Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in the Healthcare Setting

BACKGROUND

Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in protecting healthcare workers (HCWs) and patients from acquiring SARS-CoV-2.

METHODS

We performed retrospective cross-sectional analyses of viral genomics from all available SARS-CoV-2 viral samples collected at UC San Diego Health and social network analysis using the electronic medical record to derive temporospatial overlap of infections among related viromes and supplemented with contact tracing data. The outcome measure was any instance of healthcare transmission, defined as cases with closely related viral genomes and epidemiological connection within the healthcare setting during the infection window. Between November 2020 through January 2022, 12 933 viral genomes were obtained from 35 666 patients and HCWs.

RESULTS

Among 5112 SARS-CoV-2 viral samples sequenced from the second and third waves of SARS-CoV-2 (pre-Omicron), 291 pairs were derived from persons with a plausible healthcare overlap. Of these, 34 pairs (12%) were phylogenetically linked: 19 attributable to household and 14 to healthcare transmission. During the Omicron wave, 2106 contact pairs among 7821 sequences resulted in 120 (6%) related pairs among 32 clusters, of which 10 were consistent with healthcare transmission. Transmission was more likely to occur in shared spaces in the older hospital compared with the newer hospital (2.54 vs 0.63 transmission events per 1000 admissions, P < .001).

CONCLUSIONS

IP strategies were effective at identifying and preventing healthcare SARS-CoV-2 transmission.

Insulin Infusion Computer Calculator Programmed Directly Into Electronic Health Record Medication Administration Record

BACKGROUND

Computerized insulin infusion protocols have demonstrated higher staff satisfaction, better compliance with protocols, and increased time with glucose in range compared to paper protocols. At University of California San Diego Health (UCSDH), we implemented an insulin infusion computer calculator (IICC) and transitioned it from a web-based platform directly into the electronic medication administration record (eMAR) of our primary electronic health record (EHR).

METHODS

This is a retrospective analysis of 6306 adult patients at UCSDH receiving intravenous (IV) insulin infusion from March 7, 2013 to May 30, 2019. We created three periods of the study-(1) the pre-eMAR integration period; (2) the eMAR integration period; and (3) the post-eMAR integration period-and looked at the percentage of readings within goal range (90-150 mg/dL for intensive care unit [ICU], 90-180 mg/dL for non-ICU) in patients with and without hyperglycemic emergencies. As our safety endpoints, we elected to look at incidence of blood glucose (BG) readings <70 mg/dL, <54 mg/dL, and <40 mg/dL.

RESULTS

Pre-eMAR 69.8% of readings were in the 90-150 mg/dL range compared to 70.2% post-eMAR (P = .03) and 82.7% of readings were in the 90-180 mg/dL range pre-eMAR versus 82.9% (P = .09) post-eMAR in patients without hyperglycemic emergencies. Rates of hypoglycemia with BG <70 mg/dL were 0.43%, <54 mg/dL were 0.07%, and <40 mg/dL were 0.01% of readings pre- and post-eMAR.

CONCLUSIONS

At UCSDH, our IICC has shown to be safe and effective in a wide variety of clinical situations and we were able to successfully transition it from a web-based platform directly into the eMAR of our primary EHR.

[Bronchiolitis obliterans and no radiographic abnormalities in a patient with rheumatoid arthritis]

A 53-year-old woman was given a diagnosis of rheumatoid arthritis in 1988, and begun treatment with D-penicillamine in September 1992. She noticed dry coughing and exertional dyspnea that began in April 1993. Chest X-ray and CT films revealed no abnormal opacities. However, bronchiolitis obliterans was suspected because of a low FEV1% (23%). Examination of specimens obtained by thoracoscopic lung biopsy revealed constrictive obliteration by granulation tissue in proximal bronchioles and follicular bronchiolitis. Alveoli and respiratory bronchioles were intact. After corticosteroid and cyclophosphamide pulse therapy, FEV1% increased to 35%. At the time of this writing she was alive 2.5 years after hospitalization.

[Hard metal lung with diffuse small nodular shadows]

A 32-year-old woman was admitted to Niigata University Hospital with dyspnea and a non-productive cough. She had been exposed to hard metal dust for 4 years in a metal-polishing factory. Chest X-ray and CT films showed diffuse small nodular shadows in both lung fields and pulmonary-function tests revealed severe restrictive impairment. Specimens obtained by thoracoscopic lung biopsy showed fibrosis in the centers of lobules and in peribronchiolar regions. Giant-cell interstitial pneumonia-like findings were also noted. Tungsten carbide and cobalt were detected in these specimens, with an X-ray microanalyzer. Hard metal lung was diagnosed. By 1 year after she changed her place of work and began corticosteroid treatment her symptoms and pulmonary function had improved remarkably, although shadows on chest X-ray films remained to some extent.