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Article ; Online: Fractal dimension based geographical clustering of COVID-19 time series data.

Natalia, Yessika Adelwin / Faes, Christel / Neyens, Thomas / Chys, Pieter / Hammami, Naïma / Molenberghs, Geert

2023 Volume 13, Issue 1, Page(s) 4322

Abstract: Understanding the local dynamics of COVID-19 transmission calls for an approach that characterizes the incidence curve in a small geographical unit. Given that incidence curves exhibit considerable day-to-day variation, the fractal structure of the time ... ...

Abstract	Understanding the local dynamics of COVID-19 transmission calls for an approach that characterizes the incidence curve in a small geographical unit. Given that incidence curves exhibit considerable day-to-day variation, the fractal structure of the time series dynamics is investigated for the Flanders and Brussels Regions of Belgium. For each statistical sector, the smallest administrative geographical entity in Belgium, fractal dimensions of COVID-19 incidence rates, based on rolling time spans of 7, 14, and 21 days were estimated using four different estimators: box-count, Hall-Wood, variogram, and madogram. We found varying patterns of fractal dimensions across time and location. The fractal dimension is further summarized by its mean, variance, and autocorrelation over time. These summary statistics are then used to cluster regions with different incidence rate patterns using k-means clustering. Fractal dimension analysis of COVID-19 incidence thus offers important insight into the past, current, and arguably future evolution of an infectious disease outbreak.
MeSH term(s)	Humans ; Fractals ; Time Factors ; COVID-19/epidemiology ; Geography ; Belgium/epidemiology
Language	English
Publishing date	2023-03-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-30948-7
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Article ; Online: Key risk factors associated with fractal dimension based geographical clustering of COVID-19 data in the Flemish and Brussels region, Belgium.

Natalia, Yessika Adelwin / Faes, Christel / Neyens, Thomas / Hammami, Naïma / Molenberghs, Geert

Frontiers in public health

2023 Volume 11, Page(s) 1249141

Abstract: Introduction: COVID-19 remains a major concern globally. Therefore, it is important to evaluate COVID-19's rapidly changing trends. The fractal dimension has been proposed as a viable method to characterize COVID-19 curves since epidemic data is often ... ...

Abstract	Introduction: COVID-19 remains a major concern globally. Therefore, it is important to evaluate COVID-19's rapidly changing trends. The fractal dimension has been proposed as a viable method to characterize COVID-19 curves since epidemic data is often subject to considerable heterogeneity. In this study, we aim to investigate the association between various socio-demographic factors and the complexity of the COVID-19 curve as quantified through its fractal dimension. Methods: We collected population indicators data (ethnic composition, socioeconomic status, number of inhabitants, population density, the older adult population proportion, vaccination rate, satisfaction, and trust in the government) at the level of the statistical sector in Belgium. We compared these data with fractal dimension indicators of COVID-19 incidence between 1 January - 31 December 2021 using canonical correlation analysis. Results: Our results showed that these population indicators have a significant association with COVID-19 incidences, with the highest explanatory and predictive power coming from the number of inhabitants, population density, and ethnic composition. Conclusion: It is important to monitor these population indicators during a pandemic, especially when dealing with targeted interventions for a specific population.
MeSH term(s)	Humans ; Aged ; Fractals ; Belgium/epidemiology ; COVID-19/epidemiology ; Cluster Analysis ; Risk Factors
Language	English
Publishing date	2023-11-03
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2023.1249141
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Article ; Online: COVID-19 surveillance in the Flemish school system: development of systematic data collection within the public health school system and descriptive analysis of cases reported between October 2020 and June 2021.

Merckx, Joanna / Crèvecoeur, Jonas / Proesmans, Kristiaan / Hammami, Naïma / Denys, Hilde / Hens, Niel

BMC public health

2022 Volume 22, Issue 1, Page(s) 1921

Abstract: Background: The age-specific distribution of SARS-CoV-2 cases in schools is not well described. Reported statistics reflect the intensity of community transmission while being shaped by biases from age-dependent testing regimes, as well as effective age- ...

Abstract	Background: The age-specific distribution of SARS-CoV-2 cases in schools is not well described. Reported statistics reflect the intensity of community transmission while being shaped by biases from age-dependent testing regimes, as well as effective age-specific interventions. A case surveillance system was introduced within the Flemish school and health-prevention network during the 2020-2021 school year. We present epidemiological data of in-school reported cases in pre-, primary and secondary schools identified by the case surveillance system, in conjunction with test data and community cases from October 2020 to June 2021. Methods: We describe the development of the surveillance system and provide the number of reported cases and standardized rates per grade over time. We calculated absolute and relative differences in case incidence according to school grade (primary: grades 1-6, and secondary: grades 7-12) using grades 7-8 as a comparator, relating them to non-pharmaceutical infection prevention interventions. Cumulative population incidences (IP) stratified by age, province and socioeconomic status (SES) of the school population are presented with their 95% confidence intervals (CI). Results: A total of 59,996 COVID-19 cases were reported in the school surveillance system, with the highest population adjusted IP in grade 11-12 of 7.39% (95%CI 7.24-7.53) and ranging from 2.23% to 6.25% from pre-school through grade 10. Age-specific reductions in mask introduction and in-person teaching were temporally associated with decreased case incidence, while lower pupil SES was associated with an increase in cumulative cases (excess 2,739/100,000 pupils compared to highest SES tertile). Community testing volumes varied more for children compared to adults, with overall higher child test-positivity. Holidays influence capturing of cases by the system, however efficiency increased to above 75% after further automation and integration in existing structures. Conclusion: We demonstrate that effective integration of case surveillance within an electronic school health system is feasible, provides valuable data regarding the evolution of an epidemic among schoolchildren, and is an integral component of public health surveillance and pandemic preparedness. The relationship towards community transmission needs careful evaluation because of age-different testing regimens. In the Flemish region, case incidence within schools exhibited an age gradient that was mitigated through grade-specific interventions, though differences by SES remain.
MeSH term(s)	Adult ; COVID-19/epidemiology ; Child ; Child, Preschool ; Data Collection ; Humans ; SARS-CoV-2 ; Schools ; Schools, Public Health
Language	English
Publishing date	2022-10-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2041338-5
ISSN	1471-2458 ; 1471-2458
ISSN (online)	1471-2458
ISSN	1471-2458
DOI	10.1186/s12889-022-14250-1
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Article ; Online: Gram-negative central line-associated bloodstream infection incidence peak during the summer: a national seasonality cohort study.

Blot, Koen / Hammami, Naïma / Blot, Stijn / Vogelaers, Dirk / Lambert, Marie-Laurence

Scientific reports

2022 Volume 12, Issue 1, Page(s) 5202

Abstract: Central line-associated bloodstream infections (CLABSI) cause increased morbidity, mortality, and hospital costs that are partially preventable. The phenomenon of seasonality among CLABSI rates has not been fully elucidated, but has implications for ... ...

Abstract	Central line-associated bloodstream infections (CLABSI) cause increased morbidity, mortality, and hospital costs that are partially preventable. The phenomenon of seasonality among CLABSI rates has not been fully elucidated, but has implications for accurate surveillance and infection prevention trials. Longitudinal dynamic cohort of hospitals participating in hospital-wide and intensive care unit bloodstream infection surveillance for at least one full year over 2000 to 2014. Mixed-effects negative binomial regression analysis calculated the peak-to-low ratio between months as an adjusted CLABSI incidence rate ratio (IRR) with 95% confidence intervals (CI). Multivariate regression models examined the associations between CLABSI pathogens and ambient temperature and relative humidity. The study population included 104 hospital sites comprising 11,239 CLABSI. Regression analysis identified a hospital-wide increase in total CLABSI during July-August, with a higher gram-negative peak-to-low incidence rate ratio (IRR 2.52 [95% CI 1.92-3.30], p < 0.001) compared to gram-positive bacteria (IRR 1.29 [95% CI 1.11-1.48], p < 0.001). Subgroup analysis replicated this trend for CLABSI diagnosed in the intensive care unit. Only gram-negative CLABSI rates were associated with increased temperature (IRR + 30.3% per 5 °C increase [95% CI 17.3-43.6], p < 0.001) and humidity (IRR + 22.9% per 10% increase [95% CI 7.7-38.3), p < 0.001). The incidence and proportion of gram-negative CLABSI approximately doubled during the summer periods. Ambient temperature and humidity were associated with increases of hospital-acquired gram-negative infections. CLABSI surveillance, preventive intervention trials and epidemiological studies should consider seasonal variation and climatological factors when preparing study designs or interpreting their results.
MeSH term(s)	Catheter-Related Infections/epidemiology ; Catheter-Related Infections/prevention & control ; Cohort Studies ; Cross Infection/microbiology ; Humans ; Incidence ; Intensive Care Units ; Seasons ; Sepsis/complications
Language	English
Publishing date	2022-03-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-08973-9
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Article ; Online: Key performance indicators of COVID-19 contact tracing in Belgium from September 2020 to December 2021.

Kremer, Cécile / Willem, Lander / Boone, Jorden / Arrazola de Oñate, Wouter / Hammami, Naïma / Faes, Christel / Hens, Niel

PloS one

2023 Volume 18, Issue 10, Page(s) e0292346

Abstract: The goal of tracing, testing, and quarantining contacts of infected individuals is to contain the spread of infectious diseases, a strategy widely used during the COVID-19 pandemic. However, limited research exists on the effectiveness of contact tracing, ...

Abstract	The goal of tracing, testing, and quarantining contacts of infected individuals is to contain the spread of infectious diseases, a strategy widely used during the COVID-19 pandemic. However, limited research exists on the effectiveness of contact tracing, especially with regard to key performance indicators (KPIs), such as the proportion of cases arising from previously identified contacts. In our study, we analyzed contact tracing data from Belgium collected between September 2020 and December 2021 to assess the impact of contact tracing on SARS-CoV-2 transmission and understand its characteristics. Among confirmed cases involved in contact tracing in the Flemish and Brussels-Capital regions, 19.1% were previously identified as close contacts and were aware of prior exposure. These cases, referred to as 'known' to contact tracing operators, reported on average fewer close contacts compared to newly identified individuals (0.80 versus 1.05), resulting in fewer secondary cases (0.23 versus 0.28). Additionally, we calculated the secondary attack rate, representing infections per contact, which was on average lower for the 'known' cases (0.22 versus 0.25) between December 2020 and August 2021. These findings indicate the effectiveness of contact tracing in Belgium in reducing SARS-CoV-2 transmission. Although we were unable to quantify the exact number of prevented cases, our findings emphasize the importance of contact tracing as a public health measure. In addition, contact tracing data provide indications of potential shifts in transmission patterns among different age groups associated with emerging variants of concern and increasing vaccination rates.
MeSH term(s)	Humans ; COVID-19/epidemiology ; COVID-19/prevention & control ; Contact Tracing/methods ; SARS-CoV-2 ; Pandemics/prevention & control ; Belgium/epidemiology
Language	English
Publishing date	2023-10-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0292346
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Article ; Online: Seasonal variation of hospital-acquired bloodstream infections: A national cohort study.

Blot, Koen / Hammami, Naïma / Blot, Stijn / Vogelaers, Dirk / Lambert, Marie-Laurence

Infection control and hospital epidemiology

2021 Volume 43, Issue 2, Page(s) 205–211

Abstract: Background: Hospital-acquired bloodstream infections (HABSIs) cause increased morbidity, mortality, and hospital costs that are partially preventable. HABSI seasonality has been described for gram-negative bacteria but has not been stratified per ... ...

Abstract	Background: Hospital-acquired bloodstream infections (HABSIs) cause increased morbidity, mortality, and hospital costs that are partially preventable. HABSI seasonality has been described for gram-negative bacteria but has not been stratified per infection origin. Objective: To assess seasonality among all types of HABSIs and their associations with climate. Methods: Hospitals performing surveillance for at least 1 full calendar year between 2000 and 2014 were included. Mixed-effects negative binomial regression analysis calculated the peak-to-low monthly ratio as an adjusted HABSI incidence rate ratio (IRR) with 95% confidence intervals (CIs). Another regression model examined associations between HABSI rates and climate variables. These analyses were stratified by microorganism and infectious origin. Results: The study population included 104 hospitals comprising 44,111 HABSIs. Regression analysis identified an incidence rate ratio (IRR) peak in August for gram-negative HABSIs (IRR, 1.59; 95% CI, 1.49-1.71), CLABSIs (IRR, 1.49; 95% CI, 1.30-1.70), and urinary tract HABSI (IRR, 1.52; 95% CI, 1.34-1.74). The gram-negative incidence increased by 13.1% (95% CI, 9.9%-16.4%) for every 5°C increase in temperature. Seasonality was most present among E. coli, K. pneumoniae, E. cloacae, and the nonfermenters. Gram-positive and pulmonary HABSIs did not demonstrate seasonal variation. Conclusions: Seasonality with summer spikes occurred among gram-negative bacteria, CLABSIs, and urinary tract HABSIs. Higher ambient temperature was associated with gram-negative HABSI rates. The preventable causative factors for seasonality, such as the nurse-to-patient ratio, indoor room temperature or device-utilization, need to be examined to assess areas for improving patient safety.
MeSH term(s)	Cohort Studies ; Cross Infection/microbiology ; Escherichia coli ; Hospitals ; Humans ; Incidence ; Seasons ; Sepsis/epidemiology
Language	English
Publishing date	2021-05-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639378-0
ISSN	1559-6834 ; 0195-9417 ; 0899-823X
ISSN (online)	1559-6834
ISSN	0195-9417 ; 0899-823X
DOI	10.1017/ice.2021.85
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Article ; Online: Translating the COVID-19 epidemiological situation into policies and measures: the Belgian experience.

De Muylder, Géraldine / Laisnez, Valeska / Stefani, Giulietta / Boulouffe, Caroline / Faes, Christel / Hammami, Naïma / Hubin, Pierre / Molenberghs, Geert / Sans, Jasper / van de Konijnenburg, Cecile / Van der Borght, Stefaan / Brondeel, Ruben / Stassijns, Jorgen / Lernout, Tinne

Frontiers in public health

2024 Volume 12, Page(s) 1306361

Abstract: The COVID-19 pandemic led to sustained surveillance efforts, which made unprecedented volumes and types of data available. In Belgium, these data were used to conduct a targeted and regular assessment of the epidemiological situation. In addition, ... ...

Abstract	The COVID-19 pandemic led to sustained surveillance efforts, which made unprecedented volumes and types of data available. In Belgium, these data were used to conduct a targeted and regular assessment of the epidemiological situation. In addition, management tools were developed, incorporating key indicators and thresholds, to define risk levels and offer guidance to policy makers. Categorizing risk into various levels provided a stable framework to monitor the COVID-19 epidemiological situation and allowed for clear communication to authorities. Although translating risk levels into specific public health measures has remained challenging, this experience was foundational for future evaluation of the situation for respiratory infections in general, which, in Belgium, is now based on a management tool combining different data sources.
MeSH term(s)	Humans ; COVID-19/epidemiology ; Belgium/epidemiology ; SARS-CoV-2 ; Health Policy ; Public Health ; Pandemics ; Risk Assessment/methods
Language	English
Publishing date	2024-04-05
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2024.1306361
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Article ; Online: Outbreak of

Jacquinet, Stéphanie / Martini, Helena / Mangion, Jean-Paul / Neusy, Sarah / Detollenaere, Aurélie / Hammami, Naïma / Bruggeman, Lien / Hoorelbeke, Bart / Pierard, Denis / Cornelissen, Laura

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2023 Volume 28, Issue 44

Abstract: Since 2022, European countries have been facing an outbreak of mainly cutaneous diphtheria caused by ... ...

Abstract	Since 2022, European countries have been facing an outbreak of mainly cutaneous diphtheria caused by toxigenic
MeSH term(s)	Male ; Humans ; Belgium/epidemiology ; Corynebacterium diphtheriae ; Diphtheria/diagnosis ; Diphtheria/epidemiology ; Refugees ; Multilocus Sequence Typing ; Disease Outbreaks
Language	English
Publishing date	2023-11-02
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2023.28.44.2300130
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Article ; Online: Vaccine effectiveness against transmission of alpha, delta and omicron SARS-COV-2-infection, Belgian contact tracing, 2021–2022

Braeye, Toon / Catteau, Lucy / Brondeel, Ruben / van Loenhout, Joris A.F. / Proesmans, Kristiaan / Cornelissen, Laura / Oyen, Herman Van / Stouten, Veerle / Hubin, Pierre / Billuart, Matthieu / Djiena, Achille / Mahieu, Romain / Hammami, Naima / Van Cauteren, Dieter / Wyndham-Thomas, Chloé

Vaccine. 2023 Apr. 05,

2023

Abstract: Vaccine effectiveness against transmission (VET) of SARS-CoV-2-infection can be estimated from secondary attack rates observed during contact tracing. We estimated VET, the vaccine-effect on infectiousness of the index case and susceptibility of the high- ...

Abstract	Vaccine effectiveness against transmission (VET) of SARS-CoV-2-infection can be estimated from secondary attack rates observed during contact tracing. We estimated VET, the vaccine-effect on infectiousness of the index case and susceptibility of the high-risk exposure contact (HREC). We fitted RT-PCR-test results from HREC to immunity status (vaccine schedule, prior infection, time since last immunity-conferring event), age, sex, calendar week of sampling, household, background positivity rate and dominant VOC using a multilevel Bayesian regression-model. We included Belgian data collected between January 2021 and January 2022. For primary BNT162b2-vaccination we estimated initial VET at 96% (95%CI 95–97) against Alpha, 87% (95%CI 84–88) against Delta and 31% (95%CI 25–37) against Omicron. Initial VET of booster-vaccination (mRNA primary and booster-vaccination) was 87% (95%CI 86–89) against Delta and 68% (95%CI 65–70) against Omicron. The VET-estimate against Delta and Omicron decreased to 71% (95%CI 64–78) and 55% (95%CI 46–62) respectively, 150–200 days after booster-vaccination. Hybrid immunity, defined as vaccination and documented prior infection, was associated with durable and higher or comparable (by number of antigen exposures) protection against transmission. While we observed VOC-specific immune-escape, especially by Omicron, and waning over time since immunization, vaccination remained associated with a reduced risk of SARS-CoV-2-transmission.
Keywords	Bayesian theory ; antigens ; hybrids ; immunity ; risk reduction ; vaccination ; vaccines ; Vaccine Effectiveness ; mRNA-vaccine ; Viral-vector vaccine ; SARS-CoV-2 ; Alpha Variant of Concern ; Delta Variant of Concern ; Omicron Variant of Concern ; Transmission ; Infection-acquired immunity ; Vaccine-induced immunity ; Infectiousness ; Susceptibility
Language	English
Dates of publication	2023-0405
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Pre-press version ; Use and reproduction
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2023.03.069
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Article ; Online: Outbreak of Central American born Shigella sonnei in two youth camps in Belgium in the summer of 2019.

Van den Bossche, An / Ceyssens, Pieter-Jan / Denayer, Sarah / Hammami, Naïma / van den Beld, Maaike / Dallman, Timothy J / Mattheus, Wesley

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

2021 Volume 40, Issue 7, Page(s) 1573–1577

Abstract: In 2019, an outbreak of Shigella sonnei occurred during two youth camps in Belgium. The clustering of isolates from both camps was confirmed by next-generation sequencing, as well as a secondary infection of a technician. The outbreak strain clustered ... ...

Abstract	In 2019, an outbreak of Shigella sonnei occurred during two youth camps in Belgium. The clustering of isolates from both camps was confirmed by next-generation sequencing, as well as a secondary infection of a technician. The outbreak strain clustered with internationally isolated strains from patients with recent travel history to Central America. This report exemplifies enhanced surveillance and international collaboration between public health institutes by enabling to link local outbreaks to region-specific sublineages circulating abroad.
MeSH term(s)	Adult ; Belgium/epidemiology ; Central America ; Child ; Disease Outbreaks ; Dysentery, Bacillary/epidemiology ; Dysentery, Bacillary/microbiology ; Feces/microbiology ; Humans ; Phylogeny ; Shigella sonnei/genetics ; Shigella sonnei/isolation & purification
Language	English
Publishing date	2021-02-11
Publishing country	Germany
Document type	Journal Article
ZDB-ID	603155-9
ISSN	1435-4373 ; 0934-9723 ; 0722-2211
ISSN (online)	1435-4373
ISSN	0934-9723 ; 0722-2211
DOI	10.1007/s10096-021-04164-y
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