scholarly journals Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Jamie M Ellingford ◽  
Ryan George ◽  
John H McDermott ◽  
Shazaad Ahmad ◽  
Jonathan J Edgerley ◽  
...  
Keyword(s):  
Infection Control ◽  
Temporal Dynamics ◽  
Management Strategies ◽  
Healthcare Setting ◽  
Location Data ◽  
Genome Data ◽  
Healthcare Settings ◽  
Movement Data ◽  
Spatial And Temporal Dynamics ◽  
Transmission Pathways

Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. We integrated patient movement and staff location data into the analysis of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples. Incorporation of HCW location further increased the number of individuals within PCCs and identified additional links in SARS-CoV-2 transmission pathways. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location. SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters. This dynamic approach can support infection control management strategies within the healthcare setting.

Tuberculosis: Infection Control/Exposure Control Issues for Oral Healthcare Workers

2008 ◽  
Vol 9 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Geza T. Terezhalmy ◽  
Nuala B. Porteous
Keyword(s):  
Infection Control ◽  
Healthcare Workers ◽  
Healthcare Setting ◽  
Essential Elements ◽  
Exposure Control ◽  
Standard Precautions ◽  
Control Plan ◽  
Healthcare Settings ◽  
Tuberculosis Infection Control ◽  
Tb Infection Control

Abstract Aim The aim is to present the essential elements of an infection control/exposure control plan for the oral healthcare setting with emphasis on tuberculosis (TB). Methods and Materials A comprehensive review of the literature was conducted with special emphasis on TB infection-control issues in the oral healthcare setting. Results Currently available knowledge related to TB infection-control issues is supported by data derived from well-conducted trials or extensive controlled observations. In the absence of supportive data the information is supported with the best-informed, most authoritative opinion available. Conclusion Essential elements of an effective TB infection-control plan include a three-level hierarchy of administrative, environmental, and respiratory-protection controls. Clinical Significance Standard precautions provide the fabric for strategies to prevent or reduce the risk of exposure to bloodborne pathogens and other potentially infectious material. However, standard precautions are inadequate to prevent the spread of organisms through droplet nuclei 1-5 micron in diameter and additional measures are necessary to prevent the spread of Mycobacterium tuberculosis. Oral healthcare settings have been identified as outpatient settings in which patients with suspected or confirmed infectious TB disease are expected to be encountered. Therefore, oral healthcare settings must have a written TB infection-control program. Citation Porteous NB, Terezhalmy GT. Tuberculosis: Infection Control/Exposure Control Issues for Oral Healthcare Workers. J Contemp Dent Pract 2008 January; (9)1:001-013.

Hospital antibiotic use and its relationship to age-adjusted comorbidity and alcohol-based hand rub consumption

2013 ◽  
Vol 142 (2) ◽  
pp. 404-408 ◽  
Author(s):  
M. A. ALDEYAB ◽  
J. C. McELNAY ◽  
M. G. SCOTT ◽  
F. W. DARWISH ELHAJJI ◽  
M. P. KEARNEY
Keyword(s):  
Infection Control ◽  
Moving Average ◽  
Arima Model ◽  
Healthcare Setting ◽  
Antibiotic Use ◽  
Future Research ◽  
Predictive Variables ◽  
Healthcare Settings ◽  
Modifiable Factor ◽  
The Impact

SUMMARYThe objective of this study was to evaluate the effect of age-adjusted comorbidity and alcohol-based hand rub on monthly hospital antibiotic usage, retrospectively. A multivariate autoregressive integrated moving average (ARIMA) model was built to relate the monthly use of all antibiotics grouped together with age-adjusted comorbidity and alcohol-based hand rub over a 5-year period (April 2005–March 2010). The results showed that monthly antibiotic use was positively related to the age-adjusted comorbidity index (concomitant effect, coefficient 1·103, P = 0·0002), and negatively related to the use of alcohol-based hand rub (2-month delay, coefficient −0·069, P = 0·0533). Alcohol-based hand rub is considered a modifiable factor and as such can be identified as a target for quality improvement programmes. Time-series analysis may provide a suitable methodology for identifying possible predictive variables that explain antibiotic use in healthcare settings. Future research should examine the relationship between infection control practices and antibiotic use, identify other infection control predictive factors for hospital antibiotic use, and evaluate the impact of enhancing different infection control practices on antibiotic use in a healthcare setting.

scholarly journals Signatures of the collapse and incipient recovery of an overexploited marine ecosystem

2017 ◽  
Vol 4 (7) ◽  
pp. 170215 ◽  
Author(s):  
Eric J. Pedersen ◽  
Patrick L. Thompson ◽  
R. Aaron Ball ◽  
Marie-Josée Fortin ◽  
Tarik C. Gouhier ◽  
...  
Keyword(s):  
Regime Shift ◽  
Temporal Dynamics ◽  
Atlantic Cod ◽  
Marine Ecosystem ◽  
Management Strategies ◽  
Individual Species ◽  
Trawl Survey ◽  
Effective Management ◽  
Spatial And Temporal Dynamics ◽  
Wide Perspective

The Northwest Atlantic cod stocks collapsed in the early 1990s and have yet to recover, despite the subsequent establishment of a continuing fishing moratorium. Efforts to understand the collapse and lack of recovery have so far focused mainly on the dynamics of commercially harvested species. Here, we use data from a 33-year scientific trawl survey to determine to which degree the signatures of the collapse and recovery of the cod are apparent in the spatial and temporal dynamics of the broader groundfish community. Over this 33-year period, the groundfish community experienced four phases of change: (i) a period of rapid, synchronous biomass collapse in most species, (ii) followed by a regime shift in community composition with a concomitant loss of functional diversity, (iii) followed in turn by periods of slow compositional recovery, and (iv) slow biomass growth. Our results demonstrate how a community-wide perspective can reveal new aspects of the dynamics of collapse and recovery unavailable from the analysis of individual species or a combination of a small number of species. Overall, we found evidence that such community-level signals should be useful for designing more effective management strategies to ensure the persistence of exploited marine ecosystems.

scholarly journals Transmission pathways of multidrug-resistant organisms in the hospital setting: a scoping review

2019 ◽  
Vol 40 (4) ◽  
pp. 447-456 ◽  
Author(s):  
Natalia Blanco ◽  
Lyndsay M. O’Hara ◽  
Anthony D. Harris
Keyword(s):  
Scoping Review ◽  
Hospital Setting ◽  
Healthcare Setting ◽  
Multidrug Resistant ◽  
Infection Prevention And Control ◽  
Complex Nature ◽  
Original Research ◽  
Healthcare Settings ◽  
Cross Transmission ◽  
Transmission Pathways

AbstractBackground:Prevalence of multidrug-resistant microorganisms (MDROs) continues to increase, while infection control gaps in healthcare settings facilitate their transmission between patients. In this setting, 5 distinct yet interlinked pathways are responsible for transmission. The complete transmission process is still not well understood. Designing and conducting a single research study capable of investigating all 5 complex and multifaceted pathways of hospital transmission would be costly and logistically burdensome. Therefore, this scoping review aims to synthesize the highest-quality published literature describing each of the 5 individual potential transmission pathways of MDROs in the healthcare setting and their overall contribution to patient-to-patient transmission.Methods:In 3 databases, we performed 2 separate systematic searches for original research published during the last decade. The first search focused on MDRO transmission via the HCW or the environment to identify publications studying 5 specific transmission pathways: (1) patient to HCW, (2) patient to environment, (3) HCW to patient, (4) environment to patient, and (5) environment to HCW. The second search focused on overall patient-to-patient transmission regardless of the transmission pathway. Both searches were limited to transmission of methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus, multidrug-resistant A. baumannii, and carbapenem-resistant Enterobacteriaceae. After abstract screening of 5,026 manuscripts, researchers independently reviewed and rated the remaining papers using objective predefined criteria to identify the highest quality and most influential manuscripts.Results:High-quality manuscripts were identified for all 5 routes of transmission. Findings from these studies were consistent for all pathways; however, results describing the routes from the environment/HCW to a noncolonized patient were more limited and variable. Additionally, most research focused on MRSA, instead of other MDROs. The second search yielded 10 manuscripts (8 cohort studies) that demonstrated the overall contribution of patient-to-patient transmission in hospitals regardless of the transmission route. For MRSA, the reported cross-transmission was as high as 40%.Conclusions:This scoping review brings together evidence supporting all 5 possible transmission pathways and illustrates the complex nature of patient-to-patient transmission of MDROs in hospitals. Our findings also confirm that transmission of MDROs in hospitals occurs frequently, suggesting that ongoing efforts are necessary to strengthen infection prevention and control to prevent the spread of MDROs.

scholarly journals High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity

2020 ◽  
Author(s):  
San Emmanuel James ◽  
Sinaye Ngcapu ◽  
Aquillah M Kanzi ◽  
Houriiyah Tegally ◽  
Vagner Fonseca ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Genome Data ◽  
Healthcare Settings ◽  
Bottleneck Analysis ◽  
Wide Range ◽  
Rapid Spread ◽  
High Resolution Analysis ◽  
Resolution Analysis ◽  
Transmission Pathways ◽  
And Control

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes acute, highly transmissible respiratory infection in both humans and wide range of animal species. Its rapid spread globally and devasting effects have resulted into a major public health emergency prompting the need for methodological interventions to understand and control its spread. In particular, The ability to effectively retrace its transmission pathways in outbreaks remains a major challenge. This is further exacerbated by our limited understanding of its underlying evolutionary mechanism. Using NGS whole-genome data, we determined whether inter- and intra-host diversity coupled with bottleneck analysis can retrace the pathway of viral transmission in two epidemiologically well characterised nosocomial outbreaks in healthcare settings supported by phylogenetic analysis. Additionally, we assessed the mutational landscape, selection pressure and diversity of the identified variants. Our findings showed evidence of intrahost variant transmission and evolution of SARS-CoV-2 after infection These observations were consistent with the results from the bottleneck analysis suggesting that certain intrahost variants in this study could have been transmitted to recipients. In both outbreaks, we observed iSNVs and SNVs shared by putative source-recipients pairs. Majority of the observed iSNVs were positioned in the S and ORF1ab region. AG, CT and TC nucleotide changes were enriched across SARS-COV-2 genome. Moreover, SARS-COV-2 genome had limited diversity in some loci while being highly conserved in others. Overall, Our findings show that the synergistic effect of combining withinhost diversity and bottleneck estimations greatly enhances resolution of transmission events in Sars-Cov-2 outbreaks. They also provide insight into the genome diversity suggesting purifying selection may be involved in the transmission. Together these results will help in developing strategies to elucidate transmission events and curtail the spread of Sars-Cov-2

scholarly journals Incidence, Spatial Pattern and Temporal Progress of Fusarium Wilt of Bananas

2021 ◽  
Vol 7 (8) ◽  
pp. 646
Author(s):  
Daniel W. Heck ◽  
Miguel Dita ◽  
Emerson M. Del Ponte ◽  
Eduardo S. G. Mizubuti
Keyword(s):  
Fusarium Wilt ◽  
Temporal Dynamics ◽  
Secondary Infection ◽  
Regional Scale ◽  
Management Strategies ◽  
Gompertz Model ◽  
Spatial And Temporal Dynamics ◽  
Sigmoidal Curve ◽  
Average Loss ◽  
The Impact

The effective management of Fusarium wilt of bananas (FWB) depends on the knowledge of the disease dynamics in time and space. The objectives of this work were: to estimate disease intensity and impact, and to investigate the spatial and temporal dynamics of FWB. Fields planted with Silk (n = 10), Pome (n = 17), or Cavendish (n = 3) banana subgroups were surveyed in Brazil, totaling 95 ha. In each field, all plants were visually assessed, and diseased plants were georeferenced. The incidence of FWB and the impact of the disease on the yield on a regional scale were estimated. Spatial patterns were analyzed using quadrat- and distance-based methods. FWB incidence ranged from 0.09% to 41.42%, being higher in Silk fields (median = 14.26%). Impacts of epidemics on yield ranged from 18.4 to 8192.5 kg ha−1 year−1, with an average of 1856.7 kg ha−1 year−1. The higher economic impact of the disease was observed on Silk cultivar with an average loss of USD 1974.2 ha−1 year−1. Overall, estimated losses increased on average by USD 109.8 ha−1 year−1 at each 1% of incidence. Aggregation of FWB was detected by all analytical methods in 13 fields (1 of Cavendish, 11 of Pome, and 1 of Silk). In the other 17 fields, at least one analytical method did not reject the null hypothesis of randomness. One field (5 ha), composed of six plots, was selected for spatial and temporal studies during two years with bi-monthly assessments. A sigmoidal curve represented the FWB progress and the Gompertz model best-fitted disease progress. The level of aggregation varied over time, and evidence of secondary infection to neighboring and distant plants was detected. FWB is a widespread problem in Brazil and yield losses can be of high magnitude. Epidemiology-based management strategies can now be better established.

Spatial and temporal dynamics of lexico-semantic processing in American Sign Language

2011 ◽  
Author(s):  
M. Leonard ◽  
N. Ferjan Ramirez ◽  
C. Torres ◽  
M. Hatrak ◽  
R. Mayberry ◽  
...  
Keyword(s):  
American Sign Language ◽  
Sign Language ◽  
Semantic Processing ◽  
Temporal Dynamics ◽  
American Sign ◽  
Spatial And Temporal Dynamics

Spatial and temporal dynamics of Pacific capelin Mallotus catervarius in the Gulf of Alaska: implications for ecosystem-based fisheries management

2020 ◽  
Vol 637 ◽  
pp. 117-140 ◽  
Author(s):  
DW McGowan ◽  
ED Goldstein ◽  
ML Arimitsu ◽  
AL Deary ◽  
O Ormseth ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Marine Ecosystem ◽  
Gulf Of Alaska ◽  
Data Series ◽  
Limited Information ◽  
Important Species ◽  
Multiple Data ◽  
Spatial And Temporal Dynamics ◽  
Spawning Areas ◽  
Spatio Temporal

Pacific capelin Mallotus catervarius are planktivorous small pelagic fish that serve an intermediate trophic role in marine food webs. Due to the lack of a directed fishery or monitoring of capelin in the Northeast Pacific, limited information is available on their distribution and abundance, and how spatio-temporal fluctuations in capelin density affect their availability as prey. To provide information on life history, spatial patterns, and population dynamics of capelin in the Gulf of Alaska (GOA), we modeled distributions of spawning habitat and larval dispersal, and synthesized spatially indexed data from multiple independent sources from 1996 to 2016. Potential capelin spawning areas were broadly distributed across the GOA. Models of larval drift show the GOA’s advective circulation patterns disperse capelin larvae over the continental shelf and upper slope, indicating potential connections between spawning areas and observed offshore distributions that are influenced by the location and timing of spawning. Spatial overlap in composite distributions of larval and age-1+ fish was used to identify core areas where capelin consistently occur and concentrate. Capelin primarily occupy shelf waters near the Kodiak Archipelago, and are patchily distributed across the GOA shelf and inshore waters. Interannual variations in abundance along with spatio-temporal differences in density indicate that the availability of capelin to predators and monitoring surveys is highly variable in the GOA. We demonstrate that the limitations of individual data series can be compensated for by integrating multiple data sources to monitor fluctuations in distributions and abundance trends of an ecologically important species across a large marine ecosystem.

Sign in / Sign up

Export Citation Format

Share Document