TABLE 2.
Pairwise SNP differences calculated between 64 B. cereus sensu lato ST 26 isolates, including 30 emetic isolates from a 2016 foodborne outbreak in New York State (NYS), using various SNP calling pipeline/reference genome combinations
| SNP calling pipeline | Reference strain | MLSTa | ANI range (mean)b | Range (median; mean) |
Min/Max differencec | ||
|---|---|---|---|---|---|---|---|
| Within NYS outbreak | Between NYS and non-NYS outbreaks | Within non-NYS outbreak | |||||
| BactSNP | AH187d | 26 | 99.8–100.0 (99.9) | 0–8 (2; 2.7) | 58–381 (127; 149.6) | 0–477 (162; 183.3) | 50 |
| IS195 | 26 | 99.6–100.0 (99.7) | 0–8 (2; 2.7) | 58–385 (128; 153.9) | 0–483 (167; 187.7) | 50 | |
| AND1407 | 164 | 98.9–99.2 (99.1) | 0–8 (2; 2.7) | 56–378 (125; 147.3) | 0–472 (157; 178.1) | 48 | |
| MB.17 | 144 | 98.8–99.1 (99.0) | 0 to 7 (2; 2.3) | 57–370 (123; 144.3) | 0–448 (153; 175.3) | 50 | |
| MB.18 | 2056 | 97.4–97.8 (97.6) | NAe | NAe | NAe | NAe | |
| MB.22 | 869 | 97.4–97.7 (97.6) | NAf | NAf | NAf | NAf | |
| Lyve-SET | AH187d | 26 | 99.8–100.0 (99.9) | 0–7 (2; 2.6) | 61–1,840 (169; 510.4) | 0–2,246 (198; 520.9) | 54 |
| IS195 | 26 | 99.6–100.0 (99.7) | 0–6 (2; 2.3) | 61–1,421 (174; 428.1) | 0–1,834 (192; 447.7) | 55 | |
| AND1407 | 164 | 98.9–99.2 (99.1) | 0–5 (2; 2.3) | 56–1,622 (147; 449.0) | 0–1,943 (167; 451.7) | 51 | |
| MB.17 | 144 | 98.8–99.1 (99.0) | 0–5 (2; 2.0) | 56–1,479 (144; 419.2) | 0–1,830 (168; 429.7) | 51 | |
| MB.18 | 2056 | 97.4–97.8 (97.6) | 0–4 (1; 1.6) | 47–1,336 (114; 367.2) | 0–1,578 (126; 363.0) | 43 | |
| MB.22 | 869 | 97.4–97.7 (97.6) | 0–4 (1; 1.6) | 44–1,323 (115; 363.3) | 0–1,576 (127; 360.0) | 40 | |
| Parsnp | AH187d | 26 | 99.8–100.0 (99.9) | 0–44 (9; 12.0) | 59–2,404 (190; 697.4) | 0–3,250 (260; 754.1) | 15 |
| IS195 | 26 | 99.6–100.0 (99.7) | 0–43 (9; 12.1) | 62–2,414 (209; 705.3) | 0–3,280 (269; 762) | 19 | |
| AND1407 | 164 | 98.9–99.2 (99.1) | 0–44 (9; 11.8) | 59–2,399 (185; 642.9) | 0–2,832 (249–647.1) | 15 | |
| MB.17 | 144 | 98.8–99.1 (99.0) | 0–42 (9; 11.8) | 63–2,130 (189; 583.5) | 0–2,527 (245; 585.9) | 21 | |
| MB.18 | 2056 | 97.4–97.8 (97.6) | 0–41 (8; 10.6) | 56–2,191 (170; 593) | 0–2,551 (226; 596.3) | 15 | |
| MB.22 | 869 | 97.4–97.7 (97.6) | 0–37 (8; 10.5) | 57–2,180 (167; 595.1) | 0–2,567 (227; 597.3) | 20 | |
| Snippy | AH187d | 26 | 99.8–100.0 (99.9) | 0–7 (2; 2.6) | 57–372 (146; 155.5) | 0–444 (157; 177.6) | 50 |
| IS195 | 26 | 99.6–100.0 (99.7) | 0–7 (2; 2.6) | 58–370 (145; 153.6) | 0–436 (157; 176.2) | 51 | |
| AND1407 | 164 | 98.9–99.2 (99.1) | 0–18 (5; 4.9) | 55–368 (143; 152.9) | 0–434 (156; 173) | 37 | |
| MB.17 | 144 | 98.8–99.1 (99.0) | 0–20 (4; 4.4) | 60–373 (138; 151.8) | 0–436 (153; 171.9) | 40 | |
| MB.18 | 2056 | 97.4–97.8 (97.6) | 0–50 (5; 9.3) | 55–350 (128; 145.7) | 0–401 (133; 159.5) | 5 | |
| MB.22 | 869 | 97.4–97.7 (97.6) | NAf | NAf | NAf | NAf | |
Seven-gene multilocus sequence types (MLST) were determined in silico using BTyper v2.3.3.
ANI range and mean values were calculated between the respective reference genome and 64 group III B. cereus sensu lato genomes assigned to ST 26 using FastANI v1.0.
The Min/Max difference is the maximum number of SNPs identified between two outbreak isolates subtracted from the minimum number of SNPs between an outbreak and nonoutbreak isolate.
AH187 has previously been shown to be an adequate reference genome for reference-based SNP calling among emetic ST 26 genomes (7).
No SNPs identified among the 64 B. cereus sensu lato ST 26 genomes using the respective SNP calling pipeline/reference genome combination.
SNPs identified using the respective SNP calling pipeline/reference genome combination were not diverse enough for use with Gubbins/IQ-TREE.