We compared the rates of hospital-onset secondary bacterial infections in patients with coronavirus disease 2019 (COVID-19) with rates in patients with influenza and controls, and we investigated reports of increased incidence of Enterococcus infections in patients with COVID-19.

Retrospective cohort study.

An academic quaternary-care hospital in San Francisco, California.

Patients admitted between October 1, 2019, and October 1, 2020, with a positive SARS-CoV-2 PCR (N = 314) or influenza PCR (N = 82) within 2 weeks of admission were compared with inpatients without positive SARS-CoV-2 or influenza tests during the study period (N = 14,332).

National Healthcare Safety Network definitions were used to identify infection-related ventilator-associated complications (IVACs), probable ventilator-associated pneumonia (PVAP), bloodstream infections (BSIs), and catheter-associated urinary tract infections (CAUTIs). A multiple logistic regression model was used to control for likely confounders.

COVID-19 patients had significantly higher rates of IVAC and PVAP compared to controls, with adjusted odds ratios of 4.7 (95% confidence interval [CI], 1.7–13.9) and 10.4 (95 % CI, 2.1–52.1), respectively. COVID-19 patients had higher incidence of BSI due to Enterococcus but not BSI generally, and whole-genome sequencing of Enterococcus isolates demonstrated that nosocomial transmission did not explain the increased rate. Subanalyses of patients admitted to the intensive care unit and patients who required mechanical ventilation revealed similar findings.

COVID-19 is associated with an increased risk of IVAC, PVAP, and Enterococcus BSI compared with hospitalized controls, which is not fully explained by factors such as immunosuppressive treatments and duration of mechanical ventilation. The mechanism underlying increased rates of Enterococcus BSI in COVID-19 patients requires further investigation.

Effective infection prevention and control (IPC) measures are key for protecting patients from nosocomial infections and require knowledge of transmission mechanisms in different settings. We performed a detailed outbreak analysis of the transmission and outcome of coronavirus disease 2019 (COVID-19) in a geriatric ward by combining whole-genome sequencing (WGS) with epidemiological data.

Retrospective cohort study.

Tertiary-care hospital.

Patients and healthcare workers (HCWs) from the ward with a nasopharyngeal sample (NPS) positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) RNA during the outbreak period.

Patient data regarding clinical characteristics, exposure and outcome were collected retrospectively from medical records. Stored NPSs from 32 patients and 15 HCWs were selected for WGS and phylogenetic analysis.

The median patient age was 84 years and 17 (53%) of 32 were male. Also, 14 patients (44%) died within 30 days of sampling. Viral loads were significantly higher among the deceased. WGS was successful in 28 (88%) of 32 patient samples and 14 (93%) of 15 HCW samples. Moreover, 3 separate viral clades were identified: 1 clade and 2 subclades among both patient and HCW samples. Integrated epidemiological and genetic analyses revealed 6 probable transmission events between patients and supported hospital-acquired COVID-19 among 25 of 32 patients.

WGS provided an insight into the outbreak dynamics and true extent of nosocomial COVID-19. The extensive transmission between patients and HCWs indicated that current IPC measures were insufficient. We recommend increased use of WGS in outbreak investigations to identify otherwise unknown transmission links and to evaluate IPC measures.

Performance characteristics of SARS-CoV-2 nucleic acid detection assays are understudied within contexts of low pre-test probability, including screening asymptomatic persons without epidemiological links to confirmed cases, or asymptomatic surveillance testing. SARS-CoV-2 detection without symptoms may represent presymptomatic or asymptomatic infection, resolved infection with persistent RNA shedding, or a false-positive test. This study assessed the positive predictive value of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) assays by retesting positive specimens from 5 pre-test probability groups ranging from high to low with an alternate assay.

In total, 122 rRT-PCR positive specimens collected from unique patients between March and July 2020 were retested using a laboratory-developed nested RT-PCR assay targeting the RNA-dependent RNA polymerase (RdRp) gene followed by Sanger sequencing.

Significantly fewer (15.6%) positive results in the lowest pre-test probability group (facilities with institution-wide screening having ≤3 positive asymptomatic cases) were reproduced with the nested RdRp gene RT-PCR assay than in each of the 4 groups with higher pre-test probability (individual group range, 50.0%–85.0%).

Large-scale SARS-CoV-2 screening testing initiatives among low pre-test probability populations should be evaluated thoroughly prior to implementation given the risk of false-positive results and consequent potential for harm at the individual and population level.

To determine the changes in severe acute respiratory coronavirus virus 2 (SARS-CoV-2) serologic status and SARS-CoV-2 infection rates in healthcare workers (HCWs) over 6-months of follow-up.

Prospective cohort study.

HCWs in the Chicago area.

Cohort participants were recruited in May and June 2020 for baseline serology testing (Abbott anti-nucleocapsid IgG) and were then invited for follow-up serology testing 6 months later. Participants completed monthly online surveys that assessed demographics, medical history, coronavirus disease 2019 (COVID-19), and exposures to SARS-CoV-2. The electronic medical record was used to identify SARS-CoV-2 polymerase chain reaction (PCR) positivity during follow-up. Serologic conversion and SARS-CoV-2 infection or possible reinfection rates (cases per 10,000 person days) by antibody status at baseline and follow-up were assessed.

In total, 6,510 HCWs were followed for a total of 1,285,395 person days (median follow-up, 216 days). For participants who had baseline and follow-up serology checked, 285 (6.1%) of the 4,681 seronegative participants at baseline seroconverted to positive at follow-up; 138 (48%) of the 263 who were seropositive at baseline were seronegative at follow-up. When analyzed by baseline serostatus alone, 519 (8.4%) of 6,194 baseline seronegative participants had a positive PCR after baseline serology testing (4.25 per 10,000 person days). Of 316 participants who were seropositive at baseline, 8 (2.5%) met criteria for possible SARS-CoV-2 reinfection (ie, PCR positive >90 days after baseline serology) during follow-up, a rate of 1.27 per 10,000 days at risk. The adjusted rate ratio for possible reinfection in baseline seropositive compared to infection in baseline seronegative participants was 0.26 (95% confidence interval, 0.13–0.53).

Seropositivity in HCWs is associated with moderate protection from future SARS-CoV-2 infection.