scholarly journals Propagation of a hospital-associated cluster of COVID-19 in Malaysia

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Diane Woei-Quan Chong ◽  
Vivek Jason Jayaraj ◽  
Chiu-Wan Ng ◽  
I-Ching Sam ◽  
Mas Ayu Said ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Whole Genome Sequencing ◽  
Healthcare Worker ◽  
Genome Sequencing ◽  
Control Measures ◽  
Contact Tracing ◽  
Infection Prevention And Control ◽  
Whole Genome ◽  
Epidemiological Investigation ◽  
Hospital Population

Abstract Background Hospitals are vulnerable to COVID-19 outbreaks. Intrahospital transmission of the disease is a threat to the healthcare systems as it increases morbidity and mortality among patients. It is imperative to deepen our understanding of transmission events in hospital-associated cases of COVID-19 for timely implementation of infection prevention and control measures in the hospital in avoiding future outbreaks. We examined the use of epidemiological case investigation combined with whole genome sequencing of cases to investigate and manage a hospital-associated cluster of COVID-19 cases. Methods An epidemiological investigation was conducted in a University Hospital in Malaysia from 23 March to 22 April 2020. Contact tracing, risk assessment, testing, symptom surveillance, and outbreak management were conducted following the diagnosis of a healthcare worker with SARS-CoV-2 by real-time PCR. These findings were complemented by whole genome sequencing analysis of a subset of positive cases. Results The index case was symptomatic but did not fulfill the initial epidemiological criteria for routine screening. Contact tracing suggested epidemiological linkages of 38 cases with COVID-19. Phylogenetic analysis excluded four of these cases. This cluster included 34 cases comprising ten healthcare worker-cases, nine patient-cases, and 15 community-cases. The epidemic curve demonstrated initial intrahospital transmission that propagated into the community. The estimated median incubation period was 4.7 days (95% CI: 3.5–6.4), and the serial interval was 5.3 days (95% CI: 4.3–6.5). Conclusion The study demonstrated the contribution of integrating epidemiological investigation and whole genome sequencing in understanding disease transmission in the hospital setting. Contact tracing, risk assessment, testing, and symptom surveillance remain imperative in resource-limited settings to identify and isolate cases, thereby controlling COVID-19 outbreaks. The use of whole genome sequencing complements field investigation findings in clarifying transmission networks. The safety of a hospital population during this COVID-19 pandemic may be secured with a multidisciplinary approach, good infection control measures, effective preparedness and response plan, and individual-level compliance among the hospital population.

scholarly journals Utilization of Whole Genome Sequencing to Understand SARS-CoV-2 Transmission Dynamics in Long-Term Care Facilities, Correctional Facilities and Meat Processing Plants in Minnesota, March − June 2020

2021 ◽  
Author(s):  
Nicholas B Lehnertz ◽  
Xiong Wang ◽  
Jacob Garfin ◽  
Joanne Taylor ◽  
Jennifer Zipprich ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Control Measures ◽  
Infection Prevention And Control ◽  
Correctional Facilities ◽  
Whole Genome ◽  
Meat Processing ◽  
Term Care ◽  
Processing Plants ◽  
Prevention And Control Measures

Congregate settings and high-density workplaces have endured a disproportionate impact from COVID-19. In order to provide further understanding of the transmission patterns of SARS-CoV-2 in these settings, whole genome sequencing (WGS) was performed on samples obtained from 8 selected outbreaks in Minnesota from March −June, 2020. WGS and phylogenetic analysis was conducted on 319 samples, constituting 14.4% of the 2,222 total SARS-CoV-2-positive individuals associated with these outbreaks. Among the sequenced specimens, three LTCFs and both correctional facilities had spread associated with a single genetic sequence. A fourth LTCF had outbreak cases associated with two distinct sequences. In contrast, cases associated with outbreaks in the two meat processing plants represented multiple SARS-CoV-2 sequences. These results suggest that a single introduction of SARS-CoV-2 into a facility can result in a widespread outbreak, and early identification and cohorting of cases, along with continued vigilance with infection prevention and control measures is imperative.

scholarly journals Comparison of routine field epidemiology and whole genome sequencing to identify tuberculosis transmission in a remote setting

2020 ◽  
Vol 148 ◽  
Author(s):  
J. L. Guthrie ◽  
L. Strudwick ◽  
B. Roberts ◽  
M. Allen ◽  
J. McFadzen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Variable Number ◽  
Yukon Territory ◽  
Contact Tracing ◽  
Whole Genome ◽  
Attitudes And Practices ◽  
Genomic Epidemiology ◽  
Recent Transmission

Abstract Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005–2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.

scholarly journals Countrywide implementation of whole genome sequencing: an opportunity to improve tuberculosis management, surveillance and contact tracing in low incidence countries

2018 ◽  
Vol 51 (6) ◽  
pp. 1800387 ◽  
Author(s):  
Andrea Maurizio Cabibbe ◽  
Alberto Trovato ◽  
Maria Rosaria De Filippo ◽  
Arash Ghodousi ◽  
Laura Rindi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Contact Tracing ◽  
Whole Genome ◽  
Low Incidence

Utility of Whole Genome Sequencing To Describe the Persistence and Evolution of Listeria monocytogenes Strains within Crabmeat Processing Environments Linked to Two Outbreaks of Listeriosis

2018 ◽  
Vol 82 (1) ◽  
pp. 30-38 ◽  
Author(s):  
RICHARD ELSON ◽  
ADEDOYIN AWOFISAYO-OKUYELU ◽  
TREVOR GREENER ◽  
CRAIG SWIFT ◽  
ANAÏS PAINSET ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Surveillance Data ◽  
Control Measures ◽  
Whole Genome ◽  
Typing Method ◽  
Outbreak Investigations ◽  
Molecular Typing Method ◽  
Clinical Cases

ABSTRACT This article describes the identification and investigation of two extended outbreaks of listeriosis in which crabmeat was identified as the vehicle of infection. Comparing contemporary and retrospective typing data of Listeria monocytogenes isolates from clinical cases and from food and food processing environments allowed the detection of cases going back several years. This information, combined with the analysis of routinely collected enhanced surveillance data, helped to direct the investigation and identify the vehicle of infection. Retrospective whole genome sequencing (WGS) analysis of isolates provided robust microbiological evidence of links between cases, foods, and the environments in which they were produced and demonstrated that for some cases and foods, identified by fluorescent amplified fragment length polymorphism, the molecular typing method in routine use at the time, were not part of the outbreak. WGS analysis also showed that the strains causing illness had persisted in two food production environments for many years and in one producer had evolved into two strains over a period of around 8 years. This article demonstrates the value of reviewing L. monocytogenes typing data from clinical cases together with that from foods as a means of identifying potential vehicles and sources of infection in outbreaks of listeriosis. It illustrates the importance of reviewing retrospective L. monocytogenes typing alongside enhanced surveillance data to characterize extended outbreaks and inform control measures. Also, this article highlights the advantages of WGS analysis for strain discrimination and clarification of evolutionary relationships that refine outbreak investigations and improve our understanding of L. monocytogenes in the food chain.

scholarly journals XDR-TB transmission in London: Case management and contact tracing investigation assisted by early whole genome sequencing

2016 ◽  
Vol 73 (3) ◽  
pp. 210-218 ◽  
Author(s):  
Amber Arnold ◽  
Adam A. Witney ◽  
Stephania Vergnano ◽  
Anita Roche ◽  
Catherine A. Cosgrove ◽  
...  
Keyword(s):  
Case Management ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Contact Tracing ◽  
Whole Genome

scholarly journals Overlapping of independent SARS-CoV-2 nosocomial transmissions in a complex outbreak

2021 ◽  
Author(s):  
Laura Pérez-Lago ◽  
Helena Martinez Lozano ◽  
Jose Antonio pajares Diaz ◽  
Arantxa Diaz Gomez ◽  
Marina Machado ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Healthcare Workers ◽  
Virulent Strain ◽  
Control Measures ◽  
Protective Equipment ◽  
Whole Genome ◽  
Single Patient ◽  
High Fatality Rate ◽  
Depth Analysis

Abstract SARS-CoV-2 nosocomial outbreaks in the first COVID-19 wave were likely associated to a shortage of personal protective equipment and scare indications on control measures. Having covered these limitations, updates on current SARS-CoV-2 nosocomial outbreaks are required. We carried out an in-depth analysis of a 27-day nosocomial outbreak in a gastroenterology ward in our hospital, potentially involving 15 patients and three healthcare workers. Patients had stayed in one of three neighbouring rooms in the ward. The severity of the infections in six of the cases and a high fatality rate suggested the possible involvement of a single virulent strain persisting in those rooms. Whole genome sequencing of the strains from 12 patients and one healthcare worker revealed an unexpected complexity. Five different SARS-CoV-2 strains were identified, two infecting a single patient each, ruling out their relationship with the outbreak; the remaining three strains were involved in three independent overlapping limited transmission clusters with three, three, and five cases. Whole genome sequencing was key to understand the complexity of this outbreak.

scholarly journals COVID-19 Outbreak Associated with a Fitness Center — Minnesota, September–November 2020

2021 ◽  
Author(s):  
Tara Suhs ◽  
Daniel Gerlach ◽  
Jacob Garfin ◽  
Alexandra Lorentz ◽  
Melanie Firestone ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Olmsted County ◽  
Epidemiological Investigation ◽  
Prevention Strategies ◽  
Fitness Center ◽  
Department Of Health

Abstract The Minnesota Department of Health investigated a COVID-19 outbreak at a fitness center in Olmsted County, Minnesota. Twenty-three SARS-CoV-2 infections (five employees and 18 members) were identified. An epidemiological investigation supported by whole genome sequencing demonstrated that transmission of SARS-CoV-2 occurred at the fitness center despite following recommended prevention strategies.

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