Contributions of Long-Read Sequencing for the Detection of Antimicrobial Resistance
Abstract
:1. Introduction
2. Methods
2.1. Bacterial Isolates, Identification, and Carbapenemase Detection
2.2. DNA Extractions and Sequencing
2.3. WGS Data Analysis and Typing
2.4. Conjugations Assays
2.5. Validation of blaNDM Alleles
3. Results
3.1. Sequencing Output
3.2. Assembly, β-Lactamase Identification and Typing
3.3. blaNDM Alleles Confirmation
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Data Set | num_read | mean_len | min_len | med_len | max_len | N50 | total_len | ambiguous_bp | Coverage | avg_read_quality |
---|---|---|---|---|---|---|---|---|---|---|
Illumina R1 | 6,451,108 | 100 | 100 | 100 | 100 | 100 | 645,110,800 | 5704 | 234.59 | 39.31 |
Illumina R2 | 6,451,108 | 100 | 100 | 100 | 100 | 100 | 645,110,800 | 70,826 | * | 38.15 |
ONT | 630,578 | 3047.7 | 100 | 1299 | 232,397 | 6802 | 1,921,804,262 | 0 | 349.42 | 29.61 |
Assembly | num_contig | total_assembly_length | max_contig_len | min_contig_len | num_ambig_bp | N50 |
---|---|---|---|---|---|---|
Illumina_spades_contigs | 277 | 5,762,046 | 325,640 | 56 | 0 | 152,157 |
Illumina_spades_scaffolds | 250 | 5,764,032 | 658,511 | 56 | 2610 | 235,693 |
ONT_flye | 5 | 5,850,368 | 5,371,556 | 5250 | 0 | 5,371,556 |
ONT_flye_medaka | 5 | 5,850,437 | 5,371,614 | 5253 | 0 | 5,371,614 |
ONT_flye_pilon | 5 | 5,850,448 | 5,371,627 | 5251 | 0 | 5,371,627 |
Unicycler (hybrid) | 6 | 5,853,076 | 5,371,783 | 2440 | 0 | 5,371,783 |
Assembly | Col (pHAD28) | Col440II | IncFIB (pNDM-Mar) | IncHI1B (pNDM-MAR) | IncFII | IncX3 |
---|---|---|---|---|---|---|
Illumina_spades | contig 61 (92.25) | contig 47 (100) | contig 27 (99.54) | contig 22 (99.47) | contig 26 (100) | contig 29 (100) |
Unicycler | contig 6 (92.25) | contig 5 (100) | contig 2 (99.54) | contig 2 (99.47) | contig 3 (100) | contig 4 (100) |
ONT_flye | contig 6 (92.37) | contig 6 (100) | contig 3 (99.54) | contig 3 (99.47) | contig 4 (100) | contig 1 (100) |
ONT_flye_medaka | contig 6 (92.37) | contig 6 (100) | contig 3 (99.54) | contig 3 (99.47) | contig 4 (100) | contig 1 (100) |
ONT_flye_pilon | contig 6 (92.37) | contig 6 (100) | contig 3 (99.54) | contig 3 (99.47) | contig 4 (100) | contig 1 (100) |
Assembly | MLST | Resistance Gene † | Identity (%) | Contig | Size (bp) | Coverage | Circular | Location § |
---|---|---|---|---|---|---|---|---|
Illumina_spades | ST16 | blaNDM-4 | 100 | contig 57 | 3036 | 295 | no | n.d. |
blaSHV-26 * | 99.88 | contig 1 | 658,511 | 79 | no | chromosome | ||
blaTEM-1B | 100 | contig 39 | 8779 | 218 | no | n.d. | ||
Unicycler_hybrid | ST16 | blaNDM-1 | 100 | contig 2 | 352,331 | 1.37× ^ | yes | IncFIB, IncHI1B |
blaNDM-5 | 100 | contig 4 | 45,181 | 1.42× ^ | yes | IncX3 | ||
blaSHV-26 * | 99.88 | contig 1 | 5,371,783 | 1.00× ^ | yes | chromosome | ||
blaTEM-1B | 100 | contig 3 | 76,090 | 1.56× ^ | yes | IncFII | ||
ONT_flye | ST16 | blaNDM-1 | 100 | contig 3 | 352,292 | 468 | yes | IncFIB, IncHI1B |
blaNDM-5 | 100 | contig 1 | 45,181 | 844 | yes | IncX3 | ||
blaSHV-26 * | 99.88 | contig 2 | 5,371,556 | 283 | yes | chromosome | ||
blaTEM-1B | 100 | contig 4 | 76,089 | 864 | yes | IncFII | ||
ONT_flye_medaka | ST16 | blaNDM-1 | 100 | contig 3 | 352,300 | 468 | yes | IncFIB, IncHI1B |
blaNDM-5 | 100 | contig 1 | 45,181 | 844 | yes | IncX3 | ||
blaSHV-26 * | 99.88 | contig 2 | 5,371,614 | 283 | yes | chromosome | ||
blaTEM-1B | 100 | contig 4 | 76,089 | 864 | yes | IncFII | ||
ONT_flye_pilon | ST16 | blaNDM-1 | 100 | contig 3 | 352,300 | 468 | yes | IncFIB, IncHI1B |
blaNDM-5 | 100 | contig 1 | 45,181 | 844 | yes | IncX3 | ||
blaSHV-26 * | 99.88 | contig 2 | 5,371,627 | 283 | yes | chromosome | ||
blaTEM-1B | 100 | contig 4 | 76,089 | 864 | yes | IncFII |
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Sierra, R.; Roch, M.; Moraz, M.; Prados, J.; Vuilleumier, N.; Emonet, S.; Andrey, D.O. Contributions of Long-Read Sequencing for the Detection of Antimicrobial Resistance. Pathogens 2024, 13, 730. https://doi.org/10.3390/pathogens13090730
Sierra R, Roch M, Moraz M, Prados J, Vuilleumier N, Emonet S, Andrey DO. Contributions of Long-Read Sequencing for the Detection of Antimicrobial Resistance. Pathogens. 2024; 13(9):730. https://doi.org/10.3390/pathogens13090730
Chicago/Turabian StyleSierra, Roberto, Mélanie Roch, Milo Moraz, Julien Prados, Nicolas Vuilleumier, Stéphane Emonet, and Diego O. Andrey. 2024. "Contributions of Long-Read Sequencing for the Detection of Antimicrobial Resistance" Pathogens 13, no. 9: 730. https://doi.org/10.3390/pathogens13090730