TABLE 1.
Genome assembly metrics and accession numbers
| Isolate | 408F-DNA-001 | 412F-DNA-002 | 427F-DNA-001 |
|---|---|---|---|
| Assembly accession | JAYXIY000000000 | JAYXIX000000000 | JAYXIW000000000 |
| SRA accession | SRR27606653 | SRR27606652 | SRR27606651 |
| Sequencing kit | 500-cycle Nano v2 | 500-cycle Nano v2 | 600-cycle v3 |
| Sequencing format | 2 × 251 bp | 2 × 251 bpa | 2 × 301 bp |
| Total number of paired reads | 373,565 | 441,603 | 1,201,328 |
| Average depth of coverage | 113× | 124× | 436× |
| Number of contigs | 28 | 19 | 18 |
| Genome size (bp) | 1,570,731 | 1,570,272 | 1,570,218 |
| L50 | 4 | 3 | 3 |
| N50 (bp) | 176,074 | 236,910 | 236,904 |
| Length of longest contig (bp) | 266,682 | 411,760 | 411,746 |
| Average GC content | 0.39 | 0.39 | 0.39 |
| Total CDSs (PGAP) | 1,502 | 1,487 | 1,490 |
| Minimum inhibitory concentration for clarithromycin (R > 0.25 µg/mL)b | 0.125 | 1.5 | 0.5 |
| Minimum inhibitory concentration for metronidazole (R > 8 µg/mL)c |
8 | 16 | 1 |
| Mutations potentially associated with clarithromycin resistanced |
Mutations within 23S rRNA (ARO:3004134) - T510C, G722A, G760del, T896C, T976G, T1024C, C1516del, T1568C, C1648T, T2199C | ||
| Genes/mutations potentially associated with metronidazole resistancee | Presence of major facilitator superfamily antibiotic efflux pump (ARO:3003964); mutations within frxA (ARO:3007059) - V7I, A16T, Q27E, I44V, L71I, F72S, G73S, T110A, N111D, N124S, M126I, A154V, E176K, C193S; mutations within rdxA (ARO:3007055) - T31E, D59N, L62V, S88P, G98S, A118S, V123T, R131K, E175Q | ||
Reverse reads trimmed to 228 nucleotides due to sequencing quality.
Resistance breakpoint for clarithromycin—EUCAST v13.1.
Resistance breakbpoint for metronidazole—EUCAST v13.1.
Genomic data queried against features associated with clarithromycin resistance in H. pylori in the Comprehensive Antimicrobial Resistance Database. The mutations in Table 1 were identified within the 23S rRNA gene for all three isolates, but specific mutations listed within the CARD were not identified.
Genomic data queried against features associated with metronidazole resistance in H. pylori in the Comprehensive Antimicrobial Resistance Database. An antibiotic efflux pump gene was identified in all three genomes. Mutations were identified within frxA and rdxA in all three genomes; specific mutations listed within the CARD are in bold text.