Genomic investigation to identify the source of SARS-CoV-2 infection among healthcare personnel
Background: Contact tracing alone is often inadequate to determine the source of healthcare personnel (HCP) COVID-19 when SARS-CoV-2 is widespread in the community. We combined whole-genome sequencing (WGS) with traditional epidemiologic analysis to investigate the frequency with which patients or o...
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Published in | Antimicrobial stewardship & healthcare epidemiology : ASHE Vol. 2; no. S1; pp. s74 - s75 |
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Main Authors | , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
Cambridge
Cambridge University Press
01.07.2022
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Subjects | |
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Abstract | Background:
Contact tracing alone is often inadequate to determine the source of healthcare personnel (HCP) COVID-19 when SARS-CoV-2 is widespread in the community. We combined whole-genome sequencing (WGS) with traditional epidemiologic analysis to investigate the frequency with which patients or other HCP with symptomatic COVID-19 acted as the source of HCP infection at a large tertiary-care center early in the pandemic.
Methods:
Cohort samples were selected from patients and HCP with PCR-positive SARS-CoV-2 infection from a period with complete retention of samples (March 14, 2021–April 10, 2020) at Rush University Medical Center, a 664-bed hospital in Chicago, Illinois. During this period, testing was limited to symptomatic patients and HCP. Recommended respiratory equipment for HCP evolved under guidance, including a 19-day period when medical face masks were recommended for COVID-19 care except for aerosol-generating procedures. Viral RNA was extracted and sequenced (NovaSeq, Illumina) from remnant nasopharyngeal swab samples in M4RT viral transport medium. Genomes with >90% coverage underwent cluster detection using a 2 single-nucleotide variant genetic distance cutoff. Genomic clusters were independently evaluated for valid epidemiologic links by 2 infectious diseases physicians (with a third adjudicator) using metadata extracted from the electronic medical record and according to predetermined criteria (Table 1).
Results:
In total, 1,031 SARS-CoV-2 sequences were analyzed, identifying 49 genomic clusters with HCP (median, 8; range, 2–43 members per cluster; total, 268 patients and 115 HCP) (Fig. 1). Also, 20,190 flowsheet activities were documented for cohort HCP and patient interactions, including 686 instances in which a cohort HCP contributed to a cohort patient’s chart. Most HCP infections were considered not healthcare associated (88 of 115, 76.5%). We did not identify any strong linkages for patient-to-HCP transmission. Moreover, 13 HCP cases (11.3%) were attributed to patient source (weak linkage). Also, 14 HCP cases (12.2%) were attributed to HCP source (11 strong and 3 weak linkages). Weak linkages were due to lack of epidemiologic data for HCP location, particularly nonclinical staff (eg, an environmental service worker who lacked location documentation to rule out patient-specific contact). Agreement for epidemiologic linkage between the 2 evaluators was high (κ, 0.91).
Conclusions:
Using genomic and epidemiologic data, we found that most HCP COVID-19 infections were not healthcare associated. We found weak evidence to support symptomatic patient-to-HCP transmission of SARS-CoV-2 and stronger evidence for HCP-to-HCP transmission. Large genomic clusters without plausible epidemiologic links were identified, reflecting the limited utility of genomic surveillance alone to characterize chains of transmission of SARS-CoV-2 during extensive community spread.
Funding:
None
Disclosures:
None |
---|---|
AbstractList | Background:
Contact tracing alone is often inadequate to determine the source of healthcare personnel (HCP) COVID-19 when SARS-CoV-2 is widespread in the community. We combined whole-genome sequencing (WGS) with traditional epidemiologic analysis to investigate the frequency with which patients or other HCP with symptomatic COVID-19 acted as the source of HCP infection at a large tertiary-care center early in the pandemic.
Methods:
Cohort samples were selected from patients and HCP with PCR-positive SARS-CoV-2 infection from a period with complete retention of samples (March 14, 2021–April 10, 2020) at Rush University Medical Center, a 664-bed hospital in Chicago, Illinois. During this period, testing was limited to symptomatic patients and HCP. Recommended respiratory equipment for HCP evolved under guidance, including a 19-day period when medical face masks were recommended for COVID-19 care except for aerosol-generating procedures. Viral RNA was extracted and sequenced (NovaSeq, Illumina) from remnant nasopharyngeal swab samples in M4RT viral transport medium. Genomes with >90% coverage underwent cluster detection using a 2 single-nucleotide variant genetic distance cutoff. Genomic clusters were independently evaluated for valid epidemiologic links by 2 infectious diseases physicians (with a third adjudicator) using metadata extracted from the electronic medical record and according to predetermined criteria (Table
1
).
Results:
In total, 1,031 SARS-CoV-2 sequences were analyzed, identifying 49 genomic clusters with HCP (median, 8; range, 2–43 members per cluster; total, 268 patients and 115 HCP) (Fig.
1
). Also, 20,190 flowsheet activities were documented for cohort HCP and patient interactions, including 686 instances in which a cohort HCP contributed to a cohort patient’s chart. Most HCP infections were considered not healthcare associated (88 of 115, 76.5%). We did not identify any strong linkages for patient-to-HCP transmission. Moreover, 13 HCP cases (11.3%) were attributed to patient source (weak linkage). Also, 14 HCP cases (12.2%) were attributed to HCP source (11 strong and 3 weak linkages). Weak linkages were due to lack of epidemiologic data for HCP location, particularly nonclinical staff (eg, an environmental service worker who lacked location documentation to rule out patient-specific contact). Agreement for epidemiologic linkage between the 2 evaluators was high (κ, 0.91).
Conclusions:
Using genomic and epidemiologic data, we found that most HCP COVID-19 infections were not healthcare associated. We found weak evidence to support symptomatic patient-to-HCP transmission of SARS-CoV-2 and stronger evidence for HCP-to-HCP transmission. Large genomic clusters without plausible epidemiologic links were identified, reflecting the limited utility of genomic surveillance alone to characterize chains of transmission of SARS-CoV-2 during extensive community spread.
Funding:
None
Disclosures:
None Background: Contact tracing alone is often inadequate to determine the source of healthcare personnel (HCP) COVID-19 when SARS-CoV-2 is widespread in the community. We combined whole-genome sequencing (WGS) with traditional epidemiologic analysis to investigate the frequency with which patients or other HCP with symptomatic COVID-19 acted as the source of HCP infection at a large tertiary-care center early in the pandemic. Methods: Cohort samples were selected from patients and HCP with PCR-positive SARS-CoV-2 infection from a period with complete retention of samples (March 14, 2021–April 10, 2020) at Rush University Medical Center, a 664-bed hospital in Chicago, Illinois. During this period, testing was limited to symptomatic patients and HCP. Recommended respiratory equipment for HCP evolved under guidance, including a 19-day period when medical face masks were recommended for COVID-19 care except for aerosol-generating procedures. Viral RNA was extracted and sequenced (NovaSeq, Illumina) from remnant nasopharyngeal swab samples in M4RT viral transport medium. Genomes with >90% coverage underwent cluster detection using a 2 single-nucleotide variant genetic distance cutoff. Genomic clusters were independently evaluated for valid epidemiologic links by 2 infectious diseases physicians (with a third adjudicator) using metadata extracted from the electronic medical record and according to predetermined criteria (Table 1). Results: In total, 1,031 SARS-CoV-2 sequences were analyzed, identifying 49 genomic clusters with HCP (median, 8; range, 2–43 members per cluster; total, 268 patients and 115 HCP) (Fig. 1). Also, 20,190 flowsheet activities were documented for cohort HCP and patient interactions, including 686 instances in which a cohort HCP contributed to a cohort patient’s chart. Most HCP infections were considered not healthcare associated (88 of 115, 76.5%). We did not identify any strong linkages for patient-to-HCP transmission. Moreover, 13 HCP cases (11.3%) were attributed to patient source (weak linkage). Also, 14 HCP cases (12.2%) were attributed to HCP source (11 strong and 3 weak linkages). Weak linkages were due to lack of epidemiologic data for HCP location, particularly nonclinical staff (eg, an environmental service worker who lacked location documentation to rule out patient-specific contact). Agreement for epidemiologic linkage between the 2 evaluators was high (κ, 0.91). Conclusions: Using genomic and epidemiologic data, we found that most HCP COVID-19 infections were not healthcare associated. We found weak evidence to support symptomatic patient-to-HCP transmission of SARS-CoV-2 and stronger evidence for HCP-to-HCP transmission. Large genomic clusters without plausible epidemiologic links were identified, reflecting the limited utility of genomic surveillance alone to characterize chains of transmission of SARS-CoV-2 during extensive community spread.Funding: NoneDisclosures: None Background: Contact tracing alone is often inadequate to determine the source of healthcare personnel (HCP) COVID-19 when SARS-CoV-2 is widespread in the community. We combined whole-genome sequencing (WGS) with traditional epidemiologic analysis to investigate the frequency with which patients or other HCP with symptomatic COVID-19 acted as the source of HCP infection at a large tertiary-care center early in the pandemic. Methods: Cohort samples were selected from patients and HCP with PCR-positive SARS-CoV-2 infection from a period with complete retention of samples (March 14, 2021–April 10, 2020) at Rush University Medical Center, a 664-bed hospital in Chicago, Illinois. During this period, testing was limited to symptomatic patients and HCP. Recommended respiratory equipment for HCP evolved under guidance, including a 19-day period when medical face masks were recommended for COVID-19 care except for aerosol-generating procedures. Viral RNA was extracted and sequenced (NovaSeq, Illumina) from remnant nasopharyngeal swab samples in M4RT viral transport medium. Genomes with >90% coverage underwent cluster detection using a 2 single-nucleotide variant genetic distance cutoff. Genomic clusters were independently evaluated for valid epidemiologic links by 2 infectious diseases physicians (with a third adjudicator) using metadata extracted from the electronic medical record and according to predetermined criteria (Table 1). Results: In total, 1,031 SARS-CoV-2 sequences were analyzed, identifying 49 genomic clusters with HCP (median, 8; range, 2–43 members per cluster; total, 268 patients and 115 HCP) (Fig. 1). Also, 20,190 flowsheet activities were documented for cohort HCP and patient interactions, including 686 instances in which a cohort HCP contributed to a cohort patient’s chart. Most HCP infections were considered not healthcare associated (88 of 115, 76.5%). We did not identify any strong linkages for patient-to-HCP transmission. Moreover, 13 HCP cases (11.3%) were attributed to patient source (weak linkage). Also, 14 HCP cases (12.2%) were attributed to HCP source (11 strong and 3 weak linkages). Weak linkages were due to lack of epidemiologic data for HCP location, particularly nonclinical staff (eg, an environmental service worker who lacked location documentation to rule out patient-specific contact). Agreement for epidemiologic linkage between the 2 evaluators was high (κ, 0.91). Conclusions: Using genomic and epidemiologic data, we found that most HCP COVID-19 infections were not healthcare associated. We found weak evidence to support symptomatic patient-to-HCP transmission of SARS-CoV-2 and stronger evidence for HCP-to-HCP transmission. Large genomic clusters without plausible epidemiologic links were identified, reflecting the limited utility of genomic surveillance alone to characterize chains of transmission of SARS-CoV-2 during extensive community spread. Background: Contact tracing alone is often inadequate to determine the source of healthcare personnel (HCP) COVID-19 when SARS-CoV-2 is widespread in the community. We combined whole-genome sequencing (WGS) with traditional epidemiologic analysis to investigate the frequency with which patients or other HCP with symptomatic COVID-19 acted as the source of HCP infection at a large tertiary-care center early in the pandemic. Methods: Cohort samples were selected from patients and HCP with PCR-positive SARS-CoV-2 infection from a period with complete retention of samples (March 14, 2021–April 10, 2020) at Rush University Medical Center, a 664-bed hospital in Chicago, Illinois. During this period, testing was limited to symptomatic patients and HCP. Recommended respiratory equipment for HCP evolved under guidance, including a 19-day period when medical face masks were recommended for COVID-19 care except for aerosol-generating procedures. Viral RNA was extracted and sequenced (NovaSeq, Illumina) from remnant nasopharyngeal swab samples in M4RT viral transport medium. Genomes with >90% coverage underwent cluster detection using a 2 single-nucleotide variant genetic distance cutoff. Genomic clusters were independently evaluated for valid epidemiologic links by 2 infectious diseases physicians (with a third adjudicator) using metadata extracted from the electronic medical record and according to predetermined criteria (Table 1). Results: In total, 1,031 SARS-CoV-2 sequences were analyzed, identifying 49 genomic clusters with HCP (median, 8; range, 2–43 members per cluster; total, 268 patients and 115 HCP) (Fig. 1). Also, 20,190 flowsheet activities were documented for cohort HCP and patient interactions, including 686 instances in which a cohort HCP contributed to a cohort patient’s chart. Most HCP infections were considered not healthcare associated (88 of 115, 76.5%). We did not identify any strong linkages for patient-to-HCP transmission. Moreover, 13 HCP cases (11.3%) were attributed to patient source (weak linkage). Also, 14 HCP cases (12.2%) were attributed to HCP source (11 strong and 3 weak linkages). Weak linkages were due to lack of epidemiologic data for HCP location, particularly nonclinical staff (eg, an environmental service worker who lacked location documentation to rule out patient-specific contact). Agreement for epidemiologic linkage between the 2 evaluators was high (κ, 0.91). Conclusions: Using genomic and epidemiologic data, we found that most HCP COVID-19 infections were not healthcare associated. We found weak evidence to support symptomatic patient-to-HCP transmission of SARS-CoV-2 and stronger evidence for HCP-to-HCP transmission. Large genomic clusters without plausible epidemiologic links were identified, reflecting the limited utility of genomic surveillance alone to characterize chains of transmission of SARS-CoV-2 during extensive community spread. Funding: None Disclosures: None |
Author | Sansom, Sarah Lin, Michael Baied, Elias Fukuda, Christine Moore, Nicholas Kim, DO Young Thotapalli, Lahari Barbian, Hannah Hayden, Mary Snitkin, Evan |
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Copyright | The Author(s), 2022. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America. This work is licensed under the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. The Society for Healthcare Epidemiology of America 2022 2022 The Society for Healthcare Epidemiology of America |
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Snippet | Background:
Contact tracing alone is often inadequate to determine the source of healthcare personnel (HCP) COVID-19 when SARS-CoV-2 is widespread in the... Background: Contact tracing alone is often inadequate to determine the source of healthcare personnel (HCP) COVID-19 when SARS-CoV-2 is widespread in the... |
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SubjectTerms | Coronaviruses COVID-19 Disease transmission Genomics Health care Infections Infectious diseases Medical personnel Pandemics Patients Poster Presentation - Oral Presentation Public health Severe acute respiratory syndrome coronavirus 2 |
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Title | Genomic investigation to identify the source of SARS-CoV-2 infection among healthcare personnel |
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