The National Immunisation Programme in the Netherlands: surveillance and developments in 2021-2022.

Synopsis The National Immunisation Programme in the Netherlands Surveillance and developments in 2021-2022 RIVM tracks how many people fall ill due to a disease that is included in the National Immunisation Programme (NIP). In 2021, fewer people got such a disease compared to 2020. This is very likely due to COVID-19 control measures such as social distancing and handwashing. There were especially fewer people with invasive pneumococcal disease (about 1,205 people), pertussis (74), and mumps (1). The number of notifications for meningococcal disease caused by serotype W (4) decreased further, after introduction of the vaccine for adolescents into the NIP in 2020. There were no notifications of diphtheria, tetanus, measles, rubella, or polio in 2021. The number of chronic hepatitis B notifications (743) was about the same as in 2020. Between 2014 and 2019 there were many more notifications, with about 1,000 to 1,100 people being made aware they had this disease. The decrease is probably the result of a decrease in doctors’ visits and therefore diagnoses during the COVID-19 pandemic. Only Haemophilus influenzae type b (Hib) occurred more frequently than before the COVID-19 pandemic. In 2020 and 2021 there were 68 notifications per year, compared to 39 in 2019. RIVM currently investigates the cause. The vaccine seems to be as effective as in previous years. In 2021, 1,703,102 children were vaccinated as part of the NIP. They received a total of 2,219,341 vaccinations. Also, 115,886 pregnant women received a vaccination that protects their baby immediately after birth against, amongst others, whooping cough. Vaccination coverage in the Netherlands is slightly lower than last year. This is partly because of the COVID-19 pandemic, which caused some vaccinations to be given later than normally planned. The Health Council of the Netherlands recommended in June 2021 to offer rotavirus vaccination to young babies. In September 2021, the Health Council recommended inviting more risk groups for flu vaccination, including pregnant women. The ministry of Health, Welfare and Sport adopted both recommendations in 2022. Vaccination against COVID-19 works well to prevent severe illness and death, but the protection slowly decreases. Booster vaccinations increase protection again

Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning

It is important that antibiotics prescriptions are based on antimicrobial susceptibility data to ensure effective treatment outcomes. The increasing availability of next-generation sequencing, bacterial whole genome sequencing (WGS) can facilitate a more reliable and faster alternative to traditional phenotyping for the detection and surveillance of AMR. This work proposes a machine learning approach that can predict the minimum inhibitory concentration (MIC) for a given antibiotic, here ciprofloxacin, on the basis of both genome-wide mutation profiles and profiles of acquired antimicrobial resistance genes. We analysed 704 Escherichia coli genomes combined with their respective MIC measurements for ciprofloxacin originating from different countries. The four most important predictors found by the model, mutations in gyrA residues Ser83 and Asp87, a mutation in parC residue Ser80 and presence of the qnrS1 gene, have been experimentally validated before. Using only these four predictors in a linear regression model, 65% and 93% of the test samples\u2019 MIC were correctly predicted within a two- and a four-fold dilution range, respectively. The presented work does not treat machine learning as a black box model concept, but also identifies the genomic features that determine susceptibility. The recent progress in WGS technology in combination with machine learning analysis approaches indicates that in the near future WGS of bacteria might become cheaper and faster than a MIC measurement