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.

scholarly journals 6 Translating genomics for clinical benefit

2019 ◽  
Vol 95 (1130) ◽  
pp. 686.3-686
Author(s):  
Mark Caulfield
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Medicine ◽  
Health Gain ◽  
Annual Review ◽  
Whole Genome ◽  
Department Of Health ◽  
Data Points ◽  
Genome Analyses ◽  
The Uk

The UK 100,000 Genomes Project has focussed on transforming genomic medicine in the National Health Service using whole genome sequencing in rare disease, cancer and infection. Genomics England partnering with the NHS established 13 Genomic Medicine Centres, the NHS whole genome sequencing centre and the Genomics England Clinical Interpretation Partnership (3337 researchers from 24 countries). We sequenced the 100,000th genome on the 5th December 2019 and completed an initial analysis for participants in July 2019. Alongside these genomes we have assembled a longitudinal life course dataset for research and diagnosis including 2.6 billion clinical data points for the 3000 plus researchers to work on to drive up the value of the genomes for direct healthcare. In parallel we have partnered the NHS to establish one of the world’s most advanced Genomic Medicine Service where we re-evaluated 300,000 genomic tests and upgraded 25% of tests to newer technologies with an annual review. The Department of Health have announced the ambition to undertake 5 million genome analyses over the next 5 years focused on new areas tractable to health gain.

69 Outbreak of Carbapenem-polymyxin-quat-resistant Acinetobacter Baumannii Associated with Mafenide Acetate Shortages: An Interdisciplinary Approach to Eradication

2020 ◽  
Vol 41 (Supplement_1) ◽  
pp. S45-S45
Author(s):  
Irma D Fleming ◽  
Carla Tang ◽  
Lois Remington ◽  
Giavonni Lewis
Keyword(s):  
Infection Control ◽  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Interdisciplinary Approach ◽  
Environmental Services ◽  
Whole Genome ◽  
Traumatic Injuries ◽  
Department Of Health ◽  
Surgical Suite

Abstract Introduction In the wake of Hurricane Maria, many US hospitals experienced massive drug shortages requiring substitution with alternative therapies. Our regional center experienced an increased incidence of Carbapenem-Polymyxin-Quat-Resistant Acinetobacter baumannii(CPQRA) infections, compared to a previous year of no infections. Here we describe a successful interdisciplinary approach to its eradication. Methods We conducted a retrospective review of CPQRA outbreaks for November and December 2018 in the burn ICU. De-identified data was collected and analyzed. In collaboration with the state’s department of health and epidemiology section, whole-genome sequencing was carried out on bacterial isolates. In addition, we instituted adenosine triphosphate (ATP) monitoring on all surfaces, a process of rapidly measuring actively growing microorganisms. Results Resistant Acinetobacter was isolated from five ICU patients, two of whom died with CPQRA bacteremia, producing a case-fatality rate of 40%. The two cases that died both suffered traumatic injuries with multiple fractures in addition to an average TBSA of 58%.Non-fatal cases suffered no other traumatic injuries and had an average TBSA of 51%.During this period, genitourinary irrigant (neomycin-Polymyxin B) and polymyxin ointment were the primary topical agents for wound care. Whole genome sequencing revealed a qacEdelta1 positive strain and identified the primary source as a patient that returned from a long-term care facility carrying the converted A. Baumannii infection. ATP testing also showed increased levels in patient rooms and surgical suite. Conclusions As a result of these findings, we achieved eradication by developing new and reinforcing traditional practices of infection control. This included UV light therapy to all ICU rooms and surgical suite, oversight of environmental services procedures, rigorous enforcement of hospital infection control procedures, auditing hand hygiene, increased efforts in antibiotic stewardshipand discontinuing Polymyxin containing topicals. By January 2019 there were no new cases of CPQRA in the ICU. This study shows that the resistance and rapid spread of CPQRA can be controlled with the cooperation of hospital staff, environmental services, infection control, pharmacy and the state’s department of health. With the coordinated efforts of all parties, we were able to successfully eradicate a virulent and fatal resistant A. baumannii strain. Applicability of Research to Practice Describe an approach to eradicating resistant organisms and provide a roadmap to characterize the source, implement control measures to terminate an outbreak, and institute preventive measures.

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 Prospective Salmonella Enteritidis surveillance and outbreak detection using whole genome sequencing, Minnesota 2015–2017

2020 ◽  
Vol 148 ◽  
Author(s):  
J. M. Rounds ◽  
A. J. Taylor ◽  
D. Eikmeier ◽  
M. M. Nichols ◽  
V. Lappi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Cluster Size ◽  
Salmonella Enteritidis ◽  
Turnaround Time ◽  
Outbreak Detection ◽  
Polymorphism Analysis ◽  
Whole Genome ◽  
Case Definitions ◽  
Department Of Health

Abstract Clusters of Salmonella Enteritidis cases were identified by the Minnesota Department of Health using both pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) single nucleotide polymorphism analysis from 1 January 2015 through 31 December 2017. The median turnaround time for obtaining WGS results was 11 days longer than for PFGE (12 vs. 1 day). WGS analysis more than doubled the number of clusters compared to PFGE analysis, but reduced the total number of cases included in clusters by 34%. The median cluster size was two cases for WGS compared to four for PFGE, and the median duration of WGS clusters was 27 days shorter than PFGE clusters. While the percentage of PFGE clusters with a confirmed source (46%) was higher than WGS clusters (32%), a higher percentage of cases in clusters that were confirmed as outbreaks reported the vehicle or exposure of interest for WGS (78%) than PFGE (46%). WGS cluster size was a significant predictor of an outbreak source being confirmed. WGS data have enhanced S. Enteritidis cluster investigations in Minnesota by improving the specificity of cluster case definitions and has become an integral part of the S. Enteritidis surveillance process.

scholarly journals Transmission of multidrug-resistant tuberculosis in Shimen community in Shanghai, China: a molecular epidemiology study

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhiying Han ◽  
Jing Li ◽  
Guomei Sun ◽  
Kaikan Gu ◽  
Yangyi Zhang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Epidemiological Investigation ◽  
Transmission Pattern ◽  
Resistant Tuberculosis ◽  
Multidrug Resistant Tuberculosis ◽  
Recent Transmission ◽  
Mdr Tb

Abstract Background Multidrug-resistant tuberculosis (MDR-TB) has become a major public health problem in China, with mounting evidence suggesting that recent transmission accounts for the majority of MDR-TB. Here we aimed to reveal the transmission pattern of an MDR-TB outbreak in the Jing'an District of Shanghai between 2010 and 2015. Methods We used whole-genome sequencing (WGS) to conduct genomic clustering analysis along with field epidemiological investigation to determine the transmission pattern and drug resistance profile of a cluster with ten MDR-TB patients in combining field epidemiological investigation. Results The ten MDR-TB patients with genotypically clustered Beijing lineage strains lived in a densely populated, old alley with direct or indirect contact history. The analysis of genomic data showed that the genetic distances of the ten strains (excluding drug-resistant mutations) were 0–20 single nucleotide polymorphisms (SNPs), with an average distance of 9 SNPs, suggesting that the ten MDR-TB patients were infected and developed the onset of illness by the recent transmission of M. tuberculosis. The genetic analysis confirmed definite epidemiological links between the clustered cases. Conclusions The integration of the genotyping tool in routine tuberculosis surveillance can play a substantial role in the detection of MDR-TB transmission events. The leverage of genomic analysis in combination with the epidemiological investigation could further elucidate transmission patterns. Whole-genome sequencing could be integrated into intensive case-finding strategies to identify missed cases of MDR-TB and strengthen efforts to interrupt transmission.

620 Outbreak of Carbapenem-Polymyxin-Quat-Resistant Acinetobacter Baumannii Associated with Mafenide Acetate shortages: An Interdisciplinary Approach to Eradication

2021 ◽  
Vol 42 (Supplement_1) ◽  
pp. S164-S165
Author(s):  
Irma D Fleming ◽  
Carla Tang ◽  
Giavonni M Lewis
Keyword(s):  
Infection Control ◽  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Interdisciplinary Approach ◽  
Environmental Services ◽  
Whole Genome ◽  
Traumatic Injuries ◽  
Department Of Health ◽  
Surgical Suite

Abstract Introduction In the wake of Hurricane Maria, many US hospitals experienced massive drug shortages requiring substitution with alternative therapies. Our regional center experienced an increased incidence of Carbapenem-Polymyxin-Quat-Resistant Acinetobacter baumannii(CPQRA) infections, compared to a previous year of no infections. Here we describe a successful interdisciplinary approach to its eradication. Methods We conducted a retrospective review of CPQRA outbreaks for November and December 2018 in the burn ICU. De-identified data was collected and analyzed. In collaboration with the state’s department of health and epidemiology section, whole-genome sequencing was carried out on bacterial isolates. In addition, we instituted adenosine triphosphate (ATP) monitoring on all surfaces, a process of rapidly measuring actively growing microorganisms. Results Resistant Acinetobacter was isolated from five ICU patients, two of whom died with CPQRA bacteremia, producing a case-fatality rate of 40%. The two cases that died both suffered traumatic injuries with multiple fractures in addition to an average TBSA of 58%. Non-fatal cases suffered no other traumatic injuries and had an average TBSA of 51%.During this period, genitourinary irrigant (neomycin-Polymyxin B) and polymyxin ointment were the primary topical agents for wound care. Whole genome sequencing revealed a qacEdelta1 positive strain and identified the primary source as a patient that returned from a long-term care facility carrying the converted A. Baumannii infection. ATP testing also showed increased levels in patient rooms and surgical suite. Conclusions As a result of these findings, we achieved eradication by developing new and reinforcing traditional practices of infection control. This included UV light therapy to all ICU rooms and surgical suite, oversight of environmental services procedures, rigorous enforcement of hospital infection control procedures, auditing hand hygiene, increased efforts in antibiotic stewardship and discontinuing Polymyxin containing topicals. By January 2019 there were no new cases of CPQRA in the ICU. This study shows that the resistance and rapid spread of CPQRA can be controlled with the cooperation of hospital staff, environmental services, infection control, pharmacy, and the state’s department of health. With the coordinated efforts of all parties, we were able to successfully eradicate a virulent and fatal resistant A. baumannii strain.

Burkholderia cenocepacia ET12 transmission in adults with cystic fibrosis

Thorax ◽  
2019 ◽  
Vol 75 (1) ◽  
pp. 88-90 ◽  
Author(s):  
Ana C Blanchard ◽  
Lin Tang ◽  
Manal Tadros ◽  
Matthew Muller ◽  
Theodore Spilker ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Infection Control ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Data ◽  
Burkholderia Cenocepacia ◽  
Nosocomial Transmission ◽  
Whole Genome ◽  
Epidemiological Investigation

This report describes transmission of a Burkholderia cenocepacia ET12 strain (ET12-Bc) at the Toronto Adult Cystic Fibrosis (CF) Centre occurring from 2008 to 2017. Epidemiological and genomic data from 11 patients with CF were evaluated. Isolates were analysed using whole genome sequencing (WGS). Epidemiological investigation and WGS analysis suggested nosocomial transmission, despite enhanced infection control precautions. This was associated with subsequent deaths in 10 patients. ET12-Bc positive patients are no longer cared for on the same unit as ET12-Bc negative patients.

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