Volume 31, Supplement—May 2025
SUPPLEMENT ISSUE
Supplement
Effects of Decentralized Sequencing on National Listeria monocytogenes Genomic Surveillance, Australia, 2016–2023
Table
Sample processing times used in a study of effects of decentralized sequencing on national Listeria monocytogenes genomic surveillance, Australia, 2016–2023*
| Collection year | Median time, d (range) |
|||||||
|---|---|---|---|---|---|---|---|---|
| ACT | NSW | NT | QLD | SA | TAS | VIC | WA | |
| Overall referral time† | ||||||||
| All sample sources | ||||||||
| 2016 | ND | 29 (15–106) | ND | 36 (30–55) | 37 (33–61) | 34 (29–39) | 25 (15–37) | 44 (36–65) |
| 2023 | 36 (36–43) | 24 (10–65) | 75 (28–122) | 20 (12–43) | 45 (14–71) | 30 (18–32) | 26 (12–56) | 50 (26–187) |
| p value |
ND |
0.003 |
ND |
<0.001 |
NS |
NS |
NS |
NS |
| Primary referral time‡ | ||||||||
| Human samples | ||||||||
| 2016 | ND | 5 (1–14) | ND | 4 (3–7) | 2 (2–3) | 4 (4) | 5 (2–10) | 6 (2–10) |
| 2023 | 13 (12–13) | 6 (0–20) | 3 (3) | 5 (2–6) | 3 (1–5) | 9 (8–9) | 3 (1–7) | 4 (0–10) |
| p value | ND | NS | ND | NS | NS | NS | <0.001 | NS |
| Food samples | ||||||||
| 2016 | ND | 1 (1) | ND | 1 (0–11) | ND | 19 (19) | 4 (0–14) | ND |
| 2023 | 15 (15) | ND | ND | 0 (0–2) | 9 (6–17) | 9 (9) | 4 (0–25) | 32 (0–129) |
| p value | NS | ND | ND | NS | ND | 0.026 | NS | ND |
| Environmental samples | ||||||||
| 2016 | ND | 1 (0–2) | ND | 1 (1) | ND | ND | 0 | ND |
| 2023 | ND | 1 (1) | ND | ND | 29 (29) | ND | 1 (0–6) | ND |
| p value |
ND |
NS |
ND |
ND |
ND |
ND |
NS |
ND |
| Sequencing time§ | ||||||||
| Human samples | ||||||||
| 2016 | ND | 10 (3–18) | ND | 10 (8–14) | 10 (5–13) | 11 (11) | 10 (6–18) | 12 (10–20) |
| 2023 | 13 | 5 (1–12) | 11 (10–11) | 8 (2–12) | 3 (2–5) | 8 (6–11) | 8 (5–11) | 6 (1–12) |
| p value | ND | <0.001 | ND | 0.014 | NS | NS | 0.003 | NS |
| Food samples | ||||||||
| 2016 | ND | 3 (3–10) | ND | 14 (10–18) | ND | 16 (16) | 20 (15–20) | ND |
| 2023 | 9 (9) | 15 (5–15) | ND | 7 (6–14) | 9 (6–14) | 8 (7–9) | 11 (6–25) | 7 (2–8) |
| p value | ND | <0.001 | ND | NS | ND | NS | 0.002 | ND |
| Environmental samples | ||||||||
| 2016 | ND | 10 (3–14) | ND | 14 (14) | ND | ND | 17 (17) | ND |
| 2023 | ND | 5 (2–5) | ND | ND | 6 (6) | ND | 16 (9–21) | ND |
| p value |
ND |
<0.001 |
ND |
ND |
ND |
ND |
NS |
ND |
| Sequence referral time§ | ||||||||
| All sample sources | ||||||||
| 2016 | ND | 20 (9–96) | ND | 27 (13–41) | 25 (17–52) | ND | ND | 34 (21–48) |
| 2023 | ND | 12 (4–54) | ND | 12 (3–19) | 26 (7–31) | ND | ND | 12 (7–26) |
| p value |
ND |
<0.001 |
ND |
<0.001 |
NS |
ND |
ND |
0.007 |
| Genomic analysis time# | ||||||||
| 2016 | ND | 11 (0–14) | ND | 8 (1–11) | 10 (4–17) | 9 (4–14) | 8 (3–17) | 9 (2–11) |
| 2023 | 19 (15–19) | 8 (1–13) | 7 (2–12) | 1 (1–19) | 9 (3–14) | 12 (4–15) | 9 (1–21) | 14 (3–18) |
| p value | ND | 0.025 | ND | 0.002 | NS | NS | NS | <0.001 |
*Times are shown as median (range) in days for each jurisdiction for years 2016 and 2023, and adjusted p values from Dunn’s post-hoc tests of pairwise comparisons. Range defined as data points within 1.5 from each quartile, with points outside interquartile range considered outliers. ACT, Australian Capital Territory; ND, no data available; NS, not statistically significant; NSW, New South Wales; NT, Northern Territory; QLD, Queensland; SA, South Australia; TAS, Tasmania; VIC, Victoria; WA, Western Australia. †Date of collection to date genomic surveillance report issued. ‡Date of collection to date sample received at jurisdictional public health laboratory. §Date received at jurisdictional public health laboratory to date sequenced. ¶Date received at jurisdictional PHL to date sequence available for bioinformatic analysis at the National Listeria Reference Laboratory. #Date received at national Listeria reference laboratory to date national genomic report issued.