Estimating nosocomial transmission of micro-organisms in hospital settings using patient records and culture data.

Pathogenic bacteria are a major threat to patient health in hospitals. Here we leverage electronic health records from a major New York City hospital system collected during 2020-2021 to support simulation inference of nosocomial transmission and pathogenic bacteria detection using an agent-based model (ABM). The ABM uses these data to inform simulation of importation from the community, nosocomial transmission, and patient spontaneous decolonization of bacteria.

Excess Mortality in the United States, 2020-21: County-level Estimates for Population Groups and Associations with Social Vulnerability.

To assess the excess mortality burden of Covid-19 in the United States, we estimated sex, age and race stratified all-cause excess deaths in each county of the US during 2020 and 2021. Using spatial Bayesian models trained on all recorded deaths between 2003-2019, we estimated 463,187 (95% uncertainty interval (UI): 426,139 - 497,526) excess deaths during 2020, and 544,105 (95% UI: 492,202 - 592,959) excess deaths during 2021 nationally, with considerable geographical heterogeneity. Excess mortality rate (EMR) nearly doubled for each 10-year increase in age and was consistently higher among men than women.

Age-dependent seasonality in the incidence of stroke: A 21-year population-based study.

Introduction: Seasonality in the incidence of stroke has been examined in numerous studies, yet data on whether it differs with age are limited. To fill this gap, we utilized a largescale dataset from Israel.

Patients And Methods: We retrieved data of all hospitalizations for ischemic stroke (IS), transient ischemic attack (TIA) and intra cerebral hemorrhage (ICH) from 2000 to 2020.

Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations.

Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. Forecasting teams were asked to provide national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza hospital admissions for one through four weeks ahead for the 2021-22 and 2022-23 influenza seasons. Across both seasons, 26 teams submitted forecasts, with the submitting teams varying between seasons.

Data-driven clustering of infectious disease incidence into age groups.

Understanding the patterns of infectious diseases spread in the population is an important element of mitigation and vaccination programs. A major and common characteristic of most infectious diseases is age-related heterogeneity in the transmission, which potentially can affect the dynamics of an epidemic as manifested by the pattern of disease incidence in different age groups. Currently there are no statistical criteria of how to partition the disease incidence data into clusters.

Population-level implications of the Israeli booster campaign to curtail COVID-19 resurgence.

Israel was one of the first countries to administer mass vaccination against severe acute respiratory syndrome coronavirus 2. Consequently, it was among the first countries to experience substantial breakthrough infections due to the waning of vaccine-induced immunity, which led to a resurgence of the epidemic. In response, Israel launched a booster campaign to mitigate the outbreak and was the first country to do so.

Similarity of Protection Conferred by Previous SARS-CoV-2 Infection and by BNT162b2 Vaccine: A 3-Month Nationwide Experience From Israel.

The worldwide shortage of vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection while the pandemic still remains uncontrolled has led many countries to the dilemma of whether or not to vaccinate previously infected persons. Understanding the level of protection conferred by previous infection compared with that of vaccination is important for policy-making. We analyzed an updated individual-level database of the entire population of Israel to assess the protection provided by both prior infection and vaccination in preventing subsequent SARS-CoV-2 infection, hospitalization with coronavirus disease 2019 (COVID-19), severe disease, and death due to COVID-19.

The role of children in the spread of COVID-19: Using household data from Bnei Brak, Israel, to estimate the relative susceptibility and infectivity of children.

One of the significant unanswered questions about COVID-19 epidemiology relates to the role of children in transmission. This study uses data on infections within households in order to estimate the susceptibility and infectivity of children compared to those of adults. The data were collected from households in the city of Bnei Brak, Israel, in which all household members were tested for COVID-19 using PCR (637 households, average household size of 5.

A two-stage approach for estimating the parameters of an age-group epidemic model from incidence data.

Age-dependent dynamics is an important characteristic of many infectious diseases. Age-group epidemic models describe the infection dynamics in different age-groups by allowing to set distinct parameter values for each. However, such models are highly nonlinear and may have a large number of unknown parameters.

Characterizing risk of Ebola transmission based on frequency and type of case-contact exposures.

During the initial months of the 2013-2016 Ebola epidemic, rapid geographical dissemination and intense transmission challenged response efforts across West Africa. Contextual behaviours associated with increased risk of exposure included travel to high-transmission settings, caring for sick and preparing the deceased for traditional funerals. Although such behaviours are widespread in West Africa, high-transmission pockets were observed.

Modeling the spread of polio in an IPV-vaccinated population: lessons learned from the 2013 silent outbreak in southern Israel.

Background: Polio eradication is an extraordinary globally coordinated health program in terms of its magnitude and reach, leading to the elimination of wild poliovirus (WPV) in most parts of the world. In 2013, a silent outbreak of WPV was detected in Israel, a country using an inactivated polio vaccine (IPV) exclusively since 2005. The outbreak was detected using environmental surveillance (ES) of sewage reservoirs.

Multiannual forecasting of seasonal influenza dynamics reveals climatic and evolutionary drivers.

Human influenza occurs annually in most temperate climatic zones of the world, with epidemics peaking in the cold winter months. Considerable debate surrounds the relative role of epidemic dynamics, viral evolution, and climatic drivers in driving year-to-year variability of outbreaks. The ultimate test of understanding is prediction; however, existing influenza models rarely forecast beyond a single year at best.

Modeling and statistical analysis of the spatio-temporal patterns of seasonal influenza in Israel.

Background: Seasonal influenza outbreaks are a serious burden for public health worldwide and cause morbidity to millions of people each year. In the temperate zone influenza is predominantly seasonal, with epidemics occurring every winter, but the severity of the outbreaks vary substantially between years. In this study we used a highly detailed database, which gave us both temporal and spatial information of influenza dynamics in Israel in the years 1998-2009.

Modelling seasonal influenza in Israel.

Mathematical modeling approaches are used to study the epidemic dynamics of seasonal influenza in Israel. The recent availability of highly resolved ten year timeseries of influenza cases provides an opportunity for modeling and estimating important epidemiological parameters in the Israeli population. A simple but well known SIR discrete-time deterministic model was fitted to consecutive epidemics allowing estimation of the initial number of susceptibles in the population S0, as well as the reproductive number R0 each year.

Onset of a pandemic: characterizing the initial phase of the swine flu (H1N1) epidemic in Israel.

Background: The swine influenza H1N1 first identified in Mexico, spread rapidly across the globe and is considered the fastest moving pandemic in history. The early phase of an outbreak, in which data is relatively scarce, presents scientific challenges on key issues such as: scale, severity and immunity which are fundamental for establishing sound and rapid policy schemes. Our analysis of an Israeli dataset aims at understanding the spatio-temporal dynamics of H1N1 in its initial phase.

[Mathematical models as tools for studying and developing strategies in the case of a pandemic influenza outbreak].

The current spread of swine flu H1N1 raises serious concerns for public health worldwide. Mathematical modelling has proved to be an essential tool for both developing strategies in preparation for an outbreak and for predicting and evaluating the effectiveness of control policies during an outbreak. Given its growing importance, this article outlines some of the fundamental contributions of mathematical modelling in the study of infectious diseases.