Development of a Multiplex PCR and Magnetic DNA Capture Assay for Detecting Six Species Pathogens of the Genera Anaplasma and Ehrlichia in Canine, Bovine, Caprine and Ovine Blood Samples from Grenada, West Indies
Abstract
:1. Introduction
2. Results
2.1. Optimization of the xMAP Assay
2.2. Analytical Specificity
2.3. The Limit of Detection and Analytical Sensitivity
2.4. Repeatability
2.5. Testing of the Field Samples
2.6. Confirmatory PCR Assays
3. Discussion
4. Materials and Methods
4.1. Collection of the Field Specimens
4.2. DNA Extraction
4.3. Optimization of the PCR and xMAP Hybridization Assay Conditions
4.4. DNA Amplification for xMAP Assay
4.5. Oligonucleotide xMAP Assay
4.5.1. Oligonucleotide Probe Design
4.5.2. Oligonucleotide Probe Coupling to xMAP Beads
4.5.3. Direct Hybridization of Blood-Derived DNA Samples to Six Oligonucleotide Probe-Coupled xMAP Beads
4.5.4. Determination of the Analytical Specificity of the Luminex Assay
4.5.5. Determination of Limit of Detection and Analytical Sensitivity
4.5.6. Intra-Assay and Inter-Assay Variability
4.6. Confirmation of the Results by PCR and Sequencing
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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DNA Targets | MFI for Hybridization of Species-Specific Oligonucleotides to DNA Targets | |||||
---|---|---|---|---|---|---|
A. marginale | E. canis | E. ewingii | A. platys | E. chaffeensis | E. ruminantium | |
NTCs c | 23.5 ± 11.1 a (>34.6) | 24 ± 14.1 a (>38.5) | 23.1 ± 11.4 a (>35) | 24.6 ± 10.8 a (>35.8) | 23.1 ± 10.2 a (>33.5) | 25.5 ± 10.2 a (>36) |
A. marginale # | 670.5b ± 118.6 | 21.6 ± 3.7 | 24 ± 2.6 | 22 ± 2.6 | 21.6 ± 4.6 | 24 ± 3.4 |
E. canis # | 21.6 ± 1.1 | 2088.6b ± 92.5 | 21.6 ± 2 | 22 ± 2 | 22 ± 1 | 24 ± 1.7 |
E. ewingii # | 18.3 ± 1.5 | 20.3 ± 0.5 | 1605.3b ± 147 | 20.6 ± 2.5 | 19.3 ± 1.1 | 21 ± 2 |
A. platys # | 21 ± 2.6 | 22.8 ± 3.1 | 21.6 ± 1.1 | 1870.2b ± 270 | 21.3 b ± 3.2 | 24.6 ± 3 |
E. chaffeensis # | 23.5 ± 2.3 | 25.3 ± 2 | 24 ± 1.7 | 23.6 ± 1.1 | 2715.8b ± 321.4 | 27 ± 1.7 |
E. ruminantium # | 20.3 ± 1.5 | 22.3 ± 2.3 | 21.6 ± 1.5 | 21 ± 1.7 | 19.3 ± 2 | 828b ± 83.9 |
DNA Targets | MFI for Hybridization of Species-Specific Oligonucleotides to DNA Targets | |||||
---|---|---|---|---|---|---|
A. marginale | E. canis | E. ewingii | A. platys | E. chaffeensis | E. ruminantium | |
NTC c | 19.2 ± 4.5 a (>23.7) | 20.3 ± 1.5 a (>21.8) | 20.3 ± 1.5 a (>21.8) | 21.1 ± 4.2 a (>25.3) | 19.5 ± 1.5 a (>21) | 22 ± 2.4 a (>24.4) |
Neg D d | 17.8 ± 0.5 | 19 ± 0 | 18 ± 0.8 | 19.2 ± 0.5 | 18 ± 0.8 | 20.5 ± 1 |
Neg C e | 19.5 ± 0.5 | 19.8 ± 0.9 | 19.2 ± 0.9 | 20 ± 0.8 | 19.2 ± 0.5 | 21.5 ± 2 |
EC-AP f | 20 ± 0 | 1344.2b ± 16.2 | 20.5 ± 0.5 | 331.1b ± 7.3 | 20.8 ± 1.7 | 23.6 ± 1.3 |
AP-EC g | 18.9 ± 0.2 | 36b ± 2.1 | 19.8 ± 1.2 | 1242.6b ± 39.3 | 20.2 ± 2.3 | 21.6 ± 1.7 |
EC-ECH h | 21.2 ± 0.9 | 1500.5b ± 19.2 | 22.8b ± 1.8 | 22 ± 0.8 | 55b ± 0 | 24.5b ± 1.2 |
ECH-EC i | 18.8 ± 1.7 | 28.2b ± 2.6 | 18.5 ± 2 | 18.9 ± 1.6 | 2231.6b ± 80.9 | 20.4 ± 1.7 |
AM-ECH j | 1077.6b ± 26.8 | 20 ± 0.8 | 25.2b ± 0.9 | 19.8 ± 0.5 | 107.5b ± 2.6 | 21.8 ± 0.5 |
ECH-AM k | 25.8b ± 1.7 | 26.2b ± 1.2 | 23.5b ± 0.5 | 24.9 ± 1 | 3997b ± 120.8 | 27b ± 2 |
Species/# Sampled | # of Samples | Parish (# Sampled) | Year of Collection | ||||||
---|---|---|---|---|---|---|---|---|---|
SG | SA | SM | SP | SD | SJ | Uk | |||
Canine/353 | 358 * | 185 | 48 | 12 | 4 | 50 | 1 | 58 | 2014–2018 |
Caprine and Ovine/65 | 65 | 18 | 25 | - | - | 22 | - | - | 2017–2018 |
Bovine/32 | 32 | 25 | 7 | - | - | - | - | - | 2017 |
Total (%) | 455 | 228 (50.1) | 80 (17.6) | 12 (2.6) | 4 (0.8) | 72 (15.8) | 1 (0.2) | 58 (12.7) |
Bacterial sp. | Canine | Bovine | Caprine and Ovine | Total | ||
---|---|---|---|---|---|---|
Animal sp. | ||||||
Single speciesinfections | AM | - | 11/32 (34.3) | 3/65 (4.6) | 14 | |
EC | 50/358 (13.9) | - | 1/65 (1.5) | 51 | ||
AP | 59/358 (16.4) | 3/32 (9.3) | 2/65 (3) | 64 | ||
ECH | 1/358 (0.2) | - | - | 1 | ||
Total | 110/358 (30.7) | 14/32 (43.7) | 6/65 (9.2) | 130 | ||
Co-infections | EC-ECH | 2/358 (0.5) | - | - | 2 | |
EC-AP | 4/358 (1.1) | - | - | 4 | ||
EE-AP | 1/358 (0.2) | - | - | 1 | ||
Total | 7/358 (1.9) | 0/36 (0) | 0/65 (0) | 7 | ||
Grand Total | 117/358 (32.6) | 14/32 (43.7) | 6/65 (9.2) | 137 |
Species | Target Gene | # of Samples Tested | # of Samples Sequenced | Deposited Sequence GenBank #s | Length (bp) | Percentage of Identity (%) | Reference Sequence |
---|---|---|---|---|---|---|---|
A. marginale | msp1a | 8 | 2 | MW486117 MW486118 | 568 326 | 94.00 94.00 | NC_012026 NC_012026 |
E. canis | 16S rRNA | 6 | 2 | MW474807 MW474808 | 335 335 | 99.40 99.40 | NR_118741 NR_118741 |
E. chaffeensis | 16S rRNA | 10 | 6 | MW474809 MW474810 MW474811 MW474812 MW474813 MW474814 | 300 334 318 334 333 334 | 100.00 100.00 100.00 100.00 100.00 100.00 | NR_074500 NR_074500 NR_074500 NR_074500 NR_074500 NR_074500 |
E. ewingii | 16S rRNA | 6 | 1 | MW474815 | 308 | 100.00 | NR_074500 |
Optimization Conditions | Test Conditions | |
---|---|---|
PCR optimization | Primer Annealing temperature (°C) | 50, 52 |
MgCl2 concentration (mM) | 1.5, 2.5 | |
PCR cycle numbers | 30, 35, 40 | |
xMAP optimization | Hybridization Temperature (°C) | 50, 52, 55, 60 |
Hybridization time (min.) | 10, 15, 20 | |
PCR product volume (µL) | 5, 10 | |
xMAP protocol | Washed, no-wash | |
Concentration of the probes (nmol/µL) | 0.1, 0.2 |
Probes | Bacterial Species | Sequences (5′-3′) | xMAP COOH-Microsphere Regions for Probe Binding | Reference |
---|---|---|---|---|
RG270Ecan | E. canis | TATAGCCTCTGGCTATAGGAAATTGTTAG | R25 | [37] |
RG266Echaf | E. chaffeensis | CTTATAACCTTTTGGTTATAAATAATTGTTAG | R43 | [37] |
RG268Eewin | E. ewingii | CTAAATAGTCTCTGATTTAGATAGTTGTTAG | R34 | [37] |
RG260Erum | E. ruminantium | GTTATTTATAGCTTCGGCTAT | R48 | [37] |
RG272Aplat | A. platys | CGGATTTTTGTCGTAGCTTGCTATGAT | R38 | [37] |
RG262Amarg | A. marginale | CGTATACGCAGCTTGCTGCGT | R20 | This study |
Species | Mix | ||||||||
---|---|---|---|---|---|---|---|---|---|
1 ✴ | 2 ✴ | 3 ✴ | 4 ✴ | 5 ✴ | 6 ✴ | 7 and 8 ★ | 9 and 10 ★ | 11 and 12 ★ | |
E. canis | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ |
E. chaffeensis | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ |
E. ewingii | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ |
E. ruminantium | ✗ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ |
A. platys | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ | ✓ | ✗ | ✗ |
A. marginale | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ |
Species | Target Gene | Primer Name | Sequence (5′→3′) | Amplicon Size (bp) | Reference |
---|---|---|---|---|---|
A. marginale | msp1a | MSP1aF1 MSP1aRN | GCATTACAACGCAACGCTTGAG CAGGAGCACCACCAAACATCATCACA | 1638 | This study |
A. platys | 16S rRNA | EP2 EP3 | GAAGATAATGACGGTACCC CGTTTTGTCTCTGTGTTG | 385 | [83] |
E. canis | 16S rRNA | ECA HE3 | CAATTATTTATAGCCTCTGGCTATAGG TATAGGTACCGTCATTATCTTCCCTAT | 385 | [34] |
E. chaffeensis | 16S rRNA | HE1 HE3 | CAATTGCTTATAACCTTTTGGTTATAAAT TATAGGTACCGTCATTATCTTCCCTAT | 385 | [84] |
E. ewingii | 16S rRNA | EE72 HE3 | CAATTCCTAAATAGTCTCTGACTATT TATAGGTACCGTCATTATCTTCCCTAT | 385 | [85] |
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Sharma, B.; Ganta, R.R.; Stone, D.; Alhassan, A.; Lanza-Perea, M.; Matthew Belmar, V.; Karasek, I.; Cooksey, E.; Butler, C.M.; Gibson, K.; et al. Development of a Multiplex PCR and Magnetic DNA Capture Assay for Detecting Six Species Pathogens of the Genera Anaplasma and Ehrlichia in Canine, Bovine, Caprine and Ovine Blood Samples from Grenada, West Indies. Pathogens 2021, 10, 192. https://doi.org/10.3390/pathogens10020192
Sharma B, Ganta RR, Stone D, Alhassan A, Lanza-Perea M, Matthew Belmar V, Karasek I, Cooksey E, Butler CM, Gibson K, et al. Development of a Multiplex PCR and Magnetic DNA Capture Assay for Detecting Six Species Pathogens of the Genera Anaplasma and Ehrlichia in Canine, Bovine, Caprine and Ovine Blood Samples from Grenada, West Indies. Pathogens. 2021; 10(2):192. https://doi.org/10.3390/pathogens10020192
Chicago/Turabian StyleSharma, Bhumika, Roman R. Ganta, Diana Stone, Andy Alhassan, Marta Lanza-Perea, Vanessa Matthew Belmar, Inga Karasek, Elizabeth Cooksey, Catherine M. Butler, Kathryn Gibson, and et al. 2021. "Development of a Multiplex PCR and Magnetic DNA Capture Assay for Detecting Six Species Pathogens of the Genera Anaplasma and Ehrlichia in Canine, Bovine, Caprine and Ovine Blood Samples from Grenada, West Indies" Pathogens 10, no. 2: 192. https://doi.org/10.3390/pathogens10020192
APA StyleSharma, B., Ganta, R. R., Stone, D., Alhassan, A., Lanza-Perea, M., Matthew Belmar, V., Karasek, I., Cooksey, E., Butler, C. M., Gibson, K., & Wilkerson, M. J. (2021). Development of a Multiplex PCR and Magnetic DNA Capture Assay for Detecting Six Species Pathogens of the Genera Anaplasma and Ehrlichia in Canine, Bovine, Caprine and Ovine Blood Samples from Grenada, West Indies. Pathogens, 10(2), 192. https://doi.org/10.3390/pathogens10020192