Ninety-five years since penicillin was discovered
[1], and despite the technological advances of the era, continued efforts are still being made to improve health systems worldwide due to emerging pathogen epidemics and the burden of hospital-care-associated infections (HCAIs), which today are a major public health concern globally
[2][3]. In addition, the emergence of virulent and high-risk bacterial strains, such as “ESKAPE” pathogens (
Enterococcus faecium,
Staphylococcus aureus,
Klebsiella pneumoniae,
Acinetobacter baumannii,
Pseudomonas aeruginosa and
Enterobacter species), represent a global threat to human health
[4]. Therefore, the rapid detection, quantification, and adequate treatment of infectious microorganisms are challenges to protecting public health
[5]. Traditional methods for the detection of pathogenic bacteria are culture-based methods and biochemical tests, which are low cost, easy to operate, and highly standardized, but they lack differentiation between the target and other non-target endogenous microorganisms, they produce false negative/positive results, they are time- and labor-consuming procedures, and they are unable to detect viable but nonculturable cells
[6]. Antibodies have made tremendous contributions in a wide range of applications. However, there are certain limitations associated with their use; monoclonal antibodies generally are incapable of membrane penetration due to their larger size and hence are less ideal as carriers for the targeted delivery of cytotoxic molecules inside cells. The production of monoclonal antibodies is laborious, expensive, time consuming, and suffers from batch-to-batch variations; they are also immunogenic, temperature sensitive, and their target binding kinetics cannot be easily modified
[7]. In addition, detection with antibodies is not accurate when there are minimal amounts of microorganisms. In some cases, the detection is not precise due to the null specificity of some antibodies or due to false positives
[8]. Thus, aptamers are considered to be an alternative to antibodies in many biological applications
[9]. Molecular approaches such as quantitative PCR are often used for the rapid and accurate enumeration of pathogen-derived nucleic acids; however, some nucleases may inhibit the enzymes of PCR resulting in false-negative results
[10]. Aptamers are proposed as substitutes for traditional detection methods; they include having an oligonucleotide single-stranded DNA (ssDNA) or RNA with target-selective high-affinity features, considered as nucleic acid-based affinity ligands
[11][12], and which do not differ in specificity or affinity. RNA aptamers have greater flexibility and produce a greater variety of possible structural configurations
[13]. Aptamers also have high stability, rapid production (synthesis or modification), low immunogenicity, are economic—they can be used for a wide range of targets—there are no animals needed for their production, they can be created against targets such as toxic or non-immunogenic molecules, and no cold chain for transportation and maintenance is needed
[14]. DNA or RNA aptamers in comparison to antibodies can undergo reversible folding and unfolding, leading to a greater stability and a simpler elution of the bound target from the aptamer
[15]; additionally, aptamers bind to their targets with high affinity and specificity due to their three-dimensional structure
[12]. The binding of aptamers to their target results from the structure’s compatibility, electrostatic interactions, Van der Waals forces, hydrogen bonds, or a combination of these
[16]. The affinity of the aptamers for their target molecule is measured using their dissociation constant (Kd)
[17]. In the treatment of microbial infections, the aptamer-based systems have been found to be talented tools, regarding their promising anti-biofilm and antimicrobial activities. Aptamers can reduce or inhibit the effects of bacterial toxins, inhibit pathogen invasion to immune cells, and they can also be used in drug delivery systems
[18]. To design aptamers, SELEX (Systematic Evolution of Ligands by Exponential Enrichment) has been employed as a useful technique for selecting nucleic acid ligands that interact with the target molecule in a desirable manner. SELEX is an iterative process of selection and amplification, in which large pools of nucleic acid molecules (>1 trillion distinct sequences) are challenged to bind to a desired target under defined conditions such as temperature and salt concentration; later, these sequences are amplified to generate a new population of enriched molecules. In SELEX, a negative selection is completed, which involves the incubation of a cell or microorganism closely related to the nucleotide sequences previously selected and the removal of sequences that are non-specific to the target molecule
[19]. Finally, using bioinformatics programs, with secondary structures from the sequences selected, Kd, the different probable binding sites, and the structure of tertiary bonding are determined
[20].