Institutional setting and study period

Our healthcare campus hosts a 1,785-bed tertiary-care hospital (mostly 5–6-bed cohort cubicles), a 545-bed community hospital, the national cardiac center and a large cancer center. Almost 13,000 HCWs work on campus. Vaccination uptake among HCWs was high, with ≥90.0% receiving 2 doses of mRNA vaccines (Pfizer/Moderna) by the end of June 2021. In contrast, 65.0% of inpatients were fully vaccinated by the end of June 2021. The study period spanned 5 months from June 21, 2021, through November 22, 2021.

Enhanced infection prevention measures

Suspected COVID-19 cases with epidemiological risk (eg, close contact with a COVID-19 case) were admitted to negative-pressure single-bed isolation rooms, whereas patients without epidemiological risk presenting with clinical syndromes compatible with COVID-19 were isolated in reduced-density cohort cubicles in the respiratory surveillance ward until SARS-CoV-2 was excluded. ^{Reference Wee, Hsieh and Phua7} HCWs donned N95 respirators in all clinical areas as a mandatory minimum; HCWs in isolation areas donned N95 respirators and disposable gloves, long-sleeved gowns, and face shields.

Diagnosis of COVID-19 among HCWs and inpatients

All symptomatic HCWs had access to free polymerase chain reaction (PCR) testing at the staff clinic. Routine rostered testing was conducted for all asymptomatic HCWs beginning in April 2021, initially with fortnightly PCR. Given surging community transmission, HCW surveillance was stepped up to twice-weekly rapid antigen detection beginning September 29, 2021. HCWs working in high-risk inpatient areas were required to obtain confirmatory PCR testing. Inpatient screening was instituted from June 2021 via PCR testing on admission and subsequent weekly testing. HCWs and patients with significant close contact with a PCR-confirmed COVID-19 patient underwent a 14-day enhanced surveillance regimen. Patients were tested via PCR on days 1, 4, 7, and 10 and via daily rapid antigen detection until day 14. HCWs were tested via PCR on days 1 and 14 and via daily rapid antigen detection until day 14.

Definition of healthcare-associated COVID-19

All COVID-19 inpatient cases were classified into community-onset or potentially healthcare-associated infection as follows ⁸ :

• Community onset: PCR positive ≤2 days after admission

• Indeterminate healthcare associated: PCR positive 3–7 days after admission

• Probable healthcare associated: PCR positive 8–14 days after admission

• Definite healthcare associated: PCR positive ≥15 days after admission

Incubation periods were defined as 1–14 days prior to positive PCR. The infectious period was defined as 2 days prior to symptom onset if symptomatic or 7 days prior to positive PCR if asymptomatic to 10 days after positive PCR. Significant patient close contact was defined as contact within 2 m of the index case for ≥15 minutes during the index case’s infectious period. ⁸ For HCWs, significant close contact was defined as contact within 2 m of the index for ≥15 minutes. Significant unprotected contact was defined as not having utilized N95 respirators during a significant close contact episode and/or not having donned disposable gowns and gloves during episodes of prolonged physical contact. HCWs with significant unprotected contact were furloughed during the enhanced surveillance period.

Cluster definition

Epidemiological clusters were defined as ≥2 COVID-19 cases among patients and HCWs in the same setting (ie, ward or workplace). These cluster outbreaks ended when no cases were diagnosed for 14 days. Genomic clusters were detected based on whole-genome similarity analysis, when sequences were ≤3 SNPs different and fell in the same branch of the genome similarity tree. ^{Reference Yingtaweesittikul, Ko, Nurdyana, Tan, Nagarajan and Suphavilai9}

Epidemiologic and genetic analysis

Contact tracing was performed for all potentially healthcare-associated COVID-19 inpatient cases and all community-onset COVID-19 inpatient cases initially managed outside isolation areas, as well as all HCWs at work during their infective periods. Cases with a cycle threshold (Ct) value <31 were sent for WGS using the ARTIC protocol on Oxford Nanopore minION sequencers (Oxford Nanopore, Oxford, UK) to enable fortnightly turnaround. ^{Reference Yingtaweesittikul, Ko, Nurdyana, Tan, Nagarajan and Suphavilai9}

Ethics statement

Ethics approval for outbreak investigation was not required under our institutional review board guidelines.