Microbiome Toolbox: methodological approaches to derive and visualize microbiome trajectories.

MOTIVATION: The gut microbiome changes rapidly under the influence of different factors such as age, dietary changes or medications to name just a few. To analyze and understand such changes, we present a Microbiome Toolbox. We implemented several methods for analysis and exploration to provide interactive visualizations for easy comprehension and reporting of longitudinal microbiome data. RESULTS: Based on the abundance of microbiome features such as taxa as well as functional capacity modules, and with the corresponding metadata per sample, the Microbiome Toolbox includes methods for (i) data analysis and exploration, (ii) data preparation including dataset-specific preprocessing and transformation, (iii) best feature selection for log-ratio denominators, (iv) two-group analysis, (v) microbiome trajectory prediction with feature importance over time, (vi) spline and linear regression statistical analysis for testing universality across different groups and differentiation of two trajectories, (vii) longitudinal anomaly detection on the microbiome trajectory and (viii) simulated intervention to return anomaly back to a reference trajectory. AVAILABILITY AND IMPLEMENTATION: The software tools are open source and implemented in Python. For developers interested in additional functionality of the Microbiome Toolbox, it is modular allowing for further extension with custom methods and analysis. The code, python package and the link to the interactive dashboard of Microbiome Toolbox are available on GitHub https://github.com/JelenaBanjac/microbiome-toolbox. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Pertussis Epidemiology in the Autonomous Province of Vojvodina, Serbia, 1948-2023.

Pertussis continues to be a significant public health concern. We aimed to examine the epidemiological characteristics of pertussis in Vojvodina, which accounts for almost a third of Serbia's population. Our aim was to determine the overall and age-specific incidence and mortality rates of pertussis in Vojvodina from 1948 to 2023, as well as the coverage of immunization against pertussis from 1960 to 2023. In the period 1948-2023, 42,259 cases of pertussis were reported. Following the introduction of the DTwP vaccine (1960) in Serbia, the reported incidence of pertussis began to decline. In 2001, for the first time since introduction of pertussis surveillance in Vojvodina, no pertussis cases were reported. Since 2012, the reported incidence of pertussis has once again increased, and peaked (41.1/100,000) in 2023, approaching the incidence rates recorded shortly after the introduction of DTwP vaccine. A shift in the age profile of pertussis from children aged 0-6 years to school-aged children (7-14 years) occurred between 2012 and 2023, when 48.3% of pertussis cases occurred in this age group. Although the incidence rates of pertussis among individuals aged 20 years and older were significantly lower than among younger age groups, there is evidence of an increasing trend in pertussis cases, particularly among those aged 40-49 years, since 2012. Based on the findings of this study, it is imperative to introduce additional booster doses of the aP vaccine for individuals aged 14 years, along with implementing maternal immunization strategies targeting women of childbearing age.

Epidemiological Characteristics of COVID-19 during Seven Consecutive Epidemiological Waves (2020-2022) in the North Backa District, Serbia.

The COVID-19 pandemic continues to pose a threat to global public health. The purpose of this research was to determine the epidemiological characteristics of COVID-19 in the North Backa district while observing seven pandemic waves. The cross-sectional study was based on data from the COVID-19 surveillance database of the Institute for Public Health of Vojvodina during the period from March 2020 to December 2022. A total of 38,685 primary infections and 4067 reinfections caused by SARS-CoV-2 were notified. Pandemic waves caused by the Delta variant (cumulative incidence rate of 2482.37/100,000) and by the Omicron variant (cumulative incidence rate of 2994.45/100,000) emerged as significant focal points during the surveillance period. Over the course of three consecutive years (2020-2022), women were more affected (50.11%, 54.03%, and 55.68%, respectively). The highest incidence rates in age-specific categories were recorded in 2021 for the age group 40-49 (1345.32 per 10,000 inhabitants), while in 2022, they shifted towards the elderly population. Regarding vaccination status at the time of diagnosis, in 2021, around 15% of patients were vaccinated, while in 2022, the number increased to 37%. The most widely received vaccine was BBIBP-CorV (67.45%), followed by BNT162b2 (19.81%), Gam-COVID-Vac (9.31%), and ChAdOx1 nCoV-19 (3.42%) vaccine. The implementation of stringent public health measures and their mitigation, together with the emergence of new variants, influenced the dynamics of COVID-19 pandemic waves in the North Backa district. Notably, throughout the study period, the working-age population was the most affected, along with females, with a mild clinical presentation dominating. Reinfections were most frequently recorded during the latter pandemic waves. Dealing with this pandemic has provided some valuable lessons for the development of future strategies in the case of a similar public health crisis.