sensors Article Immunomagnetic Separation Improves the Detection of Mycobacteria by Paper-Based Lateral and Vertical Flow Immunochromatographic Assays Alejandra Ben Aissa 1 , Barbara Araújo 1,2 , Esther Julián 3 , Maria Valnice Boldrin Zanoni 2 and María Isabel Pividori 1,4, * 1 Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; alejandra.benaissa@eurecat.org (A.B.A.); babiiii.cas@gmail.com (B.A.) 2 Department of Analytical Chemistry, Institute of Chemistry, São Paulo State University, Araraquara 14800-060, SP, Brazil; maria.valnice@unesp.br 3 Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Esther.Julian@uab.cat 4 Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain * Correspondence: Isabel.Pividori@uab.cat; Tel.: +34-93-581-1976 Abstract: This work addresses a method that combines immunomagnetic separation (IMS) and paper- based nucleic acid immunochromatographic assay for the sensitive detection of Mycolicibacterium fortuitum (basonym Mycobacterium fortuitum) In particular, the preconcentration of the bacteria was achieved by using magnetic particles modified with an antibody specific towards mycobacteria.   Following the IMS, the bacteria were lysed, and the genome was amplified by double-tagging PCR, Citation: Ben Aissa, A.; Araújo, B.; using a set of primers specific for the 16S rRNA gene for Mycobacterium. During the amplification, Julián, E.; Boldrin Zanoni, M.V.; the amplicons were labeled with biotin and digoxigenin tags. Moreover, a comparative study of Pividori, M.I. Immunomagnetic paper-based immunochromatographic platforms, relying on vertical and lateral flow and on the use Separation Improves the Detection of of streptavidin gold nanoparticles as a signal generating system, was also performed. The visual Mycobacteria by Paper-Based readout was achieved when the gold-modified amplicons were captured by the anti-DIG antibody Lateral and Vertical Flow in the test line. The analytical performance of both methods, nucleic acid vertical flow (NAVF) Immunochromatographic Assays. and nucleic acid lateral flow (NALF), is also discussed. Although NALF showed lower limit of Sensors 2021, 21, 5992. https:// detections (LODs), both NALF and NAVF combined with IMS were able to detect the required LOD doi.org/10.3390/s21185992 in hemodialysis water, becoming two promising and useful techniques for the rapid screening of water supplies in hemodialysis centers, to prevent the exposure of immunosuppressed patients to Academic Editor: Benoît Piro contaminated sources. Received: 3 August 2021 Accepted: 31 August 2021 Keywords: rapid diagnostic tests; lateral flow assay; vertical flow assay; gold nanoparticles; my- Published: 7 September 2021 cobacteria; double-tagging PCR Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- 1. Introduction iations. The recent outbreak of a communicable disease that spread globally throughout international borders in a matter of days highlighted the need for rapid diagnostic tests (RDTs), able to provide prompt diagnosis and to help implement security measures to prevent interruption of the transmission chain. Strong research efforts are thus focused Copyright: © 2021 by the authors. on introducing RDTs in low resource settings for the rapid screening of patients requiring Licensee MDPI, Basel, Switzerland. treatment, instead of standard clinical diagnostic performed by highly qualified personnel This article is an open access article in centralized laboratories [1–5]. Furthermore, because of these rapid tests, there have been distributed under the terms and increased attention on different areas related to human and animal health [6], as well as conditions of the Creative Commons other fields, such as food safety, and water and soil quality monitoring [7]. Attribution (CC BY) license (https:// Rapidity, sensitivity, and specificity are not the only features that define these tests, creativecommons.org/licenses/by/ they are also known for their simplicity, robustness, portability and, particularly, low 4.0/). Sensors 2021, 21, 5992. https://doi.org/10.3390/s21185992 https://www.mdpi.com/journal/sensors Sensors 2021, 21, 5992 2 of 13 cost [8]. These requirements are compatible with the use of paper as a substrate [9]. Differ- ent types of rapid tests are based on cellulose, such as substrate, including immunochro- matography [10]. These devices are built by overlapping a series of pads, which enable the flow of the sample and reagents due to capillary forces. In lateral flow formats, the movement of the fluids is produced through the strip by capillarity [7]. Similarly, vertical flow assays are based on the pass of the sample through a series of layered membranes by capillarity, but in this instance, gravity also plays an important role in speeding-up the process [11]. Even though immunochromatographic tests are traditionally used for qualitative and semi-quantitative analysis [12], these devices are also connected to readout systems, such as smart phones, for quantitative applications [12,13]. However, some improvements, in terms of sensitivity, are still needed, as recently highlighted in the case of some antigen LFAs for SARS-CoV-2, attributed to a sampling procedure [14]. In this regard, the preconcentration of the sample plays an important role in improving the limits of detection and sensitivity of the technique. The magnetic particles can be an approach to solve this drawback. The use of these materials, modified with biomolecules, allows for specific biorecognition, followed by the specific capture, magnetic isolation, and preconcentration of a huge range of analytes, including cells, proteins, and small molecules, among others, from a large volume of a complex matrix [15–17]. For instance, an electrochemical magneto immunosensor, based on magnetic nanoparticles able to detect foodborne pathogens as low as 1 CFU in 25 mL of milk after 8 h of pre-enrichment, was previously reported on by our research group [18,19]. Moreover, to achieve the required limits of detection, amplification of DNA remains an ineluctable procedure for the sensitive detection of some pathogens. During this pandemic, PCR tests proved to be state-of-the-art and the dominant diagnostic tests for communicable diseases [20]. Unfortunately, the first generation of nucleic-acid amplification technolo- gies based on PCR cannot feasibly be incorporated into “classical” RDTs, since it requires thermocycling platforms, trained personnel, and infrastructure, including a reliable power supply, which constitutes a critical barrier for PCR in scarce-resource settings [21]. Nowa- days, there are different solutions to bridge these barriers. For instance, different companies offer cheap, portable, battery-operated thermocyclers [22]. Our group was pioneer in the integration of PCR in RDTs based on electrochemical genosensing devices [23]. Since this early report, different routes, based on PCR, for the amplification of the analytical signal, to increase the sensitivity of the readout, were explored. A double-tagging PCR amplification strategy with electrochemical readout was reported on [24,25]. In this approach, a double-tagged set of primers labeled with small tags (e.g., biotin, digoxigenin, fluorescein, -SH, among others) was used during amplification to achieve immobilization on the platform and further readout. This method can easily be multiplexed, up to three pathogens [26]. Even improved analytical features were achieved by combining double-tagging amplification with immunomagnetic separation (IMS) [19]. The integration of double-tagged amplicon to RDTs based on immunochromatography was also reported [27,28], showing a comparable sensitivity for the detection of double-tagged amplicons: electrochemical biosensing and lateral flow labeled with Au-NPs [28] and carbon nanoparticles [29]. In this paper, the integration of immunomagnetic separation, the double-tagging PCR amplification, and two different immunochromatography paper-based platforms are presented, for the detection of Mycobacterium fortuitum. This is one of the most common mycobacteria in contaminated hemodialysis waters, which can put immunocompromised patients at risk. Hence, it is important to continuously monitor water supplies in hemodial- ysis centers, to minimize the exposure of renal transplantation and immunocompromised individuals to contaminated sources [30]. In detail, this work presents a comparative study of the two paper-based platform configurations, based on nucleic acid immunochromatog- raphy. The role of the IMS performed with anti-Mycobacteria antibody functionalized magnetic particles was also studied [31]. Sensors 2021, 21, 5992 3 of 13 2. Materials and Methods 2.1. Instrumentation and Materials Glass fiber conjugate pad (GFCP083000) and cellulose fiber sample pad strips (CFSP203000) were purchased from Millipore (Burlington, MA, USA). Absorbent pads (CF7) and nitrocellulose membranes (FP120HP) were from GE Healthcare (Chicago, IL, USA). Whatman® Protran® nitrocellulose membrane used for vertical flow devices (Z670634) was provided by Sigma (Merck KGaA, Darmstadt, Germany). Gentle Tape 2.5 cm × 5 m roll was from Leukopor and Miriad RVF cartridges were acquired from Euromedex (Souffel- weyersheim, France). Lateral flow strips Adhesive Backing Cards were obtained from Kenosha C.V. (Amstelveen, The Netherlands). The dispensing of the test and control line was performed using a Lateral Flow Reagent Dispenser from Claremont Bio (Upland, CA, USA) combined with the KDS Legato™ 200 series syringe pump from KD Scientific, Inc. (Holliston, MA, USA). 2.2. Chemicals and Biochemical InnovaCoat® GOLD 40 nm Streptavidin gold nanoparticles (streptAv-AuNPs) were purchased from Innova Biosciences (Cambridge, UK). Dynabeads™ M-280 Tosylactivated magnetic particles (2.8 µm, 30 mg mL−1 , 2 × 109 MP mL−1 ) were provided by Invitrogen Dynal AS (Oslo, Norway). Polyclonal antibody to anti-LAM from Mycobacterium (MBS315001) was from My- BioSource (San Diego, CA, USA). All buffer solutions were prepared with Milli-Q water and all other reagents were in analytical reagent grade (supplied from Sigma). The composition of these solutions were: borate buffer (0.1 mol L−1 boric acid, pH 8.5); conjugate diluting buffer (2 mmol L−1 borate pH 7, 10% w/v sucrose); running buffer (0.01 mol L−1 phosphate buffer pH 7.4, 1% BSA, 0.05% Tween 20); ammonium sulfate buffer ((NH4 )2 SO4 3 mol L−1 in borate buffer); blocking buffer/PBS 0.5% BSA (10 mmol L−1 phosphate, 0.5% w/v BSA, pH 7.4); washing buffer/PBS 0.1% BSA (10 mmol L−1 phosphate, 0.1% w/v BSA, pH 7.4); sample pad buffer (0.01 mol L−1 phosphate buffer pH 7.4, 1% BSA, 0.05% Tween 20). 2.3. Oligonucleotides Sequences The oligonucleotides were obtained from Sigma (Berlin, Germany). These sequences, complementary to the region of 16S rRNA gene common to all members of the genus Mycobacterium, were selected from a previous publication [32]. Biotin (BIO) and digoxigenin (DIG) were used to achieve the double tagging of the amplicon, both inserted in 50 end of the primers. The primer sequences as well as the tags used for the PCR amplification are shown in Table 1. Table 1. Sequences of the set of primers for the double-tagging PCR amplification for the detection of M. fortuitum. Strain Gene Primer Sequence Type 5’ Label Size (bp) ACTTGCGCTTCGTCCCTAT Forward Biotin M. fortuitum 16 s 287 ACCACGCATTTCATGGTCT Reverse Digoxigenin 2.4. Preparation of the Devices in Vertical Flow Configuration The different pads conforming the system were assembled and placed in the cartridge, as shown in Figure 1. Afterward, 0.5 µL of the anti-digoxigenin antibody (1 mg mL−1 ) and the positive control biotinylated reporter [27] (1 mg mL−1 ) were deposited on the nitrocel- lulose membrane and were then dried at RT for 30 min. Furthermore, the streptAv-AuNPs were diluted 5 times in conjugate diluting buffer, embedded in the glass fiber conjugate pads, and then dried for 3 h at RT. Finally, the glass fiber was placed on the corresponding well of the device, in direct contact with the test and control area of the nitrocellulose. 2.5. Preparation of Devices in Lateral Flow Configuration The cellulose fiber sample pads were soaked into the sample pad buffer. The strep- tAv-AuNPs were then diluted 10 times in conjugate diluting buffer and embedded in the glass fiber conjugate pads. All of the pads were dried for 3 h at RT. The antibody (1 mg Sensors 2021, 21, 5992 mL−1) and the positive control biotinylated reporter (1 mg mL−1) [27] were dispensed4 ofon 13 the nitrocellulose membrane and dried at RT for 1h. Finally, the strips were assembled on the adhesive backing card as it is shown in Figure 1. 1. Schematic Figure 1. Figure Schematicrepresentation representationofof thethe components forming components the vertical forming and lateral the vertical flow configuration. and lateral flow config- uration. 2.5. Preparation of Devices in Lateral Flow Configuration The cellulose fiber sample pads were soaked into the sample pad buffer. The streptAv- 2.6. Covalent Immobilization of Antibodies on Magnetic Particles AuNPs were then diluted 10 times in conjugate diluting buffer and embedded in the glass fiberThe antibody conjugate to M. pads. Allfortuitum waswere of the pads covalently dried coupled for 3 h atonRT.tosyl Theactivated antibodymagnetic (1 mg mL −1 ) par- ticles (tosyl-MPs) as described in Figure 2, Panel A. − 1 and the positive control biotinylated reporter (1 mg mL ) [27] were dispensed on the A volumemembrane nitrocellulose of 35 μL ofandtosyl-MP dried atwas RT washed twice with for 1h. Finally, 1 mL were the strips of borate buffer. on assembled After- the wards, 20 μg of antibody and 100 μL of adhesive backing card as it is shown in Figure 1.ammonium sulfate buffer was added in borate buffer performing a total volume of 240 μL. 2.6. Covalent MPs were Immobilization incubated underof Antibodies on Magnetic continuous agitationParticles for a total reaction time of 18 h at 37 Sensors 2021, 21, x FOR PEER REVIEW 5 of 13 The antibody °C. After incubation,to M. MPsfortuitum was covalently were separated coupledand with a magnet on tosyl activated magnetic the supernatant was re- particlesAfterward, moved. (tosyl-MPs)1 as mL described in Figure of phosphate 2, Panel blocking A. was added to the suspension and buffer incubated under shaking for 2 h at 37 °C, in order to block the remaining tosyl groups of the magnetic particles. Finally, the antibody functionalized-magnetic microparticles were washed and re- suspended in phosphate storage buffer to reach a concentration of 5.3 mg mL−1 and were then stored at 4 °C for further use for 1 month, as recommended by the manufacturer. Figure Figure 2. 2. Panel Panel (A)(A) covalent covalent immobilization immobilization of the of the antibody antibody specific specific to xtoon x on Tosyl-MP. Tosyl-MP. Panel Panel (B1) (B1) schematic schematic procedure for the procedure for DNA extraction the DNA performed extraction after immunomagnetic performed after immunomagneticseparation and mag- separation and netic preconcentration magnetic of M. fortuitum. preconcentration Panel (B2) of M. fortuitum. Panelschematic procedure (B2) schematic for the for procedure DNA theextraction per- DNA extraction formed from culture media dilutions. performed from culture media dilutions. A volume 2.7. Bacterial Strainofand 35 Culture µL of tosyl-MP was washed twice with 1 mL of borate buffer. After- wards, 20 µg of antibody Mycolicibacterium fortuitum andsubsp. 100 µLfortuitum of ammonium ATCC®sulfate 6841™buffer strain was added in was grown in tryp- borate buffer performing a total volume of 240 µL. ticase soy broth (TSB) supplemented with 0.025% Tween 20 under continuous agitation at 37 °C for 72 h. Afterward, serial dilutions from the culture were performed in hemodial- ysis water. Hemodialysis water was used since non-tuberculous mycobacteria are associ- ated with infection, arising from contamination of water in hemodialysis patients. The hemodialysis water was kindly provided by the Servei de Nefrologia, Hospital Parc Taulí Sensors 2021, 21, 5992 5 of 13 MPs were incubated under continuous agitation for a total reaction time of 18 h at 37 ◦ C. After incubation, MPs were separated with a magnet and the supernatant was removed. Afterward, 1 mL of phosphate blocking buffer was added to the suspension and incubated under shaking for 2 h at 37 ◦ C, in order to block the remaining tosyl groups of the magnetic particles. Finally, the antibody functionalized-magnetic microparticles were washed and resus- pended in phosphate storage buffer to reach a concentration of 5.3 mg mL−1 and were then stored at 4 ◦ C for further use for 1 month, as recommended by the manufacturer. 2.7. Bacterial Strain and Culture Mycolicibacterium fortuitum subsp. fortuitum ATCC® 6841™ strain was grown in trypti- case soy broth (TSB) supplemented with 0.025% Tween 20 under continuous agitation at 37 ◦ C for 72 h. Afterward, serial dilutions from the culture were performed in hemodialysis water. Hemodialysis water was used since non-tuberculous mycobacteria are associated with infection, arising from contamination of water in hemodialysis patients. The hemodial- ysis water was kindly provided by the Servei de Nefrologia, Hospital Parc Taulí Sabadell. A total of 100 µL of each dilution was spread onto Tryptic Soy Agar plates. After incubating the plates at 37 ◦ C for 24 h, the culture colonies on the plates were counted to estimate the number of viable bacteria in Colony Forming Units (CFU mL−1 ). 2.8. Immunomagnetic Separation and DNA Extraction The magnetic separation of the mycobacteria was performed to preconcentrate the bacteria from high volume of sample under magnetic actuation, and in order to improve the limit of detection (LODs). To achieve that, 20 µL of the antibody functionalized-magnetic particles was added to 1 mL of each mycobacteria samples (ranging from 0 to 106 CFU mL−1 ) and were incubated by stirring at RT for 60 min. Afterwards, the bacteria attached to the MPs were separated with a magnet and the supernatant was removed, as depicted in Figure 2, Panel B1. Then, MPs were washed with PBST (X3) and water (X1) under shaking for 1 min at RT and 700 rpm. The particles were separated with a magnet and resuspended in 50 µL of Tris-EDTA (TE) buffer for DNA extraction. The suspension was then kept in a boiling water bath for 10 min. After cooling on ice for 5 min, 2 µL of the supernatant was used directly for the amplification. In order to assess the efficiency of the preconcentration with magnetic particles, a parallel extraction of DNA from the same solutions was performed with no magnetic preconcentration, as shown in Figure 2, Panel B2. In this case, 1 mL of each one of the dilutions of mycobacteria were centrifuged at 12,000× g for 15 min, the liquid cultures were removed, and the pellet was resuspended in 1 mL of water. After a second centrifugation at 12,000× g for 15 min, the suspension was kept in a boiling water bath for 10 min. After cooling on ice for 5 min, the samples were centrifuged and 2 µL of the supernatant was used for the amplification samples. 2.9. Double-Tagging PCR for the Amplification of Mycobacteria A set of primers tagged with biotin (BIO) and digoxigenin (DIG), respectively, was used for the amplification and the double tagging of the extracted DNA. The PCR was performed in 15 µL of reaction mixture containing 2 µL of the extracted DNA. Each reaction contained 250 µmol L−1 of each deoxynucleotide triphosphate (dATP, dGTP, dCTP, and dTTP), 100 nmol L−1 of the double-tagged set of primers, and 3 U of Taq polymerase. The reaction was carried out in Taq DNA Polymerase PCR 1x Buffer (BioTools) containing 7.5 mM Tris HCl (pH 9.0), 0.2 mM MgCl2 , 5 mM KCl, 2 mM (NH4 )2 SO4 . The amplification mixtures were treated, with an initial step at 95 ◦ C for 5 min followed by 40 cycles at 95 ◦ C for 40 s, 6 ◦ C for 30 s, and 72 ◦ C for 2 min, and a last step of 10 min at 72 ◦ C. The resulting samples were stored at 4 ◦ C. The detailed PCR programing conditions for the double-tagging PCR are presented in Table S1 in the Supplementary Material section, and schematically shown in Figure 3. matically shown in Figure 3. The performance of the multiplex double-tagging PCR was analyzed with conven- tional agarose gel electrophoresis on 2% agarose gel in TAE buffer containing 1 × GelRed dye. A molecular weight (MW) marker consisting of DNA fragments ranged from 100 to Sensors 2021, 21, 59921000 base pair (bp) was used as size amplicon control. The DNA bands were visualized 6 of 13 by UV transillumination (FastGene FAST Digital System). Figure 3. Schematic Figure representation of the double-tagging 3. Schematic representation PCR amplification, of the double-tagging PCRin order to obtain amplification, in the double-tagged order to obtain theamplicon labeled with biotin (BIO) andamplicon double-tagged digoxigenin (DIG) labeled from with (BIO) andDNA. M. fortuitum biotin digoxigenin (DIG) from M. fortuitumDNA. The performance 2.10. Nucleic Acid Vertical Flow of the multiplex double-tagging PCR was analyzed with conven- tional agarose gel electrophoresis The procedure for the detection of mycobacteriaon 2% agarose gel in TAE by Nucleic Acidbuffer containing Vertical Flow 1 × GelRed dye. A molecular (NAVF) is schematically weight described (MW) marker in Figure 4, Panelconsisting of DNAsolutions A. The amplicon fragments ranged from 100 to obtained Sensors 2021, 21, x FOR PEER REVIEW 7 of 13 1000 base pair (bp) was used as size amplicon control. The DNA from the double-tagging PCR were diluted in 75 μL of running buffer and deposited bands were onvisualized by UV transillumination (FastGene FAST Digital System). the sample zone. After 20 s, 75 μL of running buffer were added in order to drag the re- maining streptAv-AuNPs 2.10.Nucleic Nucleicacidto the Acid absorbent Vertical pad. The streptAv-AuNPs thus reacted with 2.11. Lateral FlowFlow the biotin (BIO-tag) of the amplicons. As the products moved towards the nitrocellulose, Theprocedure The procedure forfor the detection thecaptured detectionbyofofmycobacteria mycobacteria by Nucleic Acid Vertical Flow (NAVF) the streptAv-AuNPs/amplicons were the digoxigeninby(DIG-tag) Nucleic Acid on theLateral test Flow (NALF) is schematically described in Figure 4, Panel B. The amplicon solutions obtained from is schematically described in Figure 4, Panel A. The amplicon solutions obtained dot, containing the antibody anti-DIG. A valid test was considered when the streptAv- the double-tagging from the double-tagging PCR PCR were diluted in was amplifications 75 µL of running diluted in 100 μLbuffer and of PBS deposited running bufferon the AuNPs also reacted with a biotinylated reporter located on the control dot. The reporter sample and zone. After deposited on the20sample s, 75 µL of running zone. After 1 buffer were min, 100 μL added in order of running to drag buffer the remaining was added in is a biotinylated reporter previously described by our research group [27], although good streptAv-AuNPs order to the to transport the absorbent remaining pad. The streptAv-AuNPs streptAv-AuNPs thus reacted up to the absorbent with thetobiotin pad. Similarly, performance can be achieved by using other biotinylated proteins at higher concentration (BIO-tag) the verticalof theimmunoassay, flow amplicons. Asthe thestreptAv-AuNPs products movedreacted towards the the with nitrocellulose, biotin of thethe streptAv- ampli- levels [29]. cons (BIO-tag). When streptAv-AuNPs/amplicon moved through the nitrocellulose, the AuNPs/amplicons were captured by the digoxigenin (DIG-tag) on the test dot, containing After one minute, the remaining streptAv-AuNPs migrated to the absorbent of thepad and the antibody specific antibodyanti-DIG. anti-DIG A on valid the test test was considered line reacted withwhen the the streptAv-AuNPs DIG-tag alsoThe amplicons. reacted the visual readout was achieved. with a biotinylated remaining streptAv-AuNPs reporter located flowed on the nitrocellulose through control dot. up The to reporter the controlisline a biotinylated where reporter they werepreviously captured by described by our research the biotinylated reporter group [27], [27] used asalthough a positivegood performance control. After 10 can be achieved by using other biotinylated proteins at higher concentration levels min, the test revealed the lines, and the test was ready for the interpretation of the [29]. results. Schematic Figure4.4.Schematic Figure representation representation of Nucleic of Nucleic AcidAcid Vertical Vertical FlowFlow (A) Nucleic (A) and and Nucleic Acid Acid LateralLateral Flow Flow (B):(i)(i)deposition (B): depositionof of thethe amplicons amplicons in the in the sample sample area;area; (ii) streptavidin (ii) streptavidin gold nanoparticles gold nanoparticles (streptAv- (streptAv- AuNPs) captured by the biotin tag of the amplicon; (iii) streptAv-AuNPs Amplicon AuNPs) captured by the biotin tag of the amplicon; (iii) streptAv-AuNPs Amplicon capture capture in thein the test area (dot or line, respectively) by the anti-DIG antibody and capture of gold nanoparticles by test area (dot or line, respectively) by the anti-DIG antibody and capture of gold nanoparticles by the the biotinylated reporter [27]. The remaining streptAv-AuNPs flow up to the absorbent pad. biotinylated reporter [27]. The remaining streptAv-AuNPs flow up to the absorbent pad. 2.12. Data Interpretation and Analysis In order to avoid any bias in the images due to luminosity, all of the strips for a single piece of experiment were photographed in a single image, and the conditions were the same in all cases. The images were taken, at the same time, for all of the strips in a single Sensors 2021, 21, 5992 7 of 13 After one minute, the remaining streptAv-AuNPs migrated to the absorbent pad and the visual readout was achieved. 2.11. Nucleic acid Lateral Flow The procedure for the detection of mycobacteria by Nucleic Acid Lateral Flow (NALF) is schematically described in Figure 4, Panel B. The amplicon solutions obtained from the double-tagging PCR amplifications was diluted in 100 µL of PBS running buffer and deposited on the sample zone. After 1 min, 100 µL of running buffer was added in order to transport the remaining streptAv-AuNPs up to the absorbent pad. Similarly, to the vertical flow immunoassay, the streptAv-AuNPs reacted with the biotin of the amplicons (BIO-tag). When streptAv-AuNPs/amplicon moved through the nitrocellulose, the specific antibody anti-DIG on the test line reacted with the DIG-tag of the amplicons. The remaining streptAv-AuNPs flowed through the nitrocellulose up to the control line where they were captured by the biotinylated reporter [27] used as a positive control. After 10 min, the test revealed the lines, and the test was ready for the interpretation of the results. 2.12. Data Interpretation and Analysis In order to avoid any bias in the images due to luminosity, all of the strips for a single piece of experiment were photographed in a single image, and the conditions were the same in all cases. The images were taken, at the same time, for all of the strips in a single image, using a portable photographic studio based on LED lights of 1100 lm and a color temperature of 6000–6500 K. The images were taken at a distance of 23 cm with a smartphone. The rear camera was used, with a maximum resolution of 12 megapixels (4032 × 3024 pixels). Autofocus was enabled, and the flashlight was turned off during the data acquisition procedure. Then, the images were converted to an 8-bit grey-scale format using the command Image > Type > 8-bit. The test and control lines were outlined using the rectangular selection tool, and the area under each peak was then numerically integrated using the ImageJ gel analysis toolbox. 3. Results and Discussion 3.1. Double-Tagging PCR for the Amplification of Mycobacteria The double-tagging PCR procedure (schematically depicted in Figure 3) was firstly studied by end-point PCR and agarose gel electrophoresis; the results are shown in Figure 5. The resulting bands showed an molecular weight (MW), as expected, for the 16S fragment (277 bp). From the results, it can be observed that the band intensities resulting from the samples obtained by immunomagnetic separation (lanes 2 to 8) are much higher than the conventional procedure involving centrifugation (lanes 10 to 15). An expected decrease in the signal was also observed when lowering the concentration of the bacteria. Sensors 2021, 21, x FOR PEER REVIEW 8 of 13 Sensors 2021, 21, 5992 8 of 13 Figure 5. Gel electrophoresis. Lane 1 is the molecular weight (MW) marker. Lanes 2 to 8 were Figure 5. Gel electrophoresis. Lane 1 is the molecular weight (MW) marker. Lanes 2 to 8 were ob- obtained by the double tagging PCR combined with IMS. Lane 2 is the negative control of this tained by the double tagging PCR combined −1 with IMS. Lane 2 is the negative control of this proce- procedure dure and corresponds and corresponds to 0 CFUto 0mL CFU −1. mL Lanes. 3Lanes 3 to 8from to 8 range range10from 1016CFU 6 to 10 1 CFU mL−1 . Lanes 9 to to 10mL −1. Lanes 9 to 15 are the samples resulting from the double tagging PCR obtained by conventional DNADNA 15 are the samples resulting from the double tagging PCR obtained by conventional extraction, extraction, in- instead of IMS, from6 to106 101mL mL−101 (lanes 10 to 15). Lane 9 is the negative control of this stead of IMS, from10 101 to CFU CFU −1 (lanes to 15). Lane 9 is the negative control of this procedure procedure and and to correspond 0 CFU mLto−1.0 CFU mL−1 . correspond 3.2. From Nucleic theAcid Vertical results, Flow it can be observed that the band intensities resulting from the sam- Figure 6byshows ples obtained the results obtained immunomagnetic by(lanes separation NAVF. Regarding 2 to thehigher 8) are much performance than theof the con- device, it is important to highlight that the readout can be achieved in only 1 ventional procedure involving centrifugation (lanes 10 to 15). An expected decrease in the min. The results signal wasof also the tests can bewhen observed readlowering with the the naked eye, but theofmeasurement concentration the bacteria. of the intensity of the dots using the image-processing program ImageJ allows the semi-quantification and 3.2. an enhanced Nucleic evaluation Acid Vertical Flow of the data. After processing the images resulting from the addition of the amplicons to the detection area of the devices, the intensity of color Figure 6 shows the results obtained by NAVF. Regarding the performance of the de- produced for each concentration of mycobacteria was quantified, and the results are shown vice, it is important to highlight that the readout can be achieved in only 1 min. The results in Figure 6. Figure S1 (Supplementary Material) shows the relative areas for each type of the tests can be read with the naked eye, but the measurement of the intensity of the of sample pretreatment, after processing the images. These areas were used for plotting dots using the image-processing program ImageJ allows the semi-quantification and an Figure 6. In all instances, the negative control containing all reagents, except the DNA enhanced evaluation of the data. After processing the images resulting from the addition template, was also processed, showing no visual signal, and confirming negligible non- of the amplicons to the detection area of the devices, the intensity of color produced for specific adsorption of the signal generating system. Moreover, a clean white area around each concentration of mycobacteria was quantified, and the results are shown in Figure 6. the reaction dots is observed in all cases, showing only a specific reaction in the reaction Figure S1 (Supplementary Material) shows the relative areas for each type of sample pre- dot and negligible non-specific adsorption on the bare membrane, as confirmed in the bare treatment, areas showed afterin processing Figure S1 the images. TheseMaterial). (Supplementary areas were used for plotting Figure 6. In all instances, the negative control containing all reagents, except the DNA template, was also processed, showing no visual signal, and confirming negligible non-specific adsorption of the signal generating system. Moreover, a clean white area around the reaction dots is observed in all cases, showing only a specific reaction in the reaction dot and negligible non-specific adsorption on the bare membrane, as confirmed in the bare areas showed in Figure S1 (Supplementary Material). The relative areas (Figure S1, Supplementary Material) were then fitted using a non- linear regression (four parameter logistic equation—GraphPad Prism Software) for the samples submitted to immunomagnetic separation and preconcentration by magnetic ac- tuation (R2 = 0.9881, red plot) and for the samples not submitted to magnetic actuation (R2 = 0.9620, green plot), for n = 3 in any case. The IMS/NAVF method was able to visually mL−1 (green arrow, Figure 6). This difference can be attributed to a lower performance of the sample treatment obtained by the centrifugation process (depicted in Figure 2, Panel B2) compared to IMS (depicted in Figure 2, Panel B1). IMS provided high affinity and specificity of the immobilized antibody. Therefore, the IMS step followed by the magnetic Sensors 2021, 21, 5992 9 of 13 preconcentration improved, by an order of magnitude, the LOD for the detection of M. fortuitum in hemodialysis water detected by NAVF. Results6.obtained Figure 6.Figure Resultsfor the NAVF obtained forforthe different NAVFCFUs mL−1 of M. for different mL−1submitted fortuitum CFUs to immunomagnetic of M. fortuitum submitted toseparation im- and preconcentration munomagnetic by magnetic separationactuation (N) and with no magnetic and preconcentration preconcentration by magnetic (•).and actuation (▲) The with negative control for the no magnetic evaluation of non-specific binding preconcentration is negative (●). The also shown. control for the evaluation of non-specific binding is also shown. The relative areas (Figure S1, Supplementary Material) were then fitted using a non- 3.3. Nucleic Acid linear Lateralregression Flow Immunoassay (four parameter logistic equation—GraphPad Prism Software) for the The results samples combining submitted to immunomagnetic double-tagging separation PCR and lateral flowand preconcentration immunoassay by magnetic integrat- actuation ing the IMS of the (R2 = 0.9881, mycobacteria red plot) and for (or alternatively, thecentrifugation) the samples not submitted to magneticasactuation were quantified (R2 = 0.9620, previously described greenThe for NAVF. plot), for n = 3 in readouts in any this case. The IMS/NAVF instance method were obtained was after 15able fromto visually detect signals as low as 100 CFU mL −1 (red arrow, Figure 6). This strategy showed better the addition of the sample on the strip. results than those obtained from the method without IMS obtaining a result of 103 CFU Figure S1 (Supplementary Material) shows the relative areas for each type of sample mL−1 (green arrow, Figure 6). This difference can be attributed to a lower performance of pretreatment, after processing the images. These areas were used for plotting Figure 7. the sample treatment obtained by the centrifugation process (depicted in Figure 2, Panel The resultsB2) forcompared both approaches, IMS/NALF to IMS (depicted compared in Figure 2, Panelto theIMS B1). common procedure provided high affinity and based on centrifugation specificity of the immobilized antibody. Therefore, the IMS step followed by theinmagnetic are shown in Figure 7. In this case, the relative areas (showed preconcentration Figure S1, supplementary improved, data) were fittedbyusing an order of magnitude, a nonlinear the LOD regression forparameter (four the detection of M. fortuitum in hemodialysis logistic equation—GraphPad water detected Prism Software) by NAVF. (R2 = 0.9949 for IMS/NALF and 0.9445 for NALF). 3.3. Nucleic Acid Lateral Flow Immunoassay The LOD obtained from the procedure combining IMS was 10 CFU mL−1 (red arrow, The results combining double-tagging PCR and lateral flow immunoassay integrating Figure 7), 10 times lower than the value obtained from samples processed by centrifuga- the IMS of the mycobacteria (or alternatively, the centrifugation) were quantified as previ- tion (10 CFU mL , green arrow, Figure 7), being the results in agreement with those ob- 2 −1 ously described for NAVF. The readouts in this instance were obtained after 15 from the tained by NAVF.addition of the sample on the strip. Figure S1 (Supplementary Material) shows the relative areas for each type of sample pretreatment, after processing the images. These areas were used for plotting Figure 7. Sensors 2021, 21, 5992 10 of 13 Figure 7. Results Figure Figure7. 7. obtained Results Results forfor obtained thethe obtained NALF for thefor NALF for different NALF for CFU different CFU of M. of M.CFU different fortuitum fortuitum submitted submitted of M. tosubmitted immunomagnetic to immunomagnetic fortuitum separation separation to immuno- and preconcentration and by preconcentration magnetic by magnetic actuation actuation (N(N) and ) and with with no no magnetic magnetic preconcentration preconcentration ( magnetic separation and preconcentration by magnetic actuation (▲) and with no magnetic precon- • ).( ). The • The negative negative control control for thefor the evaluation evaluation of non-specific of non-specific centration binding (●). Thebinding negative is also is also shown. shown. control for the evaluation of non-specific binding is also shown. The The resultsfor results forboth both approaches, approaches, IMS/NALF IMS/NALFcompared to the compared common to the procedure common procedure Furthermore,based the based comparison onon centrifugation of the centrifugation areanalytical are shown shownininFigure performance Figure7.7.InInthis of case, this NAVF thethe case, compared relative areasareas relative to (showed in (showed in NALF showed anFigure Figure improved S1, supplementary result for data) NALF were in onefitted using order ofa nonlinear magnitude. regression The (four improvedparameter S1, supplementary data) were fitted using2 a nonlinear regression (four parameter logistic equation—GraphPad Prism Software) to the (R = 0.9949 for IMS/NALF andall0.9445 LOD of NALF can be logisticattributed to the fact that, equation—GraphPad Prismdue Software) (R2 = 0.9949 for configuration of the assay, IMS/NALF and 0.9445 for NALF). for NALF). of the gold nanoparticles, TheasLODwellobtained as the sample, were forced from the procedure to pass combining IMS bywasthe10test CFU and mL− control 1 (red arrow, The LOD obtained from the procedure combining IMS was 10 CFU mL −1 (red arrow, lines, ensuring increased contact of the reagents and providing much more opportunities Figure 7), 10 times lower than the value obtained from samples processed by centrifugation Figure for reaction. Unlikely, 7), 10mL (102although CFU times muchlower −1 , green than Figure arrow, more the value rapid, 7), obtained being since fromissamples theflow the results inalso agreementprocessed moved with by centrifugation bythose obtained gravity (10 2 CFU mL − 1 , green arrow, Figure 7), being the results in agreement with those obtained by NAVF. in the vertical flow format, some reagents (including gold nanoparticles and samples) can by NAVF. Furthermore, the comparison of the analytical performance of NAVF compared to bypass the membrane NALF without reacting showed anthe withresult improved the control for and test dotsof(as depictedThe in Fig- Furthermore, comparison of NALF in one order the analytical magnitude. performance of NAVFimproved compared to ure 4). LOD showed NALF of NALF an canimproved be attributed to thefor result fact that, due NALF to the in one configuration order of the assay, of magnitude. The all of improved For this reason, theit gold can nanoparticles, be concluded as well that, as tothe sample, ensure were detectionforced at to pass high by the test sensitivity, LOD of NALF can be attributed to the fact that, due to the configuration of the assay, all of and control the lateral flow would lines, ensuring increased contact of the reagents and providing in much moreof opportunities thebe the gold best candidate nanoparticles, to achieve as well improved as the sample, were results forced to pass termsby the LOD. test and control for reaction. Unlikely, although much more rapid, since the flow is also moved by gravity However, the time of detection and the quantity of materials required for NAVF makes in the vertical flow format, some reagents (including gold nanoparticles and samples) this format very attractive can bypass for theapplications membrane without that reacting requirewith qualitative the controlresults, and test ensuring, in in dots (as depicted any case the correctFigure 4). performance to reach the proper LOD for each necessity. For this reason, it can be concluded that, to ensure detection at high sensitivity, the lateral flow would be the best candidate to achieve improved results in terms of LOD. However, the time of detection and the quantity of materials required for NAVF makes this format very attractive for applications that require qualitative results, ensuring, in any case the correct performance to reach the proper LOD for each necessity. 4. Conclusions There has been increasing interest in commercial solutions and rapid diagnostic testing developments to meet the need of analyzing targets in complex samples, at low concentration levels, and in low-resource settings. As there is increasing demand for decentralized infectious disease testing, highlighted by the pandemic, researchers have Sensors 2021, 21, 5992 11 of 13 stepped up in their efforts to provide solutions that meet the WHO guidelines, defined by the acronym ASSURED: (A) affordable, (SS) sensitive, specific, (U) user-friendly, (R) rapid and robust, (E) equipment free, and (D) deliverable to those who need it. In line with this, the integration of technologies with proven performance records in life sciences research, such as immunoassays or PCR amplification being used with smartphones and tablets as readers, has led to cheaper, hand-held devices. In this work, the performance of immunomagnetic separation of mycobacteria, fol- lowed by double-tagging PCR and optical detection based on paper-based immunochro- matography are presented in different formats: vertical and lateral flow. First, the specific separation of the bacteria from the hemodialysis water was per- formed using magnetic particles modified with an anti-lipoarabinomannan (LAM) anti- body. LAM is a glycolipid, known as a virulence factor, associated with mycobacteria. Mycobacterial DNA was then amplified by using a set of primers for the 16S rRNA gene for Mycobacterium; the signal was amplified at the same time by labeling with biotin (BIO) and digoxigenin (DIG) to achieve a visual readout by NAVF or NALF, using both gold nanoparticles as the signal generating system. This approach solves one of the main issues regarding the implementation of LFA for the detection of the whole bacteria cell. Due to the size of the bacteria, pore size must be high, thus increasing the flow rate and compromising the sensitivity. If the flow rate is very fast, the capturing process cannot be complete, and line intensities become unclear [33], compromising the limit of detection. For the bacteria to flow, many authors reported lateral flow assays for bacterial fragments obtained by heating at 100 ◦ C [34]. LOD is quite high (105 in most of the instances) and, thus, only useful for the detection of pure cultures [34]. Our strategy relied on combining immunomagnetic separation and DNA amplification to increase the sensitivity of the approach (up to 10 CFU mL−1 ). Including immunomagnetic separation provided results, as great as one order of magnitude compared to the same method of analysis without magnetic preconcentration. NALF showed improved LODs that were able to detect as low as 10 CFU mL−1 when the IMS was included in the procedure compared to the 100 CFU mL−1 when IMS was not included. The LOD of NAVF also improved (100 CFU mL−1 ) when the IMS was performed. The results of NALF are comparable to those obtained in the literature (13 CFU mL−1 ) using magneto-ELISA using conventional benchtop equipment to achieve the readout [31], representing an improvement, in terms of time, with respect to the gold standard methods, which require at least 72 h to detect rapid growing mycobacteria. On the other hand, the time of the assay for the vertical flow format was only 1 min in front of the 15 min needed to obtain the results by using the lateral flow format. Although both platforms have differences, both methods presented in this study were able to detect concentrations of this important pathogen in application, such as dialysate fluid (<200 CFU mL−1 ). This is one of the most “found” mycobacteria in contaminated hemodialysis waters, placing immunocompromised patients at risk. Hence, it is important to continuously monitor water supplies in hemodialysis centers, in order to minimize the exposure of contaminated sources to renal transplantation patients and immunocompromised individuals [32]. Future research will focus on a clinical validation of the method, including the detection of isolations from different clinical samples. Supplementary Materials: The following are available online at https://www.mdpi.com/article/10 .3390/s21185992/s1, Table S1: Thermal cycler conditions for the double-tagging PCR, Figure S1: The relative areas obtained after processing the images, and which were plotted in Figures 6 and 7. Author Contributions: M.I.P. and M.V.B.Z. conceived the presented idea. A.B.A. and B.A. verified the analytical methods. M.I.P. and E.J. encouraged A.B.A. to investigate, and supervised the findings of this work. All authors discussed the results and contributed to the final manuscript. A.B.A. and E.J. carried out the experiment. 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