Introduction

Bacteria are single-celled microscopic organisms that are widely spread in nature. They have significant effects on human life—they are used in industrial and medicinal processes, participate in natural material cycles, and can be applied in bioremediation of polluted environments. However, some of them are pathogenic, causing infectious diseases transmitted through food, water, aerosols, and in other ways (Newell et al. 2010; Scallan et al. 2011).

At present, the diagnosis and prevention of bacterial infectious diseases mainly relies on laboratory detection. Common methods for detection of pathogenic bacteria include bacterial culture, immunological methods, and molecular biological methods (Labib and Berezovski 2014; Torres-Chavolla and Alocilja 2009). Traditional culture is the gold standard for bacterial identification. However, culture techniques require specific equipment and professional operators and are time-consuming, making widespread and non-specialist applications difficult (Rajapaksha et al. 2019). Compared with bacterial culture, immunological methods, for example, enzyme-linked immunosorbent assay, are faster, but the complicated operations and the quality of antibodies can influence the experimental results. Molecular biological methods such as polymerase chain reaction (PCR) are highly-sensitive, but may generate a false-positive signal due to many PCR inhibitors in complex samples (e.g., food samples) and any pollution of samples (Levi et al. 2003). Moreover, PCR and PCR-based methods are incapable of discriminating live bacteria from dead ones, which may be a potential shortcoming to limit the future development of PCR (Wu et al. 2020b). Therefore, it is important to develop rapid, accurate, and portable/on-site testing methods for detection of pathogenic bacteria, which is of great significance for public health and clinical diagnosis.

Aptamer is a bioaffinity ligands that can specifically bind to the target, which can be divided into peptide aptamer and oligonucleotide aptamer. The peptide aptamer is a combinatorial protein reagent and its target so far has been focused on protein only. The peptide aptamer of the target protein was commonly selected with traditional yeast two-hybrid system. The peptide aptamer can bind its targets in living cells, resulting a profound influences in functional study within cells (Acquah et al. 2020; Li et al. 2011). Oligonucleotide aptamer is a single-stranded DNA or RNA sequence selected by systematic evolution of ligands by exponential enrichment (SELEX) techniques, also called “chemical antibodies” because of their high affinity to its targets. Generally, aptamer always refer to oligonucleotide one. Compared with natural antibodies, aptamers have some obvious advantages (Table 1). First, aptamers have higher surface density and cause less steric blockage, which helps to improve the efficiency of combination with targets (Lee et al. 2010). Second, their structure allows aptamers to maintain stability at room temperature and in ordinary storage conditions, while natural antibodies need strict storage conditions and are sensitive to environmental change. Third, aptamers can be chemically synthesized, produced, and purified according to strict protocols, which can save money or time in production and decrease the differences between each batch (Ray and White 2010). The obtained aptamers even can be further modified and optimized as needed. Fourth, aptamers can bind a wide range of targets, while natural antibodies can only bind with typical immunogenic macromolecules (Zhuo et al. 2017). Aptamer can specifically bind with analyte such as metal ions (Li et al. 2019b; Liu et al. 2018a), amino acids (Idili et al. 2019; Yuan et al. 2018), nucleotides (Ji et al. 2017), small organic molecules (Liu et al. 2019a; Qiu et al. 2018), peptides (Wu et al. 2019), toxins (Frohnmeyer et al. 2019; Sun and Zhao 2018), enzymes (Chen et al. 2016), other proteins (Lee and Zeng 2017), and even cells and bacteria (Sun et al. 2019a; Wu et al. 2014) with high affinity (Hermann and Patel 2000). Therefore, aptamers have been widely used as excellent molecular recognizers, and aptamer-based biosensors and bioassay methods for bacterial detection are expected to replace traditional methods, making the detection more rapid, sensitive, specific, and reliable.

Table 1 Comparison of nucleic acid aptamers and protein antibodies
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Biosensors are devices that detect an analyte in biological or chemical reactions by generating signals proportional to the analyte concentrations. It can detect analyte at the concentration of ng/ml or even fg/ml level. Biosensors can be divided into different types on the basis of the signal that is generated, such as electricity, heat, or light. Typical biosensors consist of the analyte, bioreceptor, transducer, electronics, and display (Bhalla et al. 2016) (Fig. 1). In this review, we briefly introduce some typical aptamer-based biosensors for detection of bacteria, most of which have adopted optical, electrochemical, or surface-enhanced Raman scattering (SERS) signal (Fig. 2).

Fig. 1
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Schematic diagram of typical biosensors. Typical biosensors consist of analyte, bioreceptor, transducer, electronics and display

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Fig. 2
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Schematic representation of different type aptamer-based biosensors. When the target bacteria specifically bind to aptamer, the detection system can output different signals such as colorimetric, fluorescent, electrochemical and SERS. And bacteria can be qualitatively or quantitatively detected by the corresponding aptamer-based biosensors

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SELEX techniques

The SELEX technique is a generic means for aptamer screening. In 1990, Ellington and Tuerk used SELEX technology to screen out random oligonucleotides that could specifically bind to organic dyes and DNA polymerase, respectively, and named them “aptamers” (Ellington and Szostak 1990; Tuerk and Gold 1990). Commonly used SELEX technique mainly include conventional SELEX, cell-SELEX, and genomic SELEX. The conventional SELEX technique comprises multiple cycles, and each cycle has three stages: (i) DNA or RNA libraries synthesized in vitro are mixed with the targets to form target–aptamer complexes; (ii) the complexes are separated from the free nucleic acids to remove oligonucleotides that are not bound to targets; (iii) the remaining bound sequences are used as templates for PCR amplification for the next round of screening. After about 20 rounds of selection, aptamers with high affinity and specificity to the target can be obtained (Teng et al. 2016). The cell-SELEX technique uses the whole-cell as target, which does not require protein purification or prior knowledge of the target on cells before selection, and the aptamers selected by it can be used to discover unknown surface proteins or new biomarkers on cells in their native conformation, which is the main merit of cell-SELEX (Marton et al. 2016; Zhuo et al. 2017). In contrast to conventional SELEX, genomic SELEX uses a genomic DNA library, the diversity of which is significantly reduced (Lorenz et al. 2006, 2010). In addition to the SELEX techniques above, some other SELEX technologies have emerged including negative SELEX, capillary electrophoresis-SELEX, magnetic bead-bead SELEX, microfluidic SELEX and in vivo SELEX (Ali et al. 2019; Yan et al. 2019).

Aptamer-based optical biosensors

Optical biosensors realize the detection through the optical signal changes caused by the interaction of the analyte with bioreceptors. Because of its safety and high resolution, optical biosensors have a wide range of applications in the detection of pathogenic bacteria via combination with aptamers. Optical biosensors can be divided into two general modes: label-free and label-based. In label-free sensors, the optical signals are directly generated by interaction between the analyte and the transducer. Label-based sensor uses a label to generates optical signals, which may be colorimetric, fluorescent, or luminescent (Damborský et al. 2016). According to the recent reports for bacteria detection by optical biosensors, here we mainly introduced colorimetric biosensors and fluorescent biosensors.

Aptamer-based colorimetric biosensors

Aptamer-based colorimetric biosensors detect analyte by color change depending on structural colors (Liu et al. 2009; Sivakumar et al. 2005), cationic polymers (Bala et al. 2016), oxidation of substrate by enzyme (Wu et al. 2015), catalyzed oxidation of nanomaterials (Hu et al. 2015), or the aggregation or disaggregation of nanoparticles (Mondal et al. 2018; Yousefi and Saraji 2019). This method does not need complicated analytical instruments, making the aptamer-based colorimetric biosensor simpler than most others.

Aptamer-based colorimetric biosensors usually use a sandwich structure to capture and identify bacteria. Wu et al. designed a gold nanoparticle (AuNP)-based enzyme-linked antibody-aptamer sandwich (nano-ELAAS) method to detect Salmonella typhimurium. Magnetic microparticles (MMP) were modified with S. typhimurium-specific aptamers (MMP-aptamers) to act as capture probes, pre-enriching S. typhimurium from samples; then S. typhimurium were subsequently sandwiched by MMP-aptamers and detection antibodies. Then the sandwich complex (MMP-aptamer/S. typhimurium/detector antibody) reacted with nanoprobes with a reporter antibody and horseradish peroxidase (HRP), which caused a color change that could be seen with the naked eye. Its sensitivity was much higher than that of colorimetric ELAAS and chemiluminescent ELAAS (Wu et al. 2014). Liu et al. adopted a similar sandwich structure to detect Listeria monocytogenes ranging from 10 to 106 colony-forming units (CFU)/mL. The L. monocytogenes could be captured by aptamer-modified magnetic nanoparticles (Apt-MNPs) and then recognized by immunoglobulin Y-coated silver nanoclusters (AgNCs). The AgNCs can oxidize o-phenylenediamine, making the color of reporting system change from blue to red (Liu et al. 2018b).

Aptamer-based colorimetric biosensors coupled with PCR can also achieve bacterial detection. Liu and his group combined PCR and G-quadruplex DNAzyme catalytic reaction to realize sensitive, low-cost, convenient detection of L. monocytogenes and Helicobacter pylori. They constructed a unique modified reverse primer, which bound to an anti-DNAzyme sequence at its 5′-end via a poly-A linker. This strategy can be used to synthesize DNAzyme aptamers at the 3′-end of PCR products. After hemin was added, the aptamer section of the double-stranded products formed a G-quadruplex DNAzyme. Oxidation of 2,2′-azino-bis(3-ethylbenzthiazoline)-6-sulfonic acid was catalyzed by the G-quadruplex DNAzyme, causing the system to change from colorless to green (Fig. 3). This strategy avoids a series of complicating preparations before detection, and can be used in practical samples, so it is more serviceable than other methods (Liu et al. 2018c, d).

Fig. 3
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The H. pylori detection via aptamer-based colorimetric biosensor coupled with PCR by Liu and his group. (Liu et al. 2018c). (a) The genomic DNA from H. pylori was amplified through PCR with specific forward primer and anti-DNAzyme reverse primer (ADRP). After thermal denatured, a single chain with DNAzyme aptamer was obtained. (b) The DNAzyme aptamer on H. pylori DNA chain combined with hemin to form complete G-quadruplex DNAzyme, which can catalyze the oxidation of ABTS and output the colorimetric signal

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To improve the efficiency of aptamers in colorimetric biosensors, researchers have optimized aptamers for bacteria detection. Sun et al. obtained an optimal truncated aptamer with higher affinity after optimizing the original aptamer sequence for Vibrio parahaemolyticus by truncation and site-directed mutagenesis. Then the truncated aptamer was conjugated to magnetic nanoparticles (MNPs) to construct capture probes, and G-quadruplex DNAzyme was used to catalyze chromogenic reaction of 3,3′,5,5′-tetramethylbenzidine (TMB). This method could detect V. parahaemolyticus in the range of 102 ~ 107 CFU/mL (Sun et al. 2019b). Kim et al. also used truncated aptamers for better adsorption onto AuNPs to detect Campylobacter in chicken carcass samples by the aggregation of AuNPs which could causes color change (Kim et al. 2018).

With the successive study of aptamer-based colorimetric biosensors, techniques such as multicolor detection and colorimetric analysis associated with other methods have also been developed. Liu et al. innovatively applied gold nanorods (AuNRs) for detection of L. monocytogenes (Fig. 4). In the presence of L. monocytogenes, a sandwich-type complex formed by Apt-MNPs and nanoenzyme that could oxidize TMB to produce TMB2+ captured the target and quantitatively etched AuNRs with various aspect ratios so that the system output multicolor signals for detection (Liu et al. 2019b). Wu et al. (2018) and Das et al. (2019) associated colorimetric signals with SERS signals and electrochemical signals, making the detection of pathogenic bacteria more sensitive and accurate.

Fig. 4
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The aptamer-based colorimetric biosensor for L. monocytogenes detection. (Liu et al. 2019b). The Apt-MNP is used as capture probe for L. monocytogenes. The Apt-MNP (black), L. monocytogenes (blue) and oxidase-like nano-artificial enzyme(green) form a sandwich-type immunocomplex that can catalyze TMB to TMB2+. With the concentration of L. monocytogenes increased, more TMB2+ is generated and then etched the AuNRs with various aspect ratios, resulting vivid color change in the solution

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Aptamer-based fluorescent biosensors

Aptamer-based fluorescent biosensors achieve quantitative analyte detection through fluorescence change via the combination of aptamers and fluorophores or fluorescent nanomaterials. Compared with colorimetric biosensors, it is easier to realize sensitive and selective detection using fluorescent biosensors.

The sandwich structure applied in aptamer-based colorimetric biosensors can also be employed in aptamer-based fluorescent biosensors. Cheng et al. prepared vancomycin-stabilized fluorescent gold nanoclusters (AuNCs@Van) and aptamer-coated magnetic beads for identifying and capturing Staphylococcus aureus. This dual recognition strategy of vancomycin and aptamer greatly improved the specificity and sensitivity of the detection, and it could be used to detect about 70 CFU/mL S. aureus in complex samples (containing 3 × 108 CFU/mL other bacteria) (Cheng et al. 2016). Yu et al. designed a similar dual recognition strategy with AuNCs@Van and aptamer-modified AuNPs (Apt-AuNPs), with the AuNCs@Van as an energy donor and the Apt-AuNPs as an energy acceptor. Via a fluorescence resonance energy transfer (FRET) mechanism, S. aureus could be detected sensitively and selectively in 30 min. The FRET signal was linear with the concentration of S. aureus (Yu et al. 2017).

Aptamer-based fluorescent biosensors have also been developed to detect different pathogenic bacteria simultaneously. Li et al. reported a method with excellent recovery efficiency and rapid identification capability for simultaneous detection of multiple pathogenic bacteria. The aptamer-modified fluorescent-magnetic multifunctional nanoprobes captured Escherichia coli or S. typhimurium and effectively separated them on the basis of different magnetic responses to the external magnetic field (Li et al. 2018). Duan et al. attached aptamers labeled with fluorescent dyes to carbon nanoparticles, achieving sensitive and stable simultaneous detection of V. parahaemolyticus, S. aureus, and S. typhimurium through a multiple FRET system (Duan et al. 2016b).

Current aptamer-based fluorescence detection technology is developing in the direction of rapidity, simplicity, and convenience to meet the needs of clinical diagnosis, environmental monitoring, and food safety. Qiao et al. established a FRET assay that is expected to be applicable to clinical specimens such as nasal swabs and plasma for detection of methicillin-resistant S. aureus (MRSA) based on a PBP2a protein aptamer. Compared with traditional antimicrobial susceptibility tests, this strategy greatly decreases the time required for detection, and is not necessary to isolate and purify bacteria from clinical samples (Qiao et al. 2018). Shrivastava et al. detected pathogenic bacteria sensitively by quantitative imaging using smartphones, in which they used aptamer-conjugated fluorescent MNPs to capture target bacteria and the smartphone had a light-emitting diode that acted as an excitation source for fluorescence imaging (Fig. 5). This method can realize rapid on-site detection of S. aureus and be applied in remote regions and resource-limited settings (Shrivastava et al. 2018).

Fig. 5
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Quantitative detection of S. aureus by smartphone with aptamer-based fluorescent. (Shrivastava et al. 2018). Aptamer-conjugated fluorescent MNPs was used to capture target bacteria and the smartphone had a light-emitting diode that acted as an excitation source for fluorescence imaging

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Aptamer-based electrochemical biosensors

Aptamer-based electrochemical biosensors can be traced back to 2004. Ikebukuro et al. constructed a sandwich-type biosensor that could be used to quantitatively analyze thrombin with current as the signal, using aptamers labeled with glucose dehydrogenase (Ikebukuro et al. 2004). Since then, aptamer-based electrochemical biosensors have been extensively used in monitoring health, environmental pollution, and food safety (Li et al. 2019c; Mishra et al. 2018).

Roushani et al. constructed a method to detect Pseudomonas aeruginosa in serum by aptamer-based electrochemical biosensors. They deposited silver nanoparticles (AgNPs) on a glassy carbon electrode (GCE) to increase surface area, resulting in significant acceleration of electron transfer and enhancing electrochemical signal efficiently. P. aeruginosa could be captured by NH2-aptamer covalently attached to the AgNP/GCE surface and detected according to the charge transfer resistance in the absence or presence of the target, and the concentration of P. aeruginosa was closely related to the increased degree of impedance. This method could detect P. aeruginosa in the range of 102 to 107 CFU/mL (Roushani et al. 2019). Similarly, Muniandy et al. coated reduced graphene oxide titanium dioxide (rGO-TiO2) nanocomposite on a GCE surface to construct an rGO-TiO2/GCE platform, and combined aptamers with the rGO-TiO2 to capture S. typhimurium. The aptamer–bacteria complex (S. typhimurium/Apt/rGO-TiO2/GCE) caused a physical barrier that could restrain the electronic dynamics at the GCE surface. This strategy needs only small volumes of samples, and is able to achieve quick determination by using a portable instrument. Thus, this approach possesses a huge potential in on-site detection (Muniandy et al. 2019).

Aptamer-based electrochemical biosensors can also be used to monitor bacterial proliferation. Jo et al. developed an aptamer-functionalized capacitance sensor array to monitor bacterial growth and death and to assess bacterial tolerance to antibiotics. The aptamer was immobilized on the sensor surface, and the number of viable bacteria adhering to the sensor surface was closely related to the capacitance. Therefore, the growth of bacteria could be monitored in real-time by measuring the change of capacitance (Jo et al. 2018). Zhang et al. used aptamers linked to magnetic beads to capture target pathogenic bacteria, then the trapped bacteria were cultivated in multichannel conductometric sensors after magnetic separation. The growth kinetics of bacteria could be measured through time-dependent conductivity changes of the culture media. Consequently, a curve of normalized apparent conductivity values against incubation time could be obtained, which reflected the growth of bacteria (Zhang et al. 2019) (Fig. 6).

Fig. 6
figure 6

The procedure of aptamer-based multichannel conductometric sensor for the determination of viable bacteria. (Zhang et al. 2019). The bacteria were captured by the aptamer-functionalized magnetic beads (I, II) and separated through the magnetic separation (III). Then, the growth kinetics of bacteria are obtained by measuring the time-dependent conductivity changes with a conductometric sensor (IV)

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Aptamer-based SERS methods

SERS is an emission technique that allows analyte molecules to be absorbed onto the SERS substrate, thus the analyte is exposed to the hot spots created by the substrates, remarkably enhancing the Raman signal (Wu et al. 2020a). Roughened silver, copper or gold is usually used as the SERS substrates (Mosier-Boss 2017). SERS technology can acquire information about the chemical structure of a substance at the molecular level and provide fingerprint identification spectra. It possesses high sensitivity and selectivity, fast detection speed, and very low background interference, and is suitable for multicomponent analysis. Combining SERS detection technology and aptamer recognition ability can improve the detection accuracy and the sensitivity of the analysis (Wang et al. 2019). When analytes combine with the aptamers, the SERS signal can be increased 104 to 106 fold (Chen et al. 2008).

Díaz-Amaya et al. covalently conjugated aptamers to 4-aminothiophenol (4-ATP)-modified AuNPs (4-ATP-AuNPs) to construct nanoprobes for detection of E. coli. In the presence of target bacteria, the E. coli-aptamer-4-ATP-AuNP composite was formed and gradually precipitated, and the concentration of E. coli could be determined based on the supernatant SERS signal intensity due to their negative linear correlation, and E. coli O157:H7 could be detected in the range of 102–106 CFU/mL (Díaz-Amaya et al. 2019).

Gao and He developed a nitrocellulose membrane platform for rapid detection of pathogenic bacteria by using SERS patterns. By incorporating a vacuum filtration system, the bacteria trapped by aptamers were concentrated onto the nitrocellulose membrane, then the AuNPs deposited on the membrane combined with aptamer–bacteria complexes, dramatically enhancing the Raman signal (Gao and He 2019). Pang et al. synthesized aptamer–Fe3O4@gold magnetic nanoparticles for bacteria enrichment and vancomycin and 4-mercaptobenzoic acid (4-MBA)-modified AuNPs (Au@MBA@Van) as Van-SERS tags for sensitive quantification of S. aureus. Owing to the golden surface, aptamer-Fe3O4@gold magnetic nanoparticles also have the ability to be as SERS substrates. Therefore, this strategy provided more hot spots for the amplification of Raman signal to improve the sensitivity of bacteria detection significantly (Pang et al. 2019).

Gold nanoparticle dimers (AuNDs), whether symmetrical or asymmetrical, show stable SERS activity in solution and are excellent SERS substrates because of their uniform and dispersed structure and the strong hot spots between the AuNPs. Wu et al. constructed asymmetric AuNDs with two different sizes of AuNPs, which were modified with HRP, aptamer and Raman reporters, complementary series respectively, to realize dual signal detection of bacteria. In the presence of target bacteria, the HRP-aptamer-AuNPs captured the bacteria and deposited, the asymmetric AuNDs disassembly, the SERS signal intensity of the supernatant ascribing to the single AuNPs declined, while the resuspending solution showed a significant color change on addition of TMB and H2O2 (Wu et al. 2018). Wu et al. constructed symmetrical AuNDs as probes for Shigella sonnei detection. 4-MBA, europium chloride hexahydrate and 1,10-phenanthroline formed a compound structure named as Eu complex. Then, symmetrical AuNDs was constructed by two citrate-stabilized gold nanoparticles (cit-AuNPs) with Eu complex as the linker, and modified with S. sonnei specific aptamers subsequently. When the symmetrical AuNDs specifically captured target bacteria and nonbound symmetrical AuNDs were removed through centrifuging, the symmetrical AuNDs bound with target bacterium were determinated by SERS detector. The intensity of the SERS signal of 4-MBA was proportional to the concentration of target bacteria. The successful synthesis of AuNDs simplified the preparation of SERS substrates and Raman reporters and made the detection procedure much more convenient. This dual-function nanomaterial combined with SERS technology improved the detection performance of this biosensor (Wu et al. 2020a).

AgNPs have also been developed as SERS substrates. For example, Gao et al. took the aptamer interact with S. aureus forming a bind configuration. Then, they used the formation as the template for AgNPs synthesis in situ, synthesizing S. aureus-aptamer AgNPs as the SERS substrates to monitor the concentration of S. aureus (Fig. 7). The method can directly identify a single bacterium through the SERS mapping technique which is particularly useful in the detection and analysis of bacteria because of its capability to scan a certain area to produce heat maps (Gao et al. 2017; Gao and He 2019). Duan et al. synthesized Ag@Au core/shell nanoparticles as SERS substrates and modified them with aptamers to form nanoparticle–bacteria–aptamer sandwich complexes, and used to detect S. typhimurium in real food samples based on the SERS intensity changed with changes of the S. typhimurium concentration (Duan et al. 2016a).

Fig. 7
figure 7

The aptamer-based SERS detection for S. aureus via aptamer dependent AgNPs synthesized in situ. (Gao et al. 2017). The aptamaer were used as capture probe for S. aureus and the template for AgNP synthesized in situ. And the bacteria-aptamer@AgNP generated obvious SERS signals which was linear with the concentration of S. aureus

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Other aptamer-based methods

In addition to the above common detection methods, the association of aptamers with other sensitive techniques is also used in the detection of pathogenic bacteria.

The quartz crystal microbalance (QCM) biosensor is a mass-sensitive biosensor, which works based on the change of resonance frequency (Wang et al. 2018). On the basis of this principle, Bayramoglu et al. detected Brucella melitensis in milk and milk products. They first attached aptamers to magnetic nanoparticles and QCM chips, respectively. Then the target bacteria were pre-enriched and eluted by binding to aptamers on magnetic nanoparticles, and were quantitatively detected by the final resonance frequency signals produced after binding to aptamers attached to the QCM chip (Bayramoglu et al. 2019).

Detection of pathogenic bacteria via gas pressure change in a closed vessel is an extremely sensitive method. As illustrated in Fig. 8, Li et al. used aptamer-coated magnetic nanoprobes and vancomycin-functionalized platinum nanoparticles (PtNPs@Van) to capture S. aureus, and the PtNPs@Van catalyzed oxidation of H2O2 to O2, resulting in a marked pressure increase, realizing environmentally friendly detection of S. aureus (Li et al. 2019a).

Fig. 8
figure 8

Schematic illustration for aptamer-based detection of S. aureus via gas pressure. (Li et al. 2019a). The PtNPs@Van catalyze the decomposition of H2O2 in the presence of S. aureus resulting in the pressure increased, which was positively correlated with the concentration of S. aureus

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Polyethylene glycol silane (silane–PEG–COOH) is a splendid material for bacterial detection because of its bacteria-repelling surface, which can prevent the adsorption of nonspecific bacteria on the sensor surface. Maldonado et al. used an ultrasensitive photonic biosensor based on a bimodal waveguide interferometer and aptamer for the direct detection of MRSA. With the help of silane–PEG–COOH, the specificity of the detection was greatly improved (Maldonado et al. 2020).

Microchip capillary electrophoresis (MCE) is a technique that possesses a rapid response rate, high separation efficiency, short analysis time, and low sample and reagent consumption (Castro and Manz 2015). MCE is often coupled with laser-induced fluorescence (LIF) to detect bacteria. Zhang et al. (2018) first separated the bacteria–aptamer complex and free aptamer based on the differences in the charge-to-mass ratio by MCE and then detected target bacteria by LIF, and successfully detected S. typhimurium in milk samples. Luo et al. (2020) detected S. typhimurium and P. aeruginosa via the association of aptamer-based strategy, a novel universal primer-duplex PCR process (UP-DPCR), and MCE-LIF technology, achieving high sensitivity of different bacterium detection.

The photo electrochemical (PEC) electrode is an emerging and fast-developing sensing strategy. Compared with traditional electrochemical detection, PEC biosensors have very low background noise and high sensitivity. A high-performance PEC electrode combined with CdS quantum dots modified by an aptamer can detect E. coli with high specificity and stability (Dong et al. 2020).

Besides the aptamer-based biosensors, lateral chromatography test strips is also a simple biosensor for rapid detection of pathogenic bacteria. Liu et al. proposed a novel strategy to visually and sensitively detect viable pathogenic bacteria based on an isothermal RNA amplification reaction-based bioactive paper-based platform (Fig. 9). They devised a low-cost paper-based platform to visually detect L. monocytogenes. RNA isothermal amplification products of L. monocytogenes hybridized with AuNP-thiolated DNA on the paper-based platform. When migrating along the strip, the hybridized products combined with the capture probe embedded in test area, making AuNPs accumulated and characterized a red band. And the two-dimensional bar code of the result could be built by software which could be shared with distant investigators for faster analysis. This portable, integrated test model holds a great promise for rapid on-site analysis of pathogenic bacteria (Liu et al. 2014).

Fig. 9
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The isothermal RNA amplification and the bioactive paper-based platform devised by Liu et al. (2014). The specific RNA was isothermally amplified from infected food samples and loaded in the sample pad. As migrating to the conjugate pad, it would hybridize with AuNP-thiolated DNA, and next combined with the capture probe embedded in test area, making AuNPs accumulated and characterized a red band. The excess AuNP-thiolated DNA would continually migrate to control area, forming the second red band by hybridized with capture probe here. And the two-dimensional bar code of the result could be built by software which could be shared with distant investigators for faster analysis

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The limitations of aptamer-based methods

Aptamers have received extensive attention in the detection of pathogenic bacteria. They simplify the enrichment processes and reduce the detection time owing to their high affinity and specificity. Table 2 shows the comparison between the different type of aptamer-based biosensors. Nevertheless, aptamer-based methods for pathogenic bacteria detection still have some drawbacks, which restrict the development of their applications. Aptamers obtained by SELEX generally have 60–100 nucleotides. Too long aptamers may lead to self-folding, resulting the binding between aptamer and its target reduced (Sun et al. 2019b). And the targets of bacteria-specific aptamers are ordinarily some molecules on the bacteria surface, such as proteins, polysaccharides and so on. Due to this fact, the difficulty of screening would be increased if the bacterial surface is in negative charge when the phosphate backbone of aptamer is also in negative charge (Bayat et al. 2018; Cai et al. 2018). Moreover, although the stability of aptamers in vitro is better than that of natural antibodies, aptamers are easily degraded by nuclease in vivo (Yan et al. 2019; Zhou and Rossi 2017). The high affinity between aptamer and its target only is shown under suitable conditions, which may be difficult to apply in vivo (Keefe et al. 2010). Furthermore, there is no systematic methodology for the development of aptamer, which may hinder the application of aptamer. Therefore, it is necessary to optimize SELEX techniques or develop novel SELEX techniques, which are more suitable for the conditions in complex biologic samples or in vivo.

Table 2 Summarize of aptamer-based bacteria detection
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Conclusion and Future prospects

In summary, we reviewed the recent advances on applications of different type aptamer–based biosensors for pathogenic bacteria detection. The emergence of aptamer and their combination with other technologies has supplied many new sensitive, rapid, and specific methods for bacteria detection. Aptamer as a biomolecule can be modified on various nanomaterials through different chemical reactions. Combining with nanomaterials is able to make aptamer more stable against enzyme degradation (Liang et al. 2014). It can be estimated that, with the rapid development of novel nanomaterials, more drawbacks of aptamer can be overcame. Recent years, there are some researchers report the special nucleic acid molecules constituted by artificial bases, which are designed for great molecular recognition, high stability or other useful features (Bai et al. 2020; Jin et al. 2017; Liang et al. 2016; Wang et al. 2017). As a fast-developing technique, aptamer is expected to be a useful tool for bacteria detection in environment monitoring, food safety inspection, and diagnosis of infectious diseases.