Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma
Abstract
:1. Introduction
2. Results
2.1. B508A-S1, B508A-T2A, and B508A-T4 Genome Comparison
2.2. Virulence Factors and Antimicrobial Resistances
2.3. H. pylori Genetic Population
3. Discussion
4. Materials and Methods
4.1. H. pylori Strains and Genomic DNA Extraction and Sequencing
4.2. Genomic Comparison and Characterization
4.3. Virulence and Antimicrobial Resistance Genes
4.4. H. pylori Genetic Population Assignment
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Genome Characteristics | B508A-S1 | B508A-T2A | B508A-T4 |
---|---|---|---|
GC% | 39.0 | 39.0 | 38.9 |
Genome Size (bp) | 1,586,749 | 1,584,784 | 1,585,256 |
N50 | 200,200 | 106,266 | 124,923 |
Genes (total) | 1577 | 1577 | 1581 |
Genes (unique) | 2 | 13 | 3 |
CDS (total) | 1535 | 1535 | 1536 |
CDS (coding) | 1445 | 1442 | 1444 |
rRNAs (5S, 16S, 23S) | 1, 1, 1 | 1, 1, 1 | 2, 1 1, 1 |
tRNAs | 36 | 36 | 36 |
ncRNAs | 3 | 3 | 3 |
Pseudo Genes | 90 | 93 | 92 |
vacA (PCR) | s1-s2/m1-m2 | s1-s2/m1-m2 | s1-s2/m1-m2 |
vacA (genome) | s2/m2/i2 | s1/m2/i2 | s2/m2/i2 |
cagA | - | - | - |
GenBank Accession | QDJN00000000 | QDJM00000000 | QDJL00000000 |
Type | Number of Polymorphisms | ||
---|---|---|---|
B508A-S1 Versus -T4 | B508A-S1 Versus -T2 | B508A-T2 Versus -T4 | |
SNP 1 | 113 | 2454 | 2418 |
MNP 2 | 10 | 198 | 201 |
Complex | 29 | 618 | 619 |
Deletions | 12 | 35 | 38 |
Insertions | 5 | 39 | 40 |
Total | 169 | 3344 | 3316 |
Virulence Factors | Related Genes | B508A-S1 | B508A-T2A | B508A-T4 |
---|---|---|---|---|
Urease | 1 | 1 | 1 | 1 |
Flagella | 2 | 1 | 1 | 1 |
Lipopolysaccharide Lewis antigens | futA | 1 | 2 | 1 |
futB | 1 | - | 1 | |
futC | 2 | 2 | 1 | |
Neutrophil-activating protein | napA | 1 | 1 | 1 |
oipA/hopH | 1 | 1 | 1 | |
Vacuolating cytotoxin | vacA | 1 | 1 | 1 |
Adherence-associated lipoproteins | alpA/hopC | 1 | 1 | 1 |
alpB/hopB | 1 | 1 | 1 | |
Blood group antigen binding adhesins | babA/hopS | - | - | - |
babB/hopT | 3 | 2 | 3 | |
H. pylori adhesin A | hpaA | 1 | 1 | 1 |
HopZ | hopZ | 1 | 1 | 1 |
HorB | horB | 1 | 1 | 1 |
Sialic acid binding proteins | sabA/hopP | 1 | 1 | 1 |
sabB/hopO | - | - | - | |
Duodenal ulcer promoting | dupA | 1 | 1 | 1 |
Induced by contact with epithelium A 3 | iceA | 1 | 1 | 1 |
Gene | Mutational Position | Susceptible Strains | B508A-S1 | B508A-T2 | B508A-T4 |
---|---|---|---|---|---|
pbp1 | V374L | V | V | V | V |
E406A | E | E | E | E | |
S414R | S | S | S | S | |
T593A | T | T | T | T | |
A599G | A | A | A | A | |
V601G | V | V | V | V | |
23S rRNA | A2143G | A | A | A | A |
A2144G | A | A | A | A | |
T2183C | T | T | T | T | |
C2196T | C | C | C | C | |
A2224G | A | A | A | A | |
16S rRNA | A926T | A | A | A | A |
G927T | G | G | G | G | |
A928C | A | A | A | A | |
frxA | A32V | A | A | A | A |
A70T | A | A | A | A | |
F72S | F | F | F | F | |
G73S | G | G | G | G | |
A138V | A | A | A | A | |
A152V | A | A | A | A | |
A153V | A | A | A | A | |
C193S | C | C | C | C | |
rdxA | G3A | G | G | G | G |
C46T | C | C | C | C | |
G238A | G | G | G | G | |
G352A | G | G | G | G | |
gyrA | D86N | D | D | D | D |
N87K\I\Y | N | N | N | N | |
A88V | A | A | A | A | |
D91Y\G\N | D | D | D | D |
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Palau, M.; Piqué, N.; Ramírez-Lázaro, M.J.; Lario, S.; Calvet, X.; Miñana-Galbis, D. Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma. Pathogens 2021, 10, 331. https://doi.org/10.3390/pathogens10030331
Palau M, Piqué N, Ramírez-Lázaro MJ, Lario S, Calvet X, Miñana-Galbis D. Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma. Pathogens. 2021; 10(3):331. https://doi.org/10.3390/pathogens10030331
Chicago/Turabian StylePalau, Montserrat, Núria Piqué, M. José Ramírez-Lázaro, Sergio Lario, Xavier Calvet, and David Miñana-Galbis. 2021. "Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma" Pathogens 10, no. 3: 331. https://doi.org/10.3390/pathogens10030331
APA StylePalau, M., Piqué, N., Ramírez-Lázaro, M. J., Lario, S., Calvet, X., & Miñana-Galbis, D. (2021). Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma. Pathogens, 10(3), 331. https://doi.org/10.3390/pathogens10030331