Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Isolates and DNA Preparation
2.2. Whole-Genome Sequencing
2.3. De Novo Assembly of Both Short and Long Reads
2.4. Reference-Based Assembly of Illumina Short Reads Mapped onto the Long Reads Assembly
2.5. Plasmid Annotation
2.6. S1-PFGE
2.7. Antimicrobial Resistance Gene Identification and Location
3. Results
3.1. Quality Control of Short and Long Reads
3.2. Comparison of De Novo and Reference-Based Assembly
3.3. Plasmid Annotation by PlasmidFinder and Confirmation by S1-PFGE Analysis
3.4. Antimicrobial Resistance Gene Identification and Location
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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De Novo Assembly | Reference-Based Assembly | |||||
---|---|---|---|---|---|---|
Strains | SS09 | SS12 | SS15 | SS09 | SS12 | SS15 |
Total length (bp) | 4,769,113 | 4,859,186 | 4,829,437 | 4,767,778 | 4,857,568 | 4,826,252 |
GC (%) | 52.19 | 52.13 | 52.21 | 51.19 | 52.14 | 52.21 |
N50 | 4,684,845 | 4,671,981 | 4,713,162 | 4,686,238 | 4,672,103 | 4,712,860 |
L50 | 1 | 1 | 1 | 1 | 1 | 1 |
Contig | 5 | 8 | 6 | 3 | 7 | 5 |
Size contig 1 (bp) | 4,684,845 | 4,671,981 | 4,713,162 | 4,686,238 | 4,672,198 | 4,712,860 |
Size contig 2 (bp) | 70,463 | 67,491 | 92,935 | 70,788 | 67,818 | 93,257 |
Size contig 3 (bp) | 6747 | 58,438 | 8131 | 6745 | 58,566 | 8128 |
Size contig 4 (bp) | 4013 | 45,793 | 6079 | 4007 | 45,784 | 6106 |
Size contig 5 (bp) | 3045 | 5686 | 5907 | 5682 | 5901 | |
Size contig 6 (bp) | 4663 | 3223 | 4663 | |||
Size contig 7 (bp) | 3045 | 3042 | ||||
Size contig 8 (bp) | 2089 |
De Novo Assembly | Reference-Based Assembly | ||||||
---|---|---|---|---|---|---|---|
Replicon | Contig | Identity (%) | Coverage (%) | Replicon | Contig | Identity (%) | Coverage (%) |
SS09 | SS09 | ||||||
IncFIB(K) | 2 | 98.93 | 100 | IncFIB(K) | 2 | 98.93 | 100 |
Col156 | 3 | 98.03 | 98.7 | Col156 | 3 | 98.03 | 98.7 |
Col440II | 4 | 96.44 | 99.65 | Col440II | 4 | 96.44 | 99.65 |
SS12 | SS12 | ||||||
IncFIB(K) | 2 | 98.93 | 100 | IncFIB(K) | 2 | 98.75 | 99.82 |
IncL/M | 3 | 94.63 | 89.46 | IncL/M | 3 | 94.46 | 89.31 |
IncX1 | 4 | 98.93 | 100 | IncX1 | 4 | 98.93 | 100 |
ColRNAI | 5 | 90.84 | 100 | ColRNAI | 5 | 90.08 | 99.23 |
Col156 | 6 | 93.51 | 100 | Col156 | 6 | 93.51 | 100 |
Col(BS512) | 8 | 100 | 100 | ||||
SS15 | SS15 | ||||||
IncFIB(K) | 2 | 98.93 | 100 | IncFIB(K) | 2 | 98.93 | 100 |
IncQ1 | 3 | 100 | 81.28 | IncQ1 | 3 | 100 | 81.28 |
ColRNAI | 4 | 87.79 | 100 | ColRNAI | 4 | 83.97 | 99.23 |
De Novo Assembly | Reference-Based Assembly | ||||||
---|---|---|---|---|---|---|---|
Resistance Gene | Contig | Identity (%) | Coverage (%) | Resistance Gene | Contig | Identity (%) | Coverage (%) |
SS09 | SS09 | ||||||
AAC(3)-IV | 1 | 100 | 100 | AAC(3)-IV | 1 | 100 | 100 |
AAC(6′)-Iy | 1 | 98.4 | 100 | AAC(6′)-Iy | 1 | 98.4 | 100 |
aadA2 | 1 | 100 | 100 | aadA2 | 1 | 100 | 100 |
aadA2 | 2 | 100 | 100 | aadA2 | 2 | 99.87 | 100 |
APH(4)-Ia | 1 | 100 | 100 | APH(4)-Ia | 1 | 100 | 100 |
cmlA1 | 1 | 99.92 | 100 | cmlA1 | 1 | 99.92 | 100 |
dfrA12 | 2 | 100 | 100 | dfrA12 | 2 | 100 | 100 |
golS | 1 | 99.36 | 100 | golS | 1 | 99.36 | 100 |
mdsA | 1 | 98.78 | 100 | mdsA | 1 | 98.78 | 100 |
mdsB | 1 | 99.02 | 100 | mdsB | 1 | 99.02 | 100 |
mdsC | 1 | 98.28 | 100 | mdsC | 1 | 98.28 | 100 |
mdtK | 1 | 98.88 | 100 | mdtK | 1 | 98.88 | 100 |
qacH | 1 | 91.59 | 100 | qacH | 1 | 91.59 | 100 |
sdiA | 1 | 98.75 | 100 | sdiA | 1 | 98.75 | 100 |
sul1 | 2 | 100 | 100 | sul1 | 2 | 99.88 | 99.88 |
sul3 | 1 | 100 | 100 | sul3 | 1 | 100 | 100 |
TEM-1 | 1 | 99.88 | 100 | TEM-1 | 1 | 99.88 | 100 |
tet(A) | 2 | 100 | 97.8 | tet(A) | 2 | 99.68 | 97.65 |
SS12 | SS12 | ||||||
AAC(3)-IV | 4 | 100 | 100 | AAC(3)-IV | 4 | 99.87 | 99.87 |
AAC(6′)-Iy | 1 | 98.4 | 100 | AAC(6′)-Iy | 1 | 98.4 | 100 |
aadA2 | 1 | 100 | 100 | aadA2 | 1 | 100 | 100 |
aadA2 | 2 | 100 | 100 | aadA2 | 2 | 99.87 | 100 |
APH(4)-Ia | 4 | 100 | 100 | APH(4)-Ia | 4 | 100 | 100 |
cmlA1 | 1 | 99.92 | 100 | cmlA1 | 1 | 99.92 | 100 |
dfrA12 | 2 | 100 | 100 | dfrA12 | 2 | 100 | 100 |
floR | 4 | 99.75 | 100 | floR | 4 | 99.75 | 100 |
golS | 1 | 99.36 | 100 | golS | 1 | 99.36 | 100 |
mdsA | 1 | 98.78 | 100 | mdsA | 1 | 98.78 | 100 |
mdsB | 1 | 99.02 | 100 | mdsB | 1 | 99.02 | 100 |
mdsC | 1 | 98.28 | 100 | mdsC | 1 | 98.28 | 100 |
mdtK | 1 | 98.88 | 100 | mdtK | 1 | 98.88 | 100 |
qacH | 1 | 91.59 | 100 | qacH | 1 | 91.59 | 100 |
sdiA | 1 | 98.75 | 100 | sdiA | 1 | 98.75 | 100 |
sul2 | 1 | 100 | 100 | sul2 | 1 | 99.88 | 99.88 |
TEM-1 | 1 | 99.88 | 100 | TEM-1 | 1 | 99.88 | 100 |
TEM-1 | 4 | 99.88 | 100 | TEM-1 | 4 | 99.88 | 100 |
tet(A) | 2 | 100 | 97.8 | tet(A) | 2 | 100 | 97.8 |
SS15 | SS15 | ||||||
AAC(3)-IV | 2 | 100 | 100 | AAC(3)-IV | 2 | 100 | 100 |
AAC(6′)-Iy | 1 | 98.4 | 100 | AAC(6′)-Iy | 1 | 98.4 | 100 |
aadA2 | 2 | 99.87 | 100 | aadA2 | 2 | 99.87 | 100 |
APH(4)-Ia | 2 | 100 | 100 | APH(4)-Ia | 2 | 100 | 100 |
cmlA1 | 2 | 99.92 | 100 | cmlA1 | 2 | 99.92 | 100 |
dfrA12 | 2 | 100 | 100 | dfrA12 | 2 | 100 | 100 |
floR | 2 | 99.67 | 100 | floR | 2 | 99.59 | 99.92 |
golS | 1 | 99.36 | 100 | golS | 1 | 99.36 | 100 |
mdsA | 1 | 98.78 | 100 | mdsA | 1 | 98.78 | 100 |
mdsB | 1 | 99.02 | 100 | mdsB | 1 | 98.83 | 99.81 |
mdsC | 1 | 98.21 | 100 | mdsC | 1 | 98.21 | 100 |
mdtK | 1 | 98.88 | 100 | mdtK | 1 | 98.88 | 100 |
qacH | 2 | 91.59 | 100 | qacH | 2 | 91.59 | 100 |
sdiA | 1 | 98.75 | 100 | sdiA | 1 | 98.75 | 100 |
sul1 | 2 | 100 | 100 | sul1 | 2 | 100 | 100 |
sul3 | 2 | 100 | 100 | sul3 | 2 | 99.87 | 99.87 |
tet(A) | 2 | 100 | 97.8 | tet(A) | 2 | 99.84 | 97.65 |
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Li, I.-C.; Yu, G.-Y.; Huang, J.-F.; Chen, Z.-W.; Chou, C.-H. Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates. Microorganisms 2022, 10, 227. https://doi.org/10.3390/microorganisms10020227
Li I-C, Yu G-Y, Huang J-F, Chen Z-W, Chou C-H. Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates. Microorganisms. 2022; 10(2):227. https://doi.org/10.3390/microorganisms10020227
Chicago/Turabian StyleLi, I-Chen, Gine-Ye Yu, Jing-Fang Huang, Zeng-Weng Chen, and Chung-Hsi Chou. 2022. "Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates" Microorganisms 10, no. 2: 227. https://doi.org/10.3390/microorganisms10020227
APA StyleLi, I. -C., Yu, G. -Y., Huang, J. -F., Chen, Z. -W., & Chou, C. -H. (2022). Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates. Microorganisms, 10(2), 227. https://doi.org/10.3390/microorganisms10020227