bacterial infection” J Clin Lab Anal, 2023).

Small Molecule Inhibition of virulence gene expression

Increasing antibiotic resistance requires the development of new approaches to combating infection. Virulence gene expression in vivo represents a target for antibiotic discovery that has not yet been explored. A high-throughput, phenotypic screen has been used for example to identify a small molecule 4-[N-(1,8-naphthalimide)]-n-butyric acid, virstatin, that inhibits virulence regulation in Vibrio cholerae. By inhibiting the transcriptional regulator ToxT, virstatin prevents expression of two critical V. cholerae virulence factors, cholera toxin and the toxin coregulated pilus. See Hung

Targetting Biofilm Formation 

Degrading enzymes: The biofilm extracellular matrix serves as a protective physical barrier that shelters the resident bacteria against antibiotics and host immune defenses. Therefore, approaches to disrupt the matrix by enzymatically degrading the chemical components have been investigated. DNase I-mediated degradation of extracellular DNA appears to be effective in disrupting early S. aureus biofilms and treatment with trypsin or proteinase K disrupts the protein components of the biofilm matrix.  Likewise, dispersin B, a glycoside hydrolase produced by the periodontal pathogen Actinobacillus actinomycetemcomitans, is able to breakdown the polysaccharide components of staphylococcal biofilms and can promote antibiotic penetration, resulting in synergistic killing when combined with the antibiotics cefamandole nafate or triclosan. Additional glycoside hydrolases, α-amylase and cellulase, and lysostaphin, a glycine endopeptidase produced by Staphylococcus simulans that cleaves the pentaglycine bridge in the staphylococcal cell wall, have also been shown to significantly reduce matrix biomass of S. aureus biofilms in vitro. Although these in vitro results are promising, the application of exoenzymes as therapeutic drugs may be limited due to the possibility of protein-induced inflammatory responses in the host, toxicity, or immunity. Alternatively, these enzymes could be employed in an approach similar to an “antibiotic lock” where a high concentration is applied to catheter lumens to prevent catheter-associated S. aureus infections.  See Skaar

Targeting bacterial iron metabolism through the use of chelators and gallium-based therapeutics has been demonstrated to effectively disrupt staphylococcal biofilms.

Inhibiting quorum sensing: Virulence factor production in S. aureus is regulated by quorum sensing (QS), a cell to-cell communication mechanism bacteria use to regulate gene expression in response to cellular density. The S. aureus QS system is under the control of the accessory gene regulator (agr) system and activation of the agr system by an accumulation of auto-inducing peptide (AIP) leads to activation of the agr regulatory network that controls expression of virulence factors by RNAIII, the major effector for downstream virulence expression and biofilm dispersal. Inhibiting QS would prevent the production of QS-regulated toxins such as delta-toxin, staphylococcal enterotoxin C, and Panton-Valentine leukocidin, thus restricting S. aureus’ ability to evade the host immune system, kill host cells, and disseminate.  See Skaar

Adaptive antibiotic resistance of P. aeruginosa is a recently characterized mechanism, which includes biofilm-mediated resistance and formation of multidrug-tolerant persister cells, and is responsible for recalcitrance and relapse of infections. The discovery and development of alternative therapeutic strategies that present novel avenues against P. aeruginosa infections are increasingly demanded and gaining more and more attention. Although mostly at the preclinical stages, many recent studies have reported several innovative therapeutic technologies that have demonstrated pronounced effectiveness in fighting against drug-resistant P. aeruginosa strains.  See Cheng

–Use of Essential Oils: The biofilm formation of pathogenic bacteria is considered a big challenge for the food industry and human/animal health. The QS mechanism regulates the bacterial biofilm formation; thus, destroying and/or disrupting this mechanism can help to prevent biofilm formation and then solve many health problems. EOs are composed mainly from two groups of single substances, terpenoids (monoterpene, sesquiterpene and di-terpene) and phenylpropanoids. Many plant EOs display promising anti-QS properties by preventing biofilm formation, which could be very important in reducing the virulence and pathogenicity of drug-resistant bacteria, especially for those that are food pathogenic. In fact, the use of plant EOs in food industry do not change the organoleptic properties of foods, and their use could thus be a promising natural alternative for several synthetic food preservatives. Finally, many plant EOs can represent a possible substitute for many traditional antimicrobial drugs, which have a significant negative impact on the environment and human/animal health. See Feo