In 2024, Italy experienced a major resurgence of Bluetongue (BT), a viral disease of ruminants caused by Bluetongue virus (BTV), an RNA virus circulating in multiple serotypes transmitted by Culicoides midges. By April 2025, over 7,000 confirmed cases had been reported, mainly involving serotypes BTV-3, BTV-4, and BTV-8. We performed whole-genome sequencing (WGS) and phylogenetic analyses on...
The methylome, defined as the complete set of genome-wide methylation marks, provides an additional layer of information beyond the genetic sequence, yet remains largely underexplored in bacterial genomics. Recent advances in Nanopore sequencing now allow investigation of DNA methylation not only in isolates but also at the community level, opening new opportunities to study epigenetic...
In December 2023, the WHO reported a Ralstonia pickettii outbreak in Australia linked to contaminated saline solutions. Concurrently, German surveillance detected an increase in nosocomial R. pickettii bacteremia cases, prompting a national outbreak investigation.
From August 2023 to June 2024, 15 patient isolates were sequenced using Illumina whole genome sequencing. Five of these were...
Certain sequence types (STs) of Escherichia coli, such as ST131 and ST648, belong to high-risk clonal lineages that pose serious public health threats by combining antimicrobial resistance (AMR), fitness, and virulence. In contrast, other subtypes e.g., ST10 are typically harmless and beneficial colonizers. To identify characteristics beyond AMR, we analyzed over 22,000 E. coli genomes and...
Highly pathogenic avian influenza viruses (HPAIV) cause severe outbreaks in poultry, leading to high mortality, economic losses, and occasional human infections. While H5 and H7 subtypes have dominated poultry outbreaks in the 20th century, the genomic diversity of HPAIV before widespread surveillance in the 1980s remains poorly characterized. So far, only a few complete genomes from before...
Integrated Genomic Surveillance (IGS) enables the surveillance of various, public health-relevant bacterial and viral pathogens. For bacterial species, the identification of genomic clusters represents the foundation for outbreak investigations and epidemiological studies. Providing well-defined genomic clusters therefore represents an essential task of IGS, in order to support the...
