Environmental surface surveillance during a COVID-19 outbreak in a school community: implications for controlling indirect transmission

Environmental surface surveillance is a valuable tool for detecting and controlling infectious diseases. During the COVID-19 pandemic, concerns have been raised regarding the potential for indirect transmission of SARS-CoV-2 via contaminated surfaces. However, few studies have evaluated environmental contamination in non-clinical settings during outbreaks. We conducted a study in a school community during a major outbreak, collecting 35 surface samples from high-traffic areas and testing them for SARS-CoV-2 RNA using RT-qPCR. Our results showed that 31.4% of samples were positive, including high-touch surfaces such as drinking fountains and washbasins. These findings emphasize the importance of environmental monitoring to identify and address specific areas for attention, and implementing such strategies can help prevent the indirect transmission of COVID-19 in various settings.

Phylogenomic characterization and pangenomic insights into the surfactin-producing bacteria Bacillus subtilis strain RI4914

Bacillus subtilis is a versatile bacterial species able to produce surfactin, a lipopeptide biosurfactant. We carried out the phylogenomic characterization and pangenomic analyses using available B. subtilis complete genomes. Also, we report the whole genome of the biosurfactant-producing B. subtilis strain RI4914 that was isolated from effluent water from an oil exploration field. We applied a hybrid sequencing approach using both long- and short-read sequencing technologies to generate a highly accurate, single-chromosome genome. The pangenomics analysis of 153 complete genomes classified as B. subtilis retrieved from the NCBI shows an open pangenome composed of 28,511 accessory genes, which agrees with the high genetic plasticity of the species. Also, this analysis suggests that surfactin production is a common trait shared by members of this species since the srfA operon is highly conserved among the B. subtilis strains found in most of the assemblies available. Finally, increased surfactin production corroborates the higher srfAA gene expression in B. subtilis strain RI4914.

Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils

Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.