scholarly journals Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak

2021 ◽  
pp. 100190
Author(s):  
Fumihiro Ishikawa ◽  
Yuko Udaka ◽  
Hideto Oyamada ◽  
Keiko Ishino ◽  
Issei Tokimatsu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Epidemiology ◽  
Whole Genome ◽  
Nosocomial Outbreak ◽  
Haplotype Networks

scholarly journals Correction for Quainoo et al., “Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis”

2017 ◽  
Vol 31 (1) ◽  
Author(s):  
Scott Quainoo ◽  
Jordy P. M. Coolen ◽  
Sacha A. F. T. van Hijum ◽  
Martijn A. Huynen ◽  
Willem J. G. Melchers ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Pathogens ◽  
Whole Genome ◽  
Nosocomial Outbreak ◽  
The Future

scholarly journals Whole-Genome Sequencing: The Key to Unlocking a Nosocomial Outbreak of Coronavirus Disease 2019 (COVID-19)

2021 ◽  
Vol 1 (S1) ◽  
pp. s51-s51
Author(s):  
Lindsey Gottlieb ◽  
Emilia Sordillo ◽  
Harm van Bakel ◽  
Barbara Smith ◽  
Bernard Camins ◽  
...  
Keyword(s):  
New York ◽  
High Risk ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Positive Test ◽  
Contact Tracing ◽  
Whole Genome ◽  
Nosocomial Outbreak ◽  
Primary Case ◽  
Eye Protection

Background: Accurately tracing nosocomial transmission of coronavirus disease 2019 (COVID-19) is critical to developing effective infection prevention policies. Given the high prevalence and variable incubation period of SARS-CoV-2 infection, the utility of traditional contact tracing is limited. We describe a nosocomial outbreak in which whole-genome sequencing (WGS) was pivotal to identifying the primary case. Methods: This study was conducted at a New York City academic hospital. The index case was identified on August 13, 2020, and the last case on September 9, 2020. Hospital policy required all inpatients to be screened for COVID-19 on admission by SARS-CoV-2 molecular amplification testing. All healthcare workers (HCWs) were required to wear masks and eye protection for patient care. After a patient (patient 1), who tested SARS-CoV-2 negative on admission, was positive on preprocedure screening on hospital day 9, contact tracing was initiated. Two patients (patients 2 and 3) and 13 HCWs with high-risk exposures (HREs) to patient 1 were quarantined and referred for testing. Additional surveillance testing was performed on 18 inpatients and 84 HCWs on the affected unit. Patients 2 and 3 and 3 HCWs (HCW-1, -2, and -3), only 1 of whom had a high-risk exposure to patient 1, tested positive. WGS was performed to further investigate this outbreak. Results: The outbreak variant (clade 20A) was found in samples from 6 patients and 2 HCWs. Patients 2 and 3 were roommates of patient 1 in the 2 days before patient 1’s positive test, and they did not consistently wear masks in the room. HCW-1 placed a peripheral IV in patient 1 the day before patient 1’s positive test without wearing eye protection. Four additional cases in this cluster (patients 4–6 and HCW-4) were identified by surveillance WGS of positive tests. A review indicated that patient 1 was located ~3 m (~10 feet) away from patient 4 in the emergency department (ED) for 6 hours on hospital day 1, when the admission SARS-CoV-2 test from patient 4 was not positive. No epidemiologic link was found to patient 5 or 6 or HCW-4. The specimen from HCW-2 was inadequate for WGS. The specimen from HCW-3 was not linked to this cluster. Conclusions: This complex nosocomial outbreak highlights the importance of WGS in understanding transmission events. Patient 4 was not identified by traditional contact tracing but was linked to patient 1 and was recognized as the primary case through WGS, having likely infected patient 1 in the ED. Based on these findings, we focused our corrective actions on more promptly isolating suspected COVID-19 cases in the ED, increasing inpatient masking, and improving HCW adherence to universal eye protection.Funding: NoDisclosures: None

scholarly journals Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis

2017 ◽  
Vol 30 (4) ◽  
pp. 1015-1063 ◽  
Author(s):  
Scott Quainoo ◽  
Jordy P. M. Coolen ◽  
Sacha A. F. T. van Hijum ◽  
Martijn A. Huynen ◽  
Willem J. G. Melchers ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Health Care Professionals ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Nosocomial Outbreak ◽  
Icu Patients ◽  
Outbreak Management ◽  
Sequencing Technologies ◽  
Analysis Tools

SUMMARY Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.

scholarly journals Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole Genome Sequence Analysis

2021 ◽  
Author(s):  
Suzy E Meijer ◽  
Noam Harel ◽  
Ronen Ben-Ami ◽  
Meital Nahari ◽  
Michal Yakubovsky ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Index Patient ◽  
Added Value ◽  
Whole Genome Sequence ◽  
Contact Tracing ◽  
Whole Genome ◽  
Nosocomial Outbreak ◽  
Multiple Introductions ◽  
The One

Abstract Background The COVID-19 pandemic poses many epidemiological challenges. The investigation of nosocomial transmission is usually performed via thorough investigation of an index case and subsequent contact tracing. Notably, this approach has a subjective component and there is accumulating evidence that whole genome sequencing of the virus may provide a more objective insight. Methods We report a large nosocomial outbreak in one of the medicine departments in our institution. Following intensive epidemiological investigation, we discovered that one of the patients involved was suffering from persistent COVID-19 while initially thought to be a recovering patient. She was therefore deemed to be the most likely source of the outbreak. We then performed whole genome sequencing of the virus of fourteen infected individuals involved in the outbreak. Results Surprisingly, the results of whole genome sequencing refuted our initial hypothesis. A phylogenetic tree of the samples showed multiple introductions of the virus into the ward, one of which led to a cluster of ten of the infected individuals. Importantly, the results pointed in the direction of a specific index patient that was different from the one that arose from our initial investigation. Conclusions These results underscore the important added value of using whole genome sequencing in epidemiological investigations as it may reveal unexpected connections between cases and aid in understanding transmission dynamics, especially in the setting of a pandemic where multiple possible index cases exist simultaneously.

Utility of Whole Genome Sequencing in diagnosing complex disorders: lesson from renal tubular disorders

2018 ◽  
Author(s):  
Mark Stevenson ◽  
Alistair T Pagnamenta ◽  
Heather G Mack ◽  
Judith A Savige ◽  
Kate E Lines ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Complex Disorders ◽  
Tubular Disorders ◽  
Renal Tubular Disorders ◽  
Renal Tubular

0306 Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 146-146
Author(s):  
D. M. Bickhart ◽  
L. Xu ◽  
J. L. Hutchison ◽  
J. B. Cole ◽  
D. J. Null ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Copy Number ◽  
Large Scale ◽  
Copy Number Variants ◽  
Whole Genome
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