Explosive Nosocomial Outbreak of SARS-CoV-2 in a Rehabilitation Clinic: The Limits of Genomics for Outbreak Reconstruction

Abbas, Mohamed; Nunes, Tomás Robalo; Cori, Anne; Cordey, Samuel; Laubscher, Florian; Baggio, Stéphanie; Jombart, Thibaut; Iten, Anne; Vieux, Laure; Teixeira, Daniel; Pérez, Mónica; Pittet, Didier; Frangos, Emilia; Graf, Christophe; Zingg, Walter; Harbarth, Stéphan Juergen

doi:10.2139/ssrn.3800084

Cited by 11 publications

(20 citation statements)

References 29 publications

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“…Our results strongly emphasize the importance of HCW-to-HCWs SARS-CoV-2 transmission, as previously described [18,34] and thus non only challenge the misperception that patients are the dominant reservoirs and vectors, but also support the importance of non-pharmaceutical interventions and repeated testing of employees to limit transmission from community to healthcare settings, as well as the importance of aggressive vaccination campaigns among LTCF employees [35][36][37]. Therefore, occupational exposure is not always related to direct patient care.…”

Section: Discussionsupporting

confidence: 90%

“…As previously described [18], the outbreak reconstruction was performed combining epidemiological (date of symptom onset and trajectories) and genetic sequencing data. It includes 1) construction of an epidemic curve and estimation of the time-varying reproduction number (Rt) using the EpiEstim package [19], 2) an ancestry reconstruction (who infected whom) using the outbreaker2 package [20,21], 3) a maximum posterior tree, 4) a maximum likelihood phylogenetic tree.…”

Section: Discussionmentioning

confidence: 99%

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Occupational versus community risk of SARS-CoV-2 infection among employees of a long-term care facility: an observational study

Lenggenhager

Martischang

Sauser

et al. 2021

Preprint

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ObjectivesWe investigated the relative contribution of occupational (vs. community) exposure for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among employees of a university-affiliated long-term care facility (LTCF), during the 1st pandemic wave in Switzerland (March to June 2020).MethodsWe performed a nested analysis of a seroprevalence study among all volunteering LTCF staff to determine community and nosocomial risk factors for SARS-CoV-2 seropositivity using modified Poison regression. We also combined epidemiological and genetic sequencing data from a coronavirus disease 2019 (COVID-19) outbreak investigation in a LTCF ward to infer transmission dynamics and acquisition routes of SARS-CoV-2, and evaluated strain relatedness using a maximum likelihood phylogenetic tree.ResultsAmong 285 LTCF employees, 176 participated in the seroprevalence study, of whom 30 (17%) were seropositive for SARS-CoV-2. Most (141/176, 80%) were healthcare workers (HCWs). Risk factors for seropositivity included exposure to a COVID-19 inpatient (adjusted prevalence ratio [aPR] 2.6; 95%CI 0.9-8.1) and community contact with a COVID-19 case (aPR 1.7; 95%CI 0.8-3.5). Among 18 employees included in the outbreak investigation, the outbreak reconstruction suggests 4 likely importation events by HCWs with secondary transmissions to other HCWs and patients.ConclusionsThese two complementary epidemiologic and molecular approaches suggest a substantial contribution of both occupational and community exposures to COVID-19 risk among HCWs in LTCFs. These data may help to better assess the importance of occupational health hazards and related legal implications during the COVID-19 pandemic.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Occupational versus community risk of SARS-CoV-2 infection among employees of a long-term care facility: an observational study

Lenggenhager

Martischang

Sauser

et al. 2021

Preprint

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“…and from work 28 . Still, as mass vaccination campaigns are being planned and implemented worldwide, our results strengthen the evidence to prioritize access to healthcare workers, particularly nurses, as well as employees of nursing homes, including kitchen staff.…”

Section: Discussionmentioning

confidence: 97%

“…Sample description and prevalence of anti-SARS-CoV-2 IgG antibodies, SEROCoV-WORK + study, May-September 2020, Geneva, Switzerland. These pertain to the reference individual (Female,[18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]. 69 participants were excluded due to missing serology or sociodemographic data, or due to being outside target age range of 18-65 years.…”

mentioning

confidence: 99%

Large variation in anti-SARS-CoV-2 antibody prevalence among essential workers in Geneva, Switzerland

et al. 2021

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Limited data exist on SARS-CoV-2 infection rates across sectors and occupations, hindering our ability to make rational policy, including vaccination prioritization, to protect workers and limit SARS-CoV-2 spread. Here, we present results from our SEROCoV-WORK + study, a serosurvey of workers recruited after the first wave of the COVID-19 pandemic in Geneva, Switzerland. We tested workers (May 18—September 18, 2020) from 16 sectors and 32 occupations for anti-SARS-CoV-2 IgG antibodies. Of 10,513 participants, 1026 (9.8%) tested positive. The seropositivity rate ranged from 4.2% in the media sector to 14.3% in the nursing home sector. We found considerable within-sector variability: nursing home (0%–31.4%), homecare (3.9%–12.6%), healthcare (0%–23.5%), public administration (2.6%–24.6%), and public security (0%–16.7%). Seropositivity rates also varied across occupations, from 15.0% among kitchen staff and 14.4% among nurses, to 5.4% among domestic care workers and 2.8% among journalists. Our findings show that seropositivity rates varied widely across sectors, between facilities within sectors, and across occupations, reflecting a higher exposure in certain sectors and occupations.

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“…[6][7][8][9] Elucidating the source of transmission events on the basis of viral genetic relatedness alone also entails considerable uncertainty due to the slow evolutionary rate of SARS-CoV-2. [10] In the time scale of an outbreak, a large proportion of individuals are infected by viruses too genetically similar to each other to distinguish genuine transmission events from unrelated infections. Furthermore, data from HCWs have rarely been included in previous analyses [11] and the relative role that patients and HCWs have played in fuelling hospital outbreaks in the UK remains largely unknown.…”

Section: Introductionmentioning

confidence: 99%

Characterising within-hospital SARS-CoV-2 transmission events: a retrospective analysis integrating epidemiological and viral genomic data from a UK tertiary care setting across two pandemic waves

Lindsey

Villabona-Arenas

Campbell

et al. 2021

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Objectives - To characterise within-hospital SARS-CoV-2 transmission across two waves of the COVID-19 pandemic. Design - A retrospective Bayesian modelling study to reconstruct transmission chains amongst 2181 patients and healthcare workers using combined viral genomic and epidemiological data. Setting - A large UK NHS Trust with over 1400 beds and employing approximately 17,000 staff. Participants - 780 patients and 522 staff testing SARS-CoV-2 positive between 1st March 2020 and 25th July 2020 (Wave 1); and 580 patients and 299 staff testing SARS-CoV-2 positive between 30th November 2020 and 24th January 2021 (Wave 2). Main outcome measures - Transmission pairs including who-infected-whom; location of transmission events in hospital; number of secondary cases from each individual, including differences in onward transmission from community and hospital onset patient cases. Results - Staff-to-staff transmission was estimated to be the most frequent transmission type during Wave 1 (31.6% of observed hospital-acquired infections; 95% CI 26.9 to 35.8%), decreasing to 12.9% (95% CI 9.5 to 15.9%) in Wave 2. Patient-to-patient transmissions increased from 27.1% in Wave 1 (95% CI 23.3 to 31.4%) to 52.1% (95% CI 48.0 to 57.1%) in Wave 2, to become the predominant transmission type. Over 50% of hospital-acquired infections were concentrated in 8/120 locations in Wave 1 and 10/93 locations in Wave 2. Approximately 40% to 50% of hospital-onset patient cases resulted in onward transmission compared to less than 4% of definite community-acquired cases. Conclusions - Prevention and control measures that evolved during the COVID-19 pandemic may have had a significant impact on reducing infections between healthcare workers, but were insufficient during the second wave to prevent a high number of patient-to-patient transmissions. As hospital-acquired cases appeared to drive most onward transmissions, more frequent and rapid identification and isolation of these cases will be required to break hospital transmission chains in subsequent pandemic waves

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Explosive Nosocomial Outbreak of SARS-CoV-2 in a Rehabilitation Clinic: The Limits of Genomics for Outbreak Reconstruction

Cited by 11 publications

References 29 publications

Occupational versus community risk of SARS-CoV-2 infection among employees of a long-term care facility: an observational study

Occupational versus community risk of SARS-CoV-2 infection among employees of a long-term care facility: an observational study

Large variation in anti-SARS-CoV-2 antibody prevalence among essential workers in Geneva, Switzerland

Characterising within-hospital SARS-CoV-2 transmission events: a retrospective analysis integrating epidemiological and viral genomic data from a UK tertiary care setting across two pandemic waves

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