Background
Results
Genomic and antimicrobial susceptibility characteristics of strain 2013BJHL
Comparative genomic and genetic population structure
Virulence, antibiotic resistance and secretion system analysis
T6SS genes | Predicted functions | Identity | E-value | Accession in NCBI |
---|---|---|---|---|
tssM | Type VI secretion system membrane subunit | 100.00% | 0.00E+00 | WP_060660915.1 |
tssD | Type VI secretion system membrane subunit | 100.00% | 1.00E−125 | WP_005020432.1 |
tssG | Type VI secretion system membrane subunit | 100.00% | 0.00E+00 | WP_005020437.1 |
tssF | Type VI secretion system membrane subunit | 100.00% | 0.00E+00 | WP_060660919.1 |
tssE | Type VI secretion system membrane subunit | 100.00% | 6.00E−38 | WP_065836879.1 |
tssC | Type VI secretion system membrane subunit | 100.00% | 0.00E+00 | WP_005020440.1 |
tssB | Type VI secretion system membrane subunit | 100.00% | 0.00E+00 | WP_005020441.1 |
tssA | Type VI secretion system membrane subunit | 100.00% | 0.00E+00 | WP_060660920.1 |
tssJ | Type VI secretion system membrane subunit | 100.00% | 1.00E−101 | WP_054197454.1 |
tssK | Type VI secretion system membrane subunit | 100.00% | 0.00E+00 | WP_060660921.1 |
tssL | Type VI secretion system membrane subunit | 100.00% | 0.00E+00 | WP_060660922.1 |
tssI | Type VI secretion system membrane subunit | 100.00% | 0.00E+00 | WP_082230383.1 |
hp1 | Hypothetical protein | 100% | 1.00E−169 | WP_060660916.1 |
hp2 | Hypothetical protein | 100% | 4.00E−177 | EEquation 62550.1 |
hp3 | Hypothetical protein | 98.46% | 2.00E−37 | WP_060660917.1 |
hp4 | Hypothetical protein | 100.00% | 1.00E−42 | WP_060660918.1 |
hp5 | Hypothetical protein | 93.85% | 9.00E−37 | EAJ1438355.1 |
hp6 | Hypothetical protein | 100.00% | 6.00E−135 | WP_060660923.1 |
hp7 | Hypothetical protein | 100.00% | 4.00E−143 | WP_060660924.1 |
hp8 | Hypothetical protein | 100.00% | 3.00E−144 | WP_060662478.2 |
hp9 | Hypothetical protein | 100.00% | 0.00E+00 | WP_060662473. |
hp10 | Hypothetical protein | 100.00% | 1.00E−162 | WP_060662474.1 |
hp11 | Hypothetical protein | |||
hp12 | Hypothetical protein | 100.00% | 9.00E−88 | WP_005020456.1 |
hp13 | Hypothetical protein | 100.00% | 8.00E−161 | WP_054197458.1 |
hp14 | Hypothetical protein | 100.00% | 0.00E+00 | WP_104719495.1 |
hp15 | Hypothetical protein | 99.66% | 0.00E+00 | WP_060662472.1 |
Discussion
Conclusion
Materials and methods
Sampling, isolation and identification of strain
Antimicrobial susceptibility testing
Whole genome sequencing (WGS) for strain 2013BJHL
Helicobacter pullorum genomes from NCBI
Strain ID | Contigs | CDS | Source | Country | Assembly level | T6SS | GenBank accessions |
---|---|---|---|---|---|---|---|
NCTC13154 | 1 | 1668 | Chicken caecum | UK | Complete Genome | – | LR134509 |
UBA1817 | 31 | 1666 | Cecal contents | UK | Scaffold | – | DCEZ00000000 |
229254/12 | 138 | 1778 | Fresh chicken meat | Portugal | Scaffold | + | JNOA01000000 |
229313/12 | 60 | 1657 | Fresh chicken meat | Portugal | Scaffold | – | JNOB01000000 |
229334/12 | 229 | 2191 | Fresh chicken meat | Portugal | Scaffold | + | JNOC01000000 |
229336/12 | 91 | 1766 | Fresh chicken meat | Portugal | Scaffold | + | JNUR01000000 |
MIT98-5489 | 44 | 1926 | Human | Canada | Scaffold | + | ABQU00000000 |
NCTC13156 | 3 | 1750 | Human stool | Canada | Scaffold | – | UGJF01000000 |
NCTC12824 | 314 | 1894 | Chicken faeces | Switzerland | Scaffold | + | VZPA01000000 |
35818/8 | 43 | 1603 | Poultry feces | Belgium | Scaffold | – | FZMX01000000 |
35818/9 | 50 | 1793 | Poultry feces | Belgium | Scaffold | + | FZMV01000000 |
NAP10B8 | 105 | 1632 | Chicken caecum(broiler) | India | Scaffold | – | MAOZ00000000 |
NAP11B31 | 139 | 1819 | Chicken caecum(broiler) | India | Scaffold | + | MAJF00000000 |
NAP12B32 | 130 | 1814 | Chicken caecum(broiler) | India | Scaffold | + | MAJG00000000 |
NAP13B35 | 123 | 1811 | Chicken caecum(broiler) | India | Scaffold | + | MANJ00000000 |
NAP14B36 | 101 | 1821 | Chicken caecum(broiler) | India | Scaffold | + | MANK00000000 |
NAP1W4 | 162 | 1886 | Chicken caecum | India | Scaffold | + | LXWI00000000 |
NAP2W5 | 140 | 1742 | Chicken caecum | India | Scaffold | – | MAPE00000000 |
NAP3W17 | 74 | 1662 | Chicken caecum | India | Scaffold | – | MAPD00000000 |
NAP5W19 | 127 | 1668 | Chicken caecum | India | Scaffold | – | MAPC00000000 |
NAP6W24 | 108 | 1614 | Chicken caecum | India | Scaffold | – | MAPB00000000 |
NAP8W25 | 134 | 1751 | Chicken caecum | India | Scaffold | – | MAPA00000000 |
2013BJHL* | 34 | 1855 | Fresh chicken liver | China | Scaffold | + | JXTX01000000 |