Mechanisms of antibiotic resistance in Urinary Tract Infections: Why does Anti-Microbial Resistance Pose a Challenge?

Antimicrobial resistance (AMR) is a major global health issue, and in the urology and urogynecology sub-specialties poses a significant clinical challenge for healthcare providers.¹ Infectious disease experts worry that “the golden age of antibiotic therapy is coming to an end”¹ and that “there are limited successful treatments for infectious diseases caused by bacteria”.¹ Along with increasing morbidity and mortality rates, resistant infections are an economic burden to our healthcare system.¹

As the first organisms on Earth, bacteria are believed to have existed more than 3 billion years ago.² Antibiotics were subsequently introduced in the 20^th century to combat pathologic infections in humans.³ Soon after their introduction, isolates of antibiotics with acquired resistance were identified and this pattern of resistance has followed with each new antibiotic introduction. Modern medicine continues to struggle to adequately control the rising rate of multi-drug resistant organisms. According to the Centers for Disease Control and Prevention, about one-third of antibiotic use in people is not needed nor appropriate. In 2014, for example, outpatient health care providers in the United States wrote over 266 million antibiotic prescriptions, amounting to 835 antibiotic prescriptions for every 1,000 people.⁴

Antibiotic resistance describes the ability of certain bacteria to thrive and grow in the presence of antibiotics.⁵  Traditional methods to understand antibiotic resistance have been phenotypic in nature. One example of this is culturing bacteria found in the urine of suspected urinary tract infection (UTI) patients. The emergence of molecular technologies has enabled study of antibiotic resistance genes and improved understanding of how they contribute to antimicrobial resistance.

Antibiotic resistance (ABR) genes encode deoxyribonucleic acid (DNA) for the ability of bacteria to successfully thrive in the presence of antibiotics.⁵ Over billions of years, bacteria, along with their ABR genes, have evolved and developed resistance to antibiotics through intrinsic or acquired resistance mechanisms.⁶  ABR genes can be impacted by genetic mutations or shared amongst bacteria via horizontal gene transfer and are fully transmissible. This is one reason why the infectious disease community is still challenged to this day in controlling antibiotic resistance.

Intrinsic Mechanisms of Antibiotic Resistance⁶

DNA that is encoded in ABR genes allow bacteria to carry out certain intrinsic mechanisms which ultimately lead to phenotypic antibiotic resistance. Such mechanisms fall into 3 groups.

• Prevention of antibiotic access/entry into bacteria (minimization of bacterial intracellular antibiotic concentration)

Bacteria can prevent access of antibiotics into bacterial cells by reducing their own cell wall permeability. There are also efflux pumps intrinsic to bacteria that allow them to transport antibiotics out of the bacterial intracellular space thus reducing intracellular antibiotic concentration.

• Modification of antibiotic target proteins/sites in bacteria

Bacteria also modify antibiotic target protein sites via mutations. When the target protein sites of bacteria undergo mutational changes, the antibiotics can’t bind to bacteria with high affinity, rendering a reduced or inconsequential bactericidal effect. Alternatively, target site protection can occur when bacteria alter and modify the drug-binding site, preventing the antibiotic from ever successfully attaching to bacteria.

• Destruction of antibiotics via bacterial enzymatic-catalyzed hydrolysis

Bacteria secrete various enzymes that degrade antibiotics. As a result, this leads to antibiotic destruction and hence, resistance. Such enzymes may also modify the chemical structure of the antibiotic, preventing the antibiotic from binding to the bacteria’s target protein and exerting its bactericidal effect.

Acquired Antibiotic Resistance via Horizontal Gene Transfer¹

There are 3 major mechanisms whereby bacteria engage in horizontal gene transfer (HGT): conjugation, natural transformation, and transduction.¹

• Conjugation occurs when bacteria share DNA with each other via cell-to-cell contact, mating, or transfer of plasmid DNA.¹

• Natural transformation occurs when bacteria absorb free DNA from their environment and incorporate it into their own genome.¹ This process takes place when DNA is released and dispersed by donor bacteria into the environment. The DNA persists in the environment until recipient strains of bacteria uptake the DNA and incorporate it. Donor ABR genes are then expressed in the recipient bacteria.

• Transduction occurs when a bacteriophage, that has previously replicated in another bacterial cell, packages a small amount of the donor genome and transfers the genes to a recipient bacterial cell. Transduction is considered to play an important role in transferring ABRs.¹

Identification of ABR genes is important to fully understand resistance epidemiology and for identification of resistant strains, especially when ABR genes are either weakly or not expressed in vitro. Polymerase Chain Reaction (PCR) is a reliable source to detect and identify ABR genes as it is a highly sensitive test, provides rapid results, and provides health care professionals (HCPs) with the information about the presence or absence of specific ABR genes.⁵

Although ABR genes exist within the bacteria, it is important to note that methods used for detection of resistance markers only indicate the potential for the expression of actual phenotypic antibiotic resistance.⁵ ABR gene identification by PCR may not always translate to antibiotic resistance phenotypically in the clinical setting nor does the lack of ABR identification necessarily translate into antibiotic susceptibility. It’s very possible that the ABR gene may not be fully expressed or the gene may have mutated to a non-functional form. Additionally, the ABR gene may also be incomplete, leading to a disagreement between genotypic and phenotypic antibiotic resistance information.⁵ The phenomenon describing the lack of agreement between ABR genotype and antibiotic resistance phenotype is known as discordance. 

Discordance can arise due to ABR gene mutations; when mutations occur, the ABR gene is not fully expressed.⁷  From a biochemistry perspective, mutations may occur when bacteria are transcribing the ABR gene to mRNA, when the ribosomes are translating the mRNA to protein, or when protein activation takes place. Additionally, frameshift mutations in the coding area of the ABR gene may occur, rendering lack of protein production.⁷

Luby et al state that “Although the vast majority of molecular methods detect or quantify ARGs [ABR genes], the possible disconnect between genetic potential and phenotypic reality calls for complementary methods that provide better links between the two layers of information.”⁵  Providing both pooled resistance/phenotype and resistance genes/genotype information allows the physician to see what resistance patterns exist (phenotype) and what resistance might emerge (genotype).  Newer phenotyping  technologies such as Pooled Antibiotic Susceptibility Testing have emerged with supportive clinical evidence to demonstrate utility to aid in UTI diagnostics and treatment selection.

Request Infographic: Urinary Tract Infections

About the Author

Dr. William Lai has over 20 years of collective Global Medical Affairs experience in the pharmaceutical, biotechnology, and medical device industries encompassing over 20 therapeutic areas (including infectious diseases). Dr. Lai practiced clinical pharmacy at the University of Pennsylvania Medical Center and was part of an award-winning antibiotic stewardship program. He’s also served as a Professor of Clinical Pharmacy at two schools of pharmacy at the University of Southern California and the Keck Graduate Institute. At USC, he served as Director of the MannKind/University of Southern California School of Pharmacy Post-doctoral Industry Fellowship Program. Dr. Lai previously served as a Chapter President within the American Society of Health System Pharmacists (ASHP), held national level positions within ASHP, and served on the Advisory Council of North American for the Drug Information Association (DIA).

References

1. Huddleston JR. Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes. Infect Drug Resist. 2014; 7:167-176.
2. Alegado RA, King N. Bacterial influences on animal origins. Cold Spring Harb Perspect Biol. 2014; 6:1-16.
3. Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes.
   J Antimicrob Chemother. 2012; 67: 2640-2644.
4. Centers for Disease Control and Prevention, “Outpatient Antibiotic Prescriptions—United States, 2014,” accessed Dec. 12, 2016, https://cdc.gov/getsmart/community/pdfs/annual-reportsummary_2014.pdf.
5. Luby E, Ibekwe AM, Zilles J, et al. Molecular Methods for Assessment of Antibiotic Resistance in Agricultural Ecosystems: Prospects and Challenges. J Environ Qual. 2016; 45: 441-453.
6. Blair JMA, Webber MA, Baylay AJ, et al. Molecular mechanisms of antibiotic resistance. Nat Rev Microbiol. 2015; 13: 42-51.
7. Baunoch D, Luke N, Wang D, et al. Concordance between antibiotic resistance genes and susceptibility in symptomatic urinary tract infections. Infec Drug Resist. 2021; 14: 3275-3286.