Table 2. Per hospital-onset COVID-19 infection (HOCI) implementation and outcome summary by study intervention phase, overall and within the 7/14 sites included in the ’per protocol’ sensitivity analysis.
| All study sites | Sensitivity analysis | ||||
|---|---|---|---|---|---|
| Study phase | Total | Study phase | |||
| Longer-turnaround | Rapid | Longer-turnaround | Rapid | ||
| N HOCI cases | 373 | 947 | 1320 | 143 | 533 |
| Implementation | |||||
| Sequence returned within expected timeline, n (%)* | 229 (61.4) | 377 (39.8) | 606 (45.9) | 81 (56.6) | 204 (38.3) |
| Sequence returned within study period, n (%)* | 277 (74.3) | 596 (62.9) | 873 (66.1) | 98 (68.5) | 347 (65.1) |
| SRT report returned within target timeline (10 days for longer-turnaround, 2 days for rapid), n (%) | 79 (21.2) | 44 (4.6) | 123 (9.3) | 35 (24.5) | 44 (8.3) |
| SRT report returned within study period, n (%) | 215 (57.6) | 435 (45.9) | 650 (49.2) | 92 (64.3) | 317 (59.5) |
| Time from sample to report return (days), median (IQR, range) [n] | 13 (9–15, 0–36) [215] | 5 (3-11, 2-84) [430] | 9 (4-14, 0-84) [645] | 13 (9–17, 6–29) [92] | 4 (3-6, 2-64) [312] |
| Sequencing results | |||||
| SRT-suggestive patient acquired infection post-admission, n/N (%) | 196/212 (92.5) | 384/423 (90.8) | 580/635 (91.3) | 85/92 (92.4) | 287/311 (92.3) |
| SRT-suggestive patient is part of ward outbreak, n/N (%) | 151/212 (71.2) | 260/423 (61.5) | 411/635 (64.7) | 65/92 (70.7) | 202/311 (65.0) |
| Linkage identified not suspected at initial IPC investigation: | |||||
| All HOCIs in phase n/N (%†, 95% CI) | 24/348 (6.8, 1.7–11.8) | 46/915 (6.7, 2.0–11.3) | 70/1263 (5.5) | 11/139 (7.9, 3.4–12.4) | 39/512 (7.6, 5.3–9.9) |
| When SRT returned n/N (%) | 24/190 (12.6) | 46/403 (11.4) | 70/593 (11.8) | 11/88 (12.5) | 39/296 (13.2) |
| SRT excluded IPC-identified hospital outbreak, n/N (%) | 14/213 (6.6) | 27/428 (6.3) | 41/641 (6.4) | 9/92 (9.8) | 25/310 (8.1) |
| Impact on IPC | |||||
| SRT changed IPC practice: | |||||
| All HOCIs in phase n/N (%†, 95% CI) | 25/373 (7.4, 1.1–13.6) | 74/941 (7.8, 2.4–13.2) | 99/1314 (7.5) | 1/143 (0.7, 0.0–2.1) | 52/527 (9.9, 7.3–12.4) |
| When SRT returned n/N (%) | 25/215 (11.6) | 74/429 (17.2) | 99/644 (15.4) | 1/92 (1.1) | 52/311 (16.7) |
| SRT changed IPC practice for ward, n/N (%) | 13/215 (6.0) | 31/429 (7.2) | 44/644 (6.8) | 0/92 (0.0) | 28/311 (9.0) |
| SRT used in IPC decisions beyond ward, n/N (%) | 12/215 (5.6) | 45/428 (10.5) | 57/643 (8.9) | 1/92 (1.1) | 27/310 (8.7) |
| IPC team reported SRT to be useful, n/N (%) | |||||
| Yes | 107/215 (49.8) | 303/428 (70.8) | 410/643 (63.8) | 25/92 (27.2) | 245/310 (79.0) |
| No | 67/215 (31.2) | 71/428 (16.6) | 138/643 (21.5) | 50/92 (54.3) | 57/310 (18.4) |
| Unsure | 41/215 (19.1) | 54/428 (12.6) | 95/643 (14.8) | 17/92 (18.5) | 8/310 (2.6) |
| HCW absence on ward | |||||
| Proportion of HCWs on sick leave due to COVID-19, median (IQR, range) [n] | 0.09 (0.00–0.15, 0.00–0.30) [49] | 0.13 (0.07–0.29, 0.00–1.00) [162] | 0.13 (0.04–0.27, 0.00–1.00) [321] ‡ | 0.09 (0.00–0.15, 0.00–0.30) [49] | 0.13 (0.08–0.29, 0.00–1.00) [143] |
HCW, healthcare worker; HOCI, hospital-onset COVID-19 infection; IPC, infection prevention and control; IQR, interquartile range; SRT, sequence reporting tool.
*
As recorded by site, not based on recorded date or availability on central CLIMB server.
†
Estimated marginal value from mixed effects model, not raw %, evaluated on intention-to-treat basis with lack of SRT report classified as ‘no’.
‡
Includes data for baseline phase: 0.13 (0.00–0.30, 0.00–0.88) [110].