| Literature DB >> 35646723 |
Lei Wang1,2, Dunpo Sun3, Li Chen1, Ping Zhou1, Kun Wang1, Fang Wang1, Xingqi Lei1, Yan Wang1, Yingzhi Lu1, Guanhong Huang1, Xuzhu Gao1.
Abstract
Acinetobacter baumannii is a worldwide, primary cause of respiratory tract infections, septicemia, urinary apparatus infections, and secondary meningitis. It can be fatal. Rapid and accurate detection methods are needed to control the spread of carbapenem-resistant A. baumannii (CRAB). Current molecular diagnostic methods are limited and not suitable for on-site detection. In this study, an isothermal detection method using recombinase polymerase amplification (RPA) combined with a lateral flow strip (LFS) was developed to target the bla OXA-51 and bla OXA-23 genes of A. baumannii. The reaction was completed in about 40 min at 37°C. This method can also effectively distinguish A. baumannii and CRAB. The limit of detection of 100-101 CFU/reaction was equal to that of other detection methods. The detection accuracy was equal to that of the qPCR method with the use of clinical samples. The RPA-LFS assay is portable, rapid, and accurate and could replace existing detection methods for on-site detection of A. baumannii and CRAB.Entities:
Keywords: blaOXA-23 gene; blaOXA-51 gene; carbapenem-resistant Acinetobacter baumannii; lateral flow strip; recombinase polymerase amplification
Mesh:
Substances:
Year: 2022 PMID: 35646723 PMCID: PMC9131934 DOI: 10.3389/fcimb.2022.876552
Source DB: PubMed Journal: Front Cell Infect Microbiol ISSN: 2235-2988 Impact factor: 6.073
Bacteria strains used in this study.
| Species | Source | Strain designation | Number of samples |
|---|---|---|---|
|
| Reference strain | ATCC 19606 | 1 |
|
| Sputum isolated strain | #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 | 10 |
|
| Sputum isolated strain | #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 | 10 |
| Clinical samples | Sputum | N/A | 78 |
| Clinical samples | Swab of the wound | N/A | 49 |
| Clinical samples | Urine | N/A | 86 |
|
| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Reference strain | ATCC 10231 | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
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| Sputum isolated strain | N/A | 1 |
ATCC, American Type Culture Collection, Manassas, VA, USA.
Figure 1Screening of the primer-probe sets. (A) The RPA results of the four different primer sets targeting bla OXA-51 and bla OXA-23. The name of each set is shown at the top of each lane. A NTC was used in the reactions. All reactions were performed at 37°C for 30 min. The image represents the results of three independent experiments. (B, C) Pairing analysis and sequence modifications of the primer-probe sets for detection of bla OXA-51 and bla OXA-23 with Primer Premier 5 software. Relevant DNA bases of the probes and primers were excluded. The DNA strands are shown as horizontal lines and matching bases are indicated with vertical lines. Molecular markers are listed under the (C). (D) Effectiveness of the primer-probe sets for the RPA-LFS assay. The name of each set is shown at the top of each lane. A NTC was used in the reactions. The positions of the test and control lines are indicated on the right. All reactions were performed at 37°C for 30 min. The images represent the results of three independent experiments.
Primers and probes used in this study.
| Primers/Probes | Primer Sequences | Size (bp) | Reaction name | Targeting area | Production Size(bp) |
|---|---|---|---|---|---|
|
| CTATTCCGGTTTATCAAGATTTAGCTCGTCG | 31 | RPA | 2228255..2228343 | 89 |
|
| ATCTGCATTGCCATAACCAACACGCTTCACT | 31 | |||
| blaOXA-51-F2 | AGCTATGGTAATGATCTTGCTCGTGCTTCGA | 31 | 2228062..2222178 | 117 | |
| blaOXA-51-R2 | AAATACTTCTGTGGTGGTTGCCTTATGGTGC | 31 | |||
| blaOXA-23-F1 | TTTAATGGTCCTACCAACCAGAAATTATCAACCT | 35 | 411..513 | 103 | |
| blaOXA-23-R1 | GTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAA | 34 | |||
| blaOXA-23-F2 | CTTGAACAATCTGACTCGGGGTTTCATTTATT | 35 | 820..910 | 91 | |
| blaOXA-23-R2 | TTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTC | 32 | |||
| blaOXA-51-P | FITC-AGCTATGGTAATGATCTTGCTCGTGCTTCGA[THF]CGAGGATGTAGCTGCT-C3 Spacer | 47 | RPA-LFS | 2228035..2228178 | 144 |
| blaOXA-51-R2B | Biotin-AAATACTTCTGTGGTGGTTGCCTTATGGTGC | 31 | |||
| blaOXA-51-F3 | GTTATCCAACAAGGCCAAACTCAACAAAGCT | 31 | |||
| blaOXA-23-P | FITC-CTTGTACAATCTGACTCGAGGTTTCATTTA[THF]TACACTATGCTGTGC-C3 Spacer | 45 | 645..910 | 266 | |
| blaOXA-23-R2B | Biotin-TTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTC | 35 | |||
| blaOXA-23-F3 | TGGTTCTCCAATCCGATCAGGGCATTCAACATT | 33 | |||
| blaOXA-51-qF | GCAACCACCACAGAAG | 16 | qPCR | 2228158..2228292 | 135 |
| blaOXA-51-qR | TCCAATACGACGAGCT | 16 | |||
| blaOXA-23-qF | CCTGATAGACTGGGACT | 16 | 526..661 | 136 | |
| blaOXA-23-qR | ATCGGATTGGAGAACC | 17 |
F, forward primer; R, reverse primer; P, probe.
Figure 2Applicability of the primer-probe sets. (A) The image shows the detection results of the RPA-LFS assay for 10 A. baumannii (bla OXA-51 without OXA-23) isolates using the primer-probe sets bla OXA-51-F3/R2B/P (#1-1, #2-1, #3-1, #4-1, #5-1, #6-1, #7-1, #8-1, #9-1, #10-1) and bla OXA-23-F3/R2B/P (#1-2, #2-2, #3-2, #4-2, #5-2, #6-2, #7-2, #8-2, #9-2, #10-2). (B) The image shows the detection results of the RPA-LFS assay for 10 A. baumannii (bla OXA-51 and OXA-23) isolates using the primer-probe sets bla OXA-51-F3/R2B/P (#1-1, #2-1, #3-1, #4-1, #5-1, #6-1, #7-1, #8-1, #9-1, #10-1) and bla OXA-23-F3/R2B/P (#1-2, #2-2, #3-2, #4-2, #5-2, #6-2, #7-2, #8-2, #9-2, #10-2). NTC-1, no template control with the primer-probe set bla OXA-51-F3/R2B/P. NTC-2, no template control with the primer-probe set bla OXA-23-F3/R2B/P. The name of each set is shown at the top of each lane. The positions of the test and control lines are indicated on the right. All reactions were performed at 37°C for 30 min. The images represent the results of three independent experiments.
Figure 3Specificity of the primer-probe sets. The image shows the detection results of the RPA-LFS assay with different bacterial templates using the primer-probe set bla OXA-51-F3/R2B/P. The name of the bacterium used for each reaction is shown at the top of each lane. NTC, no template control. The positions of the test and control lines are indicated on the right. All reactions were performed at 37°C for 30 min. The image represents the results of three independent experiments.
Figure 4LOD of the RPA-LFS assay. (A) The image shows the detection results of the RPA-LFS assay with different CFUs of A. baumannii (bla OXA-51) using the primer-probe set bla OXA-51-F3/R2B/P. (B) The image shows the detection results of the RPA-LFS assay with different CFUs of A. baumannii (bla OXA-51) and 107 CFU of E. coli O157 using the primer-probe set bla OXA-51-F3/R2B/P. (C) The image shows the detection results of the RPA-LFS assay with different CFUs of A. baumannii (bla OXA-23) using the primer-probe set bla OXA-23-F3/R2B/P. (D) The image shows the detection results of the RPA-LFS assay with different CFUs of A. baumannii (bla OXA-23) and 107 CFU of E. coli O157 using the primer-probe set bla OXA-23-F3/R2B/P. NTC, no template control. All reactions were performed at 37°C for 30 min. The CFUs are indicated at the top of the strips. The positions of the test and control lines are indicated on the right. The images represent the results of three independent experiments.
Prevalence of carbapenemase genes in 213 clinical samples of A. baumannii using RPA-LFS and PCR (summarized).
| Method |
| N (%) |
| N (%) |
|---|---|---|---|---|
| RPA-LFS | 206 | 96.7 | 95 | 44.6 |
| qPCR | 206 | 96.7 | 95 | 44.6 |
| Coincidence rate (%) | N/A | 100% | N/A | 100% |
N, number.