Investigation of healthcare-associated COVID-19 in a large French hospital group by whole-genome sequencing

Factors associated with extent of COVID-19 outbreaks: A prospective study in a large hospital network

BACKGROUND

The COVID-19 pandemic has generated numerous hospital outbreaks. This study aimed to identify factors related to the extent of nosocomial COVID-19 outbreaks in the largest French public health institution.

METHODS

An observational study was conducted from July 2020 to September 2021. Outbreaks were defined as at least 2 cases, patients and/or health care workers (HCWs), linked by time and geographic location. Logistic regression was performed to identify risk factors for large outbreaks among nine variables: variant, medical ward, COVID-19 vaccination rate and incidence among HCWs and Paris population, number of weekly COVID-19 tests among HCWs and the positivity rate, epidemic waves.

RESULTS

Within 14 months, 799 outbreaks were identified: 450 small ones (≤6 cases) and 349 large ones (≥7 cases), involving 3,260 patients and 3,850 HCWs. In univariate analysis, large outbreaks were positively correlated to geriatrics wards, COVID-19 incidence, and rate of weekly positive tests among HCWs; and negatively correlated to intensive care units, variant Delta, fourth wave, vaccination rates of the Paris region's population and that of the HCWs. In multivariate analysis, factors that remained significant were the type of medical ward and the vaccination rate among HCWs.

CONCLUSIONS

Intensive care unit and high vaccination rates among HCWs were associated with a lower risk of large COVID-19 outbreaks, as opposed to geriatric wards, which are associated with a higher risk.

A systematic outbreak investigation of SARS-CoV-2 transmission clusters in a tertiary academic care center

BACKGROUND

We sought to decipher transmission pathways in healthcare-associated infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within our hospital by epidemiological work-up and complementary whole genome sequencing (WGS). We report the findings of the four largest epidemiologic clusters of SARS-CoV-2 transmission occurring during the second wave of the pandemic from 11/2020 to 12/2020.

METHODS

At the University Hospital Basel, Switzerland, systematic outbreak investigation is initiated at detection of any nosocomial case of SARS-CoV-2 infection, as confirmed by polymerase chain reaction, occurring more than five days after admission. Clusters of nosocomial infections, defined as the detection of at least two positive patients and/or healthcare workers (HCWs) within one week with an epidemiological link, were further investigated by WGS on respective strains.

RESULTS

The four epidemiologic clusters included 40 patients and 60 HCWs. Sequencing data was available for 70% of all involved cases (28 patients and 42 HCWs), confirmed epidemiologically suspected in house transmission in 33 cases (47.1% of sequenced cases) and excluded transmission in the remaining 37 cases (52.9%). Among cases with identical strains, epidemiologic work-up suggested transmission mainly through a ward-based exposure (24/33, 72.7%), more commonly affecting HCWs (16/24, 66.7%) than patients (8/24, 33.3%), followed by transmission between patients (6/33, 18.2%), and among HCWs and patients (3/33, 9.1%, respectively two HCWs and one patient).

CONCLUSIONS

Phylogenetic analyses revealed important insights into transmission pathways supporting less than 50% of epidemiologically suspected SARS-CoV-2 transmissions. The remainder of cases most likely reflect community-acquired infection randomly detected by outbreak investigation. Notably, most transmissions occurred between HCWs, possibly indicating lower perception of the risk of infection during contacts among HCWs.

Molecular Characterization and Cluster Analysis of SARS-CoV-2 Viral Isolates in Kahramanmaraş City, Turkey: The Delta VOC Wave within One Month

The SARS-CoV-2 pandemic has seriously affected the population in Turkey. Since the beginning, phylogenetic analysis has been necessary to monitor public health measures against COVID-19 disease. In any case, the analysis of spike (S) and nucleocapsid (N) gene mutations was crucial in determining their potential impact on viral spread. We screened S and N regions to detect usual and unusual substitutions, whilst also investigating the clusters among a patient cohort resident in Kahramanmaraş city, in a restricted time span. Sequences were obtained by Sanger methods and genotyped by the PANGO Lineage tool. Amino acid substitutions were annotated comparing newly generated sequences to the NC_045512.2 reference sequence. Clusters were defined using phylogenetic analysis with a 70% cut-off. All sequences were classified as Delta. Eight isolates carried unusual mutations on the S protein, some of them located in the S2 key domain. One isolate displayed the unusual L139S on the N protein, while few isolates carried the T24I and A359S N substitutions able to destabilize the protein. Phylogeny identified nine monophyletic clusters. This study provided additional information about SARS-CoV-2 epidemiology in Turkey, suggesting local transmission of infection in the city by several transmission routes, and highlighting the necessity to improve the power of sequencing worldwide.

Clinical Outcome and Prognosis of a Nosocomial Outbreak of COVID-19

Nosocomial coronavirus disease 2019 (COVID-19) outbreaks have been reported despite widespread quarantine methods to prevent COVID-19 in society and hospitals. Our study was performed to investigate the clinical outcome and prognosis of a nosocomial outbreak of COVID-19. We retrospectively analyzed the medical records of patients diagnosed with nosocomial COVID-19 of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) at a university teaching hospital between 1 November 2021 and 31 April 2022. Nosocomial COVID-19 was defined as a positive SARS-CoV-2 polymerase chain reaction (PCR) test result 4 or more days after admission in asymptomatic patients who had a negative SARS-CoV-2 PCR test on admission. In this study, 167 patients were diagnosed with nosocomial COVID-19 (1.14%) among a total of 14,667 patients admitted to hospital during the study period. A total of 153 patients (91.6%) survived, but 14 patients (8.4%) died. The median time between admission and COVID-19 diagnosis was 11 days, and the median duration of hospital stay was 24 days. After adjusting for other factors, no vaccination (adjusted HR = 5.944, 95% CI = 1.626–21.733, p = 0.007) and chronic kidney disease (adjusted HR = 6.963, 95% CI = 1.182–41.014, p = 0.032) were found to increase mortality risk. Despite strict quarantine, a significant number of nosocomial COVID-19 cases with a relatively high mortality rate were reported. As unvaccinated status or chronic kidney disease were associated with poor outcomes of nosocomial COVID-19, more active preventive strategies and treatments for patients with these risk factors are needed.

Transmission dynamics and associated mortality of nosocomial COVID-19 throughout 2021: a retrospective study at a large teaching hospital in London

BACKGROUND

The impact of nosocomial SARS-CoV-2 infections has changed significantly since 2020. However, there is a lack of up-to-date evidence of the epidemiology of these infections which is essential in order to appropriately guide infection control policy.

AIMS

To identify the secondary attack rate of SARS-CoV-2 infection and associated mortality across different variants of concern.

METHODS

A single-centre retrospective study of all nosocomial SARS-CoV-2 exposure events was conducted between 31^st December 2020 and 31^st December 2021. A secondary attack rate was calculated for nosocomial acquisition of SARS-CoV-2 infection and time to positivity. Positive contacts were assessed for all-cause 30-day mortality.

RESULTS

A total of 346 sequential index exposure events were examined, and 1378 susceptible contacts identified. Two hundred susceptible contacts developed SARS-CoV-2 infection (secondary attack rate of 15.5%). The majority of index cases (59%) did not result in any secondary SARS-CoV-2 infection. Where close contacts developed SARS-CoV-2 infection, 80% were detected within the first five days since last contact with the index case. The overall associated mortality among positive contacts across 2021 was 9%, with an estimated reduction of 68% when comparing periods of high Omicron versus Alpha transmission.

CONCLUSION

Our findings describe that most SARS-CoV-2 infections are detected within five days of contact with an index case; we have also demonstrated a considerably lower mortality rate with the Omicron variant in comparison to previous variants. These findings have important implications for informing and supporting infection control protocols to allow movement through the hospital, and ensure patients access care safely.